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Clark, AG, Kao, T-H. Excess nonsynonymous substitution at shared polymorphic sites among self incompatibility alleles of Solanaceae. Proc Natl Acad Sci USA, 88: 9823-9827
Abstract
The function of the self-incompatibility locus (S locus) of many plant species dictates that natural selection will favor high levels of protein diversity. Pairwise sequence comparisons between S alleles from four species of Solanaceae reveal remarkably high sequence diversity and evidence for shared polymorphism. The level of amino acid constraint was found to be significantly heterogeneous among different regions of the gene, with some regions being highly constrained and others appearing to be virtually unconstrained. In some regions of the protein, there was an excess of nonsynonymous over synonymous substitution, consistent with the strong diversifying selection that must operate on this locus. These hypervariable regions are candidates for the sites that determine functional allelic identity. Simple contingency table tests show that sites that have polymorphism shared between species have more nonsynonymous substitution than polymorphic sites that do not exhibit shared polymorphism. This is consistent with the idea that adaptive evolution favoring amino acid replacement is occurring at sites with shared polymorphism. Tests of clustered polymorphism reveal that an unusually low rate of recombination must be occurring in this locus, allowing very ancient alleles to preserve their identity.
... Second, the flanking regions of different alleles of the S-RNase gene share virtually no sequence similarity and contain abundant repetitive sequences (Kaufmann et al., 1991;Coleman and Kao, 1992;Matton et al., 1995), indicative of a lack of recombination in the vicinity of the S-RNase gene. Third, no evidence of intragenic recombination was found when sensitive statistical methods were used to examine cDNA sequences for 12 alleles of the S-RNase gene for clustering of polymorphic sites (Clark and Kao, 1991). Last, the S locus of Lycopersicon peruvianum has been shown by genetic mapping to be located close to the centromere of chromosome I (Bernatzky, 1993), and the S locus of Petunia hybrida has been shown by fluorescence in situ hybridization to be located close to the centromere of chromosome III (Entani et al., 1999), the centromere being a region where recombination is known to be suppressed. ...
... Second, the high degree of sequence diversity in the flanking regions of the S genes might prevent intergenic, but not intragenic recombination. Moreover, the S-RNases available to Clark and Kao (1991) for examining the possibility of intragenic recombination by statistical methods are too divergent in sequence to allow detection of any ancient recombination events because accumulation of neutral mutations over long evolutionary time would have obscured the exchanges. ...
For Solanaceae type self-incompatibility, discrimination between self and nonself pollen by the pistil is controlled by the highly polymorphic S-RNase gene. To date, the mechanism generating the allelic diversity of this gene is largely unknown. Natural populations offer a good opportunity to address this question because they likely contain different alleles that share recent common progenitors. We identified 19 S haplotypes from a natural population ofPetunia inflata in Argentina, used reverse transcriptase-polymerase chain reaction to obtain cDNAs for 15 alleles of the S-RNase gene, and sequenced all the cDNAs. Phylogenetic studies revealed that five of these alleles and two previously identified alleles form a major clade, and that the 5′ region ofS 19 allele was derived from an ancestor allele closely related to S 2, whereas its 3′ region was derived from an ancestor allele closely related to S 8. A similar evolutionary relationship was found among S 3,S 12, andS 15 alleles. These findings suggest that intragenic recombination contributed to the generation of the allelic diversity of the S-RNase gene. Two additional findings emerged from the sequence comparisons. First, the nucleotide sequence of theS 1 allele identified in this work is completely identical to that of the previously identifiedS 1 allele of a different origin. Second, in the two hypervariable regions HVa and HVb, thought to be involved in determining S allele specificity,S 6 andS 9 alleles differ only by four nucleotides, all in HVb, resulting in two amino acid differences. The implications of these findings are discussed.
... Because no recombination was found between the S locus and three of the markers (CP100, CP108 and 48A), the order of these markers with respect to each other could not be determined. This finding is consistent with earlier reports suggesting that recombination at the S locus is suppressed (Clark and Kao 1991; Coleman and Kao 1992). ...
... The 167A locus is also polymorphic and may be a second example of a gene hitchhiking on the S locus. The two possible mechanisms for maintaining 48A polymorphisms (selection and hitchhiking) can be distinguished from each other using appropriate statistical tests (see for example Clark and Kao 1991), but this would require complete 48A sequences from several different S alleles. ...
The S locus of solanaceous plants includes separate genes that control the self-incompatibility phenotype of the pistil and of
the pollen. The gene controlling the self-incompatibility phenotype of the pistil encodes an extracellular ribonuclease, the
S-RNase. The gene(s) controlling the self-incompatibility phenotype of pollen (the pollen-S gene) has yet to be identified. As part of a long-term strategy to clone the pollen-S gene by chromosome walking, a detailed map of the region near the S locus of Nicotiana alata was generated using a total of 251 F2 plants. The map spans an interval of approximately 2.6 cM and contains five markers as well as the S-RNase gene. Two markers
were detected with heterologous probes that also detect sequences linked to the S locus of Solanum tuberosum and the homologous region of the Lycopersicon genome. Three markers were identified by differential display using N. alata pollen RNA as a template. One of these markers is a pollen-expressed sequence, 48A, which detects a polymorphic marker no more than 0.5 cM from the S locus. RNA blot analysis indicates that the 48A gene is expressed primarily during pollen development after the completion of meiosis and is therefore a candidate for the
pollen-S gene. The utility of these markers and the possible involvement of 48A in the molecular mechanism of self- incompatibility are discussed.
... Although the variation at the b locus is of direct importance to the population genetic structure and pathogenicity of U. maydis, little is known about the evolutionary processes maintaining its diversity. Recent molecular analyses of fungal and mating compatibility type genes demonstrated that different mating types are highly divergent in sequence and have likely been maintained in population for long periods (Clark and Kao 1991 ;Gillissen, et al., 1992 ;Kronstad and Leong , 1990 ;and Richman,et al.,1996). ...
... These allorecognition systems typically exhibit exceptional specificity and presumably corresponding high levels of genetic polymorphism (i.e., allotypic diversity), sometimes exceeding by an order of magnitude levels of variation found at almost all other polymorphic loci (Wright 1939;Grosberg 1988;Potts and Wakeland 1990;Charlesworth 1995;Parham and Ohta 1996). In the absence of exceptionally high mutation rates, the evolution and persistence of extensive allotypic diversity likely involves some form of balancing selection (Grosberg 1988;Potts and Wakeland 1993), resulting in: (1) unusually high levels of sequence divergence among alleles (Potts and Wakeland 1993); (2) high ratios of non synonymous to synonymous substitutions (Clark and Kao 1991); and (3) transpecific coalescence of allelic genealogies (Haring et al. 1990). These patterns are most likely the outcome of some combination of either overdominant (Hughes andNei 1988, 1992) or frequency-dependent (Slade and McCallum 1992;Potts and Wakeland 1993) selection acting on allorecognition phenotypes (Hedrick 1994;Apanius et al. 1997). ...
Many sessile colonial organisms intensively compete with conspecifics for growing space. This competition can result in either cooperative fusion or aggressive rejection between colonies, and some species have evolved highly polymorphic genetic systems that mediate the outcome of these interactions. Here we demonstrate the potential for interactions among close kin as the basis for the evolutionary maintenance of a genetically polymorphic allorecognition system in the colonial hydroid Hydractinia symbiolongicarpus, which lives on gastropod shells occupied by hermit crabs. Fusion between hydroids in the laboratory is restricted mainly to encounters between full siblings, whereas other encounters result in aggressive rejection. Natural selection acting on the costs or benefits of fusion between colonies could be responsible for the present maintenance of such a highly specific behavioral response, but only if encounters between fusible colonies still occur in contemporary populations. The large size of these hydroid populations and the mobility of the crabs should limit the potential for interactions among closely related hydroids on the same shell. However, RAPD polymorphisms among a large sample of hydroids from a population off the coast of Massachusetts indicate that genetically similar colonies are often found together on the same shell. Some genetic distances between colonies on the same shell were low relative to genetic distances between colonies on different shells or genetic distances between known full siblings from laboratory matings. We conservatively estimate that 2-18% of co-occurring colonies may be full sibling pairs. These observations suggest that encounters between genetically similar hydroids are common, despite the mobile nature of their habitat, and these encounters may provide frequent opportunities for natural selection to influence the evolution of cooperative and agonistic behaviors and their polymorphic genetic basis.
... The problem has been approached by computer analysis and by experimental manipulation of S-RNase sequences. Several authors have analysed multiple sequence alignments to identify regions that are responsible for allelic specificity in S-RNases of the Solanaceae and Rosaceae (loerger, Clark and Kao, 1990;Clark and Kao, 1991;loerger et al., 1991;Tsai et al., 1992;Sims, 1993;Ishimizu et al., 1998). It is apparent that S-RNases contain a patchwork of small conserved domains and larger variable domains. ...
... With simple modifications such as the use of sliding windows to find localized regions of positive selection within otherwise conserved genes, it led to a flood of studies that collectively showed that positive selection is not as rare as many neutralists had assumed. Positive selection was readily detectable in genes involved in various forms of inter-organism and inter-species interactions, such as host/pathogen interactions (Hughes 1991), self/non-self recognition in plant selfincompatibility systems (Clark and Kao 1991), sperm/egg recognition in marine invertebrates (Swanson and Vacquier 1995), and many more (Endo et al. 1996). Hughes was nevertheless critical of a weakening of stringent criteria used in detecting positive selection and sought improvements in methodologies used in the analyses (Hughes 2007;Hughes and Friedman 2008). ...
In this minireview, we highlight the contributions of the late Austin L. Hughes to two areas of molecular evolution: the role of positive (Darwinian) selection, and the impact of gene duplications during genome evolution.
... Rh. glutinis CBS 20 T 97 1 5 9 13 17 21 25 29 33 37 41 45 49 53 57 61 65 69 73 77 81 85 89 93 97 101 105 109 113 117 121 125 129 systems such as the S-loci of plants [60,61]. Additionally, sites within the homeodomain motif exhibited low ω (ω < 0.26) indicative of strong purifying selection. ...
... Overall, these results weaken previous suggestions that Slocus regions have unusually low recombination rates (Clark and Kao, 1991;Coleman and Kao, 1992;Boyes et al., 1997), and suggest that some exchange process occurs in these regions; the inverted arrangement of some of the genes in this region in certain Brassica S-haplotypes (Suzuki et al., 1999) suggests that reciprocal recombination between some haplotypes could be rare, but gene conversion events may perhaps occur. It is thus likely that the selfincompatibility recognition locus (or loci) is very close to the highly polymorphic SLG and SRK loci, if not within one or both of them, since high sequence diversity is expected only at sites very close to those under balancing selection. ...
Here we review some of the unsolved problems in understanding plant self-incompatibility and attempt to show how a population
genetics approach is integral to many interesting questions, including some of the problems involved in making inferences
about which parts of the sequences of the known genes are involved in recognition functions. We describe preliminary results
from work on a species in the Brassica family, Arabidopsis (formerly Arabis) lyrata. Our data indicate that this species has sporophytic self-incompatibility, with extensive dominance/recessivity of alleles.
We have not yet attempted to estimate allele numbers in samples from natural populations, but there must be many alleles,
since unrelated plants are usually cross-compatible. Using primers based on Brassica SLG and SRK sequences, we have amplified several S-domain loci from A. lyrata genomic DNA and estimate that at least seven such loci are present. Using plants from geographically separated populations,
we find that sequence diversity differs greatly from locus to locus. One set of sequences, representing one locus or at most
a few loci, shows linkage with incompatibility groups segregating within several independent families, consistent with this
set of sequences representing alleles of a self-incompatibility gene. However, further work is needed to test whether these
sequences represent more than a single locus and whether expression patterns of these sequences are consistent with their
having a role in self-incompatibility.
... 1.65 Mb. This number is likely to be considerably larger for the S-locus linkage group because of recombination suppression (Clark and Kao, 1991). The approach of chromosome walking from the S-RNase gene to identify the pollen S-gene has hitherto been deemed unfeasible due to the repetitive nature of the flanking regions of the S-RNase gene. ...
Petunia inflata has been used as a model to study solanaceous type self-incompatibility (SI), an RNase-mediated self/non-self recognition mechanism. Pistil proteins that co-segregate with S -alleles (termed S-proteins or S-RNases) were identified, and their role in SI was demonstrated by gain-of-function and loss-of-function experiments. Several lines of evidence strongly suggest that the S -locus contains another gene, termed the pollen S -gene, whose allelic products presumably interact with S-RNases to trigger the SI response. Thus, ultimate understanding of the molecular/biochemical basis of SI requires the identification of the pollen S -gene. A number of approaches that have been used to accomplish this objective are discussed. Differential display and subtractive hybridization have yielded the most promising results: cDNAs corresponding to 13 pollen-expressed genes that lie within 1 cM of the S-RNase gene have been identified. They will be used as markers to identify large S -linked genomic fragments which will then be examined for the presence of the pollen S -gene by plant transformation.
... The S alleles of the Solanaceae species encoding the S-RNase are highly divergent, with amino acid sequence identities ranging from 38 to 98% Clark and Kao, 1991;Tsai et al., 1992). The degree of amino acid sequence divergence within a species is similar to the degree of amino acid sequence divergence between species. ...
Self-incompatibility is a common mechanism by which flowering plants can exert some control over the process of fertilization. Typically, the self-incompatibility response involves the recognition and rejection of self-incompatible pollen which leads to a block in self-fertilization and, as a consequence, promotes outcrossing. In recent years, considerable progress has been made in the molecular understanding of several self-incompatibility systems. Interestingly, a common mechanism for self-incompatibility is not employed by all flowering plants, but in fact quite diverse mechanisms have been recruited for the rejection of self-incompatible pollen. In this review, the recent advances in the self-incompatibility systems of the Solanaceae, Papaveraceae, and Brassicaceae will be described as well as some of the molecular work that is emerging for the Poaceae and the heteromorphic self-incompatibility systems.
... d N /d S ratios > 1 have been found in many plant families, both in gametophytic and sporophytic SI systems (Clark and Kao 1991;Ishimizu et al. 1998;Sato et al. 2002;Takebayashi et al. 2003;Igic et al. 2007;Guo et al. 2011). d N /d S ratios > 1 were corroborated with additional data to infer the action of balancing selection: significantly positive Tajima's D values, little population structure compared to neutral markers, and low recombination for SRK and SCR in Brassica cretica (Edh et al. 2009), trans-species polymorphisms in SRK and SCR in several Arabidopsis species (Sato et al. 2002;Guo et al. 2011). ...
Allorecognition is the ability of an organism to differentiate self or close relatives from unrelated individuals. The best known applications of allorecognition are the prevention of inbreeding in hermaphroditic species (e.g., the self-incompatibility [SI] systems in plants), the vertebrate immune response to foreign antigens mediated by MHC loci, and somatic fusion, where two genetically independent individuals physically join to become a chimera. In the few model systems where the loci governing allorecognition outcomes have been identified, the corresponding proteins have exhibited exceptional polymorphism. But information about the evolution of this polymorphism outside MHC is limited. We address this subject in the ascidian Botryllus schlosseri, where allorecognition outcomes are determined by a single locus, called FuHC (Fusion/HistoCompatibility). Molecular variation in FuHC is distributed almost entirely within populations, with very little evidence for differentiation among different populations. Mutation plays a larger role than recombination in the creation of FuHC polymorphism. A selection statistic, neutrality tests, and distribution of variation within and among different populations all provide evidence for selection acting on FuHC, but are not in agreement as to whether the selection is balancing or directional.
... Much progress has been made in understanding the molecular evolution of S-genes in Solanaceae (Richman and Kohn 2000 ). Point mutations and cross-species-diversifying selection are the primary sources for S-gene polymorphism in gametophytic SI systems (Ebert et al. 1989; Ioerger et al. 1990; Clark and Kao 1991; Coleman and Kao 1992; Saba-El-Leil et al. 1994, Charlesworth and Guttman 1997). A similar conclusion was reached after the S-RNase genes of Rosaceae were analysed evolutionarily (Ishimizu et al. 1998; Ma and Oliveira, unpublished data). ...
Almond (Prunus dulcis) displays gametophytic self-incompatibility. In the work reported here, we cloned two novel S-RNase genes from almond cultivar Ferragnès (genotype S1S3) using PCR. The S1-RNase gene has the same coding region as the Sb gene cloned from almond cultivated in the USA; however, their introns are different in sequence. S1 was cloned and sequenced
from six different cultivars originating in Europe. The full-length of the S3-RNase gene was cloned using two primers corresponding to the start and stop codons contexts. Two introns are present in the
S3 gene, unique among the S-RNase genes. Sequence-specific PCR was performed to confirm that the two cloned genes co-segregate
with the S-locus using progenies of a controlled cross between Tuono (S1Sf) and Ferragnès (S1S3). Based on the structural differences of S- and S-like RNase genes, we discuss the evolutionary relationship between the two groups of RNase genes.
... Comparisons of different S-RNase alleles in rosaceous and solanaceous species revealed a single variable (RHV) and two hypervariable (HVa and HVb) regions, respectively (Ioerger et al. 1991;Kheyr-Pour et al. 1990;Ushijima et al. 1998). The hypervariable regions appear to be under positive selection (Clark andKao 1991, Ishimizu et al. 1998) and are believed to be important for allelespecific recognition and triggering of the GSI response. Since we anticipate that S-RNase and SFB interact in an allele-specific manner, we expect the presence of variable regions, which would interact with the variable regions of the S-RNases, to be under positive selection in SFB. ...
The gene SFB encodes an F-box protein that has appropriate S-haplotype-specific variation to be the pollen determinant in the S-RNase-based gametophytic self-incompatibility (GSI) reaction in Prunus (Rosaceae). To further characterize Prunus SFB, we cloned and sequenced four additional alleles from sweet cherry (P. avium), SFB
1
, SFB
2
, SFB
4
, and SFB
5
. These four alleles showed haplotype-specific sequence diversity similar to the other nine SFB alleles that have been cloned. In an amino acid alignment of Prunus SFBs, including the four newly cloned alleles, 121 out of the 384 sites were conserved and an additional 65 sites had only conservative replacements. Amino acid identity among the SFBs ranged from 66.0% to 82.5%. Based on normed variability indices (NVI), 34 of the non-conserved sites were considered to be highly variable. Most of the variable sites were located at the C-terminal region. A window-averaged plot of NVI indicated that there were two variable and two hypervariable regions. These variable and hypervariable regions appeared to be hydrophilic or at least not strongly hydrophobic, which suggests that these regions may be exposed on the surface and function in the allele specificity of the GSI reaction. Evidence of positive selection was detected using maximum likelihood methods with sites under positive selection concentrated in the variable and hypervariable regions.
Amino acid replacements in the peptide-binding region (PBR) of the functional major histocompatibility complex (Mhc) genes appear to be driven by balancing selection. Of the various types of balancing selection, we have examined a model equivalent to overdominance that confers heterozygote advantage. As discussed by A. Robertson, overdominance selection tends to maintain alleles that have more or less the same degree of heterozygote advantage. Because of this symmetry, the model makes various testable predictions about the genealogical relationships among different alleles and provides ways of analyzing DNA sequences of Mhc alleles. In this paper, we analyze DNA sequences of 85 alleles at the HLA-A, -B, -C, -DRB1 and -DQB1 loci with respect to the number of alleles and extent of nucleotide differences at the PBR, as well as at the synonymous (presumably neutral) sites. Theory suggests that the number of alleles that differ at the sites targeted by selection (presumably the nonsynonymous sites in the PBR) should be equal to the mean number of nucleotide substitutions among pairs of alleles. We also demonstrate that the nucleotide substitution rate at the targeted sites relative to that of neutral sites may be much larger than 1. The predictions of the presented model are in surprisingly good agreement with the actual data and thus provide means for inferring certain population parameters. For overdominance selection in a finite population at equilibrium, the product of selection intensity (s) against homozygotes and the effective population size (N) is estimated to be 350-3000, being largest at the B locus and smallest at the C locus. We argue that N is of the order of 10(5) and s is several percent at most, if the mutation rate per site per generation is 10(-8).
The properties of gene and allelic genealogies at a gametophytic self-incompatibility locus in plants have been investigated analytically and checked against extensive numerical simulations. It is found that, as with overdominant loci, there are two genealogical processes with markedly different time scales. First, functionally distinct allelic lines diverge on an extremely long time scale which is inversely related to the mutation rate to new alleles. These alleles show a genealogical structure which is similar, after an appropriate rescaling of time, to that described by the coalescent process for genes at a neutral locus. Second, gene copies sampled within the same functional allelic line show genealogical relationships similar to neutral gene genealogies but on a much shorter time scale, which is on the same order of magnitude as the harmonic mean of the number of gene copies within an allelic line. These results are discussed in relation to data showing trans-specific polymorphisms for alleles at the gametophytic self-incompatibility locus in the Solanaceae. It is shown that population sizes on the order of 4 x 10(5) and a mutation rate per locus per generation as high as 10(-6) could account for estimated allelic divergence times in this family.
Self-incompatibility (SI) is a genetically controlled cell–cell recognition system that acts as a barrier to self-pollination in a wide range of flowering plant species. Several different SI mechanisms have been identified.
The floral polymorphism tristyly involves three style morphs with a reciprocal arrangement of stigma and anther heights governed by two diallelic loci (S and M). Tristyly functions to promote cross-pollination, but modifications to stamen position commonly cause transitions to selfing. Here, we integrate whole genome sequencing and genetic mapping to investigate the genetic architecture of the M locus and the genetic basis of independent transitions to selfing in tristylous Eichhornia paniculata. We crossed independently derived semi-homostylous selfing variants of the long- and mid-styled morph fixed for alternate alleles at the M locus (ssmm and ssMM, respectively) and backcrossed the F1 to the parental ssmm genotype. We phenotyped and genotyped 462 backcross progeny using 1450 genotyping-by-sequencing (GBS) markers and performed composite interval mapping to identify quantitative trait loci (QTL) governing style length and anther height variation. A QTL associated with the primary style-morph differences (style length and anther height) mapped to linkage group 5 and spanned ~13-27.5 Mbp of assembled sequence. Bulk segregant analysis identified 334 genes containing SNPs potentially linked to the M locus. The stamen modifications characterizing each selfing variant were governed by loci on different linkage groups. Our results provide an important step towards identifying the M locus and demonstrate that transitions to selfing have originated by independent sets of mating-system modifier genes unlinked to the M locus, a pattern inconsistent with a recombinational origin of selfing variants at a putative supergene. This article is protected by copyright. All rights reserved.
Self-incompatibility is a cell-cell recognition system in higher plants that is based on the ability of the pistil to discriminate “self”-pollen from “non-self”-pollen. In the simplest systems, this recognition response is controlled by a single locus — the S-locus — with multiple alleles. Pollination of a pistil with pollen bearing an S-allele recognition factor identical to that expressed in the host plant stigma or style results in rejection of the “self”-pollen. Most of the studies on the molecular genetics of self-incompatibility that are summarized in this review have had as their goal the identification and characterization of the gene product(s) associated with the self-incompatibility response. These studies have provided a great deal of new and important information about self-incompatibility — despite the fact that many critical questions remain unresolved. Taken together, the present evidence from these studies indicates that the self-incompatibility response is likely to be far more complex than suggested by historical models.
Sexual reproduction in any organism must fulfill two primary functions, maintain stability of the species and provide a reasonable degree of genetic variability within it. These functions are attained through the ability to recognize and select suitable gametes for fertilization. Different groups of plants display variations in the operation of the recognition process. In cryptogams, male and female gametes are released free into an aqueous medium and hence are in direct contact; thus recognition is dependent on the gametes themselves — no other cell or tissue being involved.
A central problem of biology is the description, classification and management of organic diversity. In one form or another this theme pervades biological science from the ecosystem level down to the population level. Diversity also has a central role in the science of genetics which originated from attempts to uncover the rules that govern the transmission of phenotypic variations between generations. Every student of introductory biology learns that the Mendelian method requires alternate allelic forms of a gene for any genetic analysis. Similarly, plant and animal improvement programs are absolutely dependent on useful genetic variants to achieve their goals of greater agricultural productivity (Brown et al., 1988; Day et al., 1991).
During the course of evolution, recognition mechanisms that prevent self-fertilization. in flowering plants have been selected. These mechanisms, named self-incompatibility, allow self-pollen rejection by the pistil. In most cases, the self-incompatibility response is under die genetic control of a single multiallelic locus, the S (Self-incompatibility) locus. Depending on the genetic control of the self-pollen rejection, two major classes of self-incompatibility systems have been described. The most common systems correspond to the gametophytic self-incompatibility, which has been well characterized in the Solanacene and in the Papaveraceae. The second type of self-incompatibility systems corresponds to the sporophytic self-incompatibility, particularly well studied in the Brassicaceae. In the review article, we present recent advances in understanding the molecular events that lead to pollen recognition and rejection in both systems. Interestingly, different molecules and signaling pathways of a have been recruited during evolution of flowering plants to answer the same biological question: how to discriminate male partners and to efficiently prevent self-fertilization by the pistil of hermaphroditic flowers ? The origin and molecular evolution of these multiallelic systems is discussed.
Self-incompatibility (SI), ‘the inability of a fertile hermaphrodite seed plant to produce zygotes after self-pollination’ (de Nettancourt 1977), is one of the mechanisms that has evolved to encourage outbreeding in flowering plants. The effectiveness of self-incompatibility in promoting outbreeding is believed to be one of the most important factors which ensured the evolutionary success of flowering plants (Whitehouse 1951). In many cases, it is controlled by a multi-allelic single locus, the S-locus. There have been a number of key reviews of the early work on the subject, the most significant of which is the classic work Incompatibility in Angiosperms by de Nettancourt (1977). Other early reviews are by Lewis (1949, 1979), Pandey (1979), Heslop-Harrison (1975, 1982, 1983) and de Nettancourt (1984). More recent reviews are by Ebert et al. (1989), Haring et al. (1990), Mau et al. (1991), Thompson and Kirch (1992), Sims (1993) and Newbigin and Clarke (1993).
Genetically determined self-incompatibility has arisen many times in the course of evolution, and there is a broad diversity of mechanisms by which these loci prevent self-fertilization (de Nettancourt 1977). Population geneticists have provided a rich theory for the origin and maintenance of genetically-determined self-incompatibility, and the problem is sufficiently intricate that there remain many unanswered questions about the evolution of self-incompatibility. Recent progress in the molecular basis for self-incompatibility has revealed common features, including highly divergent molecular sequences of alleles. High allelic sequence divergence has been observed in mating system genes of Neurospora (Glass et al. 1988), Ustilago (Schulz et al. 1990), sporophytic incompatibility loci in Brassica (Nasrallah et al. 1985, 1987; Nasrallah and Nasrallah 1989), and the gametophytic self-incompatibility locus in Solanaceae (Ioerger et al. 1990; Newbigin et al. (Chapter 1), this volume). This chapter will focus on the gametophytic system of self-incompatibility in Solanaceae. A more general review of the evolution of self-incompatibility, including the special case of heterostyly, can be found in Barrett (1988; see also Barrett (Chapter 10), this volume).
The self-incompatibility (S) gene in flowering plants has long been appreciated as an example of extreme allelic polymorphism maintained by frequency-dependent selection. Recent studies of population samples of S-allele sequences obtained by RT-PCR from five species of Solanaceae now reveal a picture of conspicuous inter-specific variation in both S-allele number and age. Explanations for this variation are examined with reference to current theory. We propose that changes in species’ effective population size, particularly those associated with the evolution of different life histories, best account for interspecific differences in both the number and average age of S alleles.
The most famous, if not necessarily the first, description of gametophytic self-incompatibility in Petunia was given by Charles Darwin (1876), who noted:
... for protected flowers, with their own pollen placed on the stigma, never yielded nearly a full complement of seed; whilst those left uncovered produced fine capsules, showing that pollen from other plants must have been brought to them, probably by moths. Plants growing vigorously and flowering in pots in the greenhouse, never yielded a single capsule...
Since that time, Petunia,especially Petunia hybrida, has been a system of choice not only for many studies on gametophytic self-incompatibility, but also for research in different areas of plant molecular genetics (Linskens 1975; de Nettancourt 1977; Hanson and Kool 1984). There are several reasons for the popularity of this organism for experimental studies. The plant is grown easily under a variety of greenhouse conditions and clonal stocks are easily propagated by vegetative cuttings. Flowering in Petunia is indeterminate, non-obligate (quantitative, LDP) for photoperiod (Armitage 1985), and the plants flower profusely. The large size of flowers and floral organs makes collection of material for biochemical studies relatively painless. Petunia hybrida varieties are readily transformed using vectors from Agrobacterium tumefaciens,and transformed cells easily regenerated to give fertile plants (Horsch et al. 1988). Because of the long history of Petunia as a garden bedding plant, a wide variety of genetic material is available. This includes the di-haploid Petunia hybrida cv. Mitchell, used for a majority of molecular genetic studies, commercial hybrid lines, and inbred lines. In addition to Petunia hybrida, non-commercial Petunia species have been used for studies of gametophytic self-incompatibility as well as for investigations of Petunia taxonomy (Ascher 1984; Sink 1984; Ai et al. 1990). Several of the Petunia species having 2n = 14 chromosomes, can form sexual or somatic hybrids with each other (Hanson and Kool 1984). Besides P. hybrida,these include: P. inflata, P. axillaris, P. violacea,P. parodii, and P. parvora.
This chapter examines homomorphic self-incompatibility. To escape inbreeding, angiosperms have developed well-organized systems such as dichogamy and self-incompatibility. Plants having self-incompatibility cannot achieve fertilization with the sperm of self-pollen, although they produce functional male and female organs. Self-incompatibility involves a recognition reaction between self and non-self in higher plants. In higher plants, recognition reactions are only known in the pollination system, involving self- and interspecific incompatibility, and in plant–pathogen interactions. The homomorphic type of self-incompatibility includes sporophytic and gametophytic systems, which are defined by the action of S genes. In the sporophytic system, the behavior of pollen tubes is determined by the phenotype of the sporophyte, by which the pollen is produced. The self-incompatibility system is composed of three stages: (1) germination of the pollen grain, (2) ability of the pollen tube to penetrate the cuticle of the stigmatic papilla, and (3) interaction of substances secreted by the pollen tube with products of the stigmatic cytoplasm. A signal transduction system appears to be involved in sporophytic incompatibility, as SRK (S-receptor kinase) genes are found. Such genes have not been found to be involved in gametophytic incompatibility.
Influenza A viruses are known for their rapid mutations, frequent reassortments, and RNA recombinations. The availability of the genomic sequences provides an opportunity for us to understand evolutionary process better than in the past. In this chapter, we will review recent research progresses and challenges in molecular evolution for both seasonal influenza and avian influenza viruses. The topics discussed include positive selection, reassortant identification, genotyping, RNA recombination, and the molecular clock in influenza A virus. Both common and uncommon features of previous pandemic strains, seasonal influenza viruses, swine influenza viruses, avian influenza viruses (especially H5N1), and other influenza A viruses are reviewed. The challenges for influenza molecular evolution studies will also be discussed.
Pigmentation traits in adult Drosophila melanogaster were used in this study to investigate how phenotypic variations of continuous ecological traits can be maintained in a natural population. First, pigmentation variation in the adult female was measured at seven different body positions in 20 strains from the Drosophila melanogaster Genetic Reference Panel (DGRP) originating from a natural population in North Carolina. Next, to assess the contributions of cis-regulatory polymorphisms of the genes involved in the melanin biosynthesis pathway, allele-specific expression levels of four genes were quantified by amplicon sequencing using a 454 GS Junior. Among those genes, ebony was significantly associated with pigmentation intensity of the thoracic segment. Detailed sequence analysis of the gene regulatory regions of this gene indicated that many different functional cis-regulatory alleles are segregating in the population and that variations outside the core enhancer element could potentially play important roles in the regulation of gene expression. In addition, a slight enrichment of distantly associated SNP pairs was observed in the ~10 kb cis-regulatory region of ebony, which suggested the presence of interacting elements scattered across the region. In contrast, sequence analysis in the core cis-regulatory region of tan indicated that SNPs within the region are significantly associated with allele-specific expression level of this gene. Collectively, the data suggest that the underlying genetic differences in the cis-regulatory regions that control intraspecific pigmentation variation can be more complex than those of interspecific pigmentation trait differences, where causal genetic changes are typically confined to modular enhancer elements. This article is protected by copyright. All rights reserved.
Tyrosine kinase 2 (TYK2), Janus kinase 1 (JAK1), and signal transducer and activator of transcription 3 (STAT3) all play critical roles in innate and acquired immunity. In this study, we investigated the association between the TYK2, JAK1, and STAT3 genes and genetic susceptibility to nonspecific digestive disorder (NSDD) in rabbits. Five coding single-nucleotide polymorphisms (cSNPs) in TYK2 were detected in New Zealand White (NZW) rabbits with direct sequencing, and two of them, c.1477 (C>T) and c.2013 (C>T), from two different linkage disequilibrium blocks, were further genotyped. A case-control association analysis revealed that allele C (c.1477) in TYK2 increases the risk of NSDD (odds ratio [OR]: 1.21; 95% confidence interval [CI] 1.036-2.145; P=0.021), whereas allele C (c.2013) plays a potentially protective role against NSDD (OR: 0.41; 95% CI 0.2996-0.5705; P<0.001). A gene×gene interaction analysis with a multifactor dimensionality reduction (MDR) method indicated that the combination of c.1477 from TYK2 and c.831 from STAT3 is associated with the susceptibility to NSDD (OR: 7.2567; 95% CI: 4.7306-11.1317; P<0.0001). Together, our data demonstrate that the TYK2 gene is associated with NSDD in rabbits. The TYK2, JAK1, and STAT3 combination model may be used to assist breeders in selecting rabbits.
This chapter discusses some practical consequences of disconnections between organizational and hierarchical levels when molecular data are used to reconstruct phylogeny. Crossing from a lower to a higher level—from genes to species or from genotype to phenotype—can simultaneously introduce new kinds of homoplasy and mask homoplasy from the lower level. Sources of homoplasy in reconstructions of “phylogenies” of nucleic acid sequences are presented to illustrate the concept of gene trees. The relationship of homoplasy in single gene trees to homoplasy in multiple gene trees is also discussed. Combining the gene trees help in reconstructing the phylogeny of something other than that of genes themselves, resulting in “species trees” or “organism trees.” The chapter presents species-level problems and deals with the issue of homoplasy in combined data sets involving closely related species. The chapter also provides a discussion on the role of character independence in phylogeny.
The field of systematic biology has been revitalized and transformed during the last few decades by the confluence of phylogenetic thinking with ready access to the tools of molecular biology. Indeed, the title of this volume and the fact that it is already in its second edition offers ample testimony to the impact that molecular approaches have had on efforts to reconstruct the phylogenetic history of plants. Concomitant with the proliferation of molecular tools has been a growing awareness that reliance on a single data set may often result in insufficient phylogenetic resolution or misleading inferences. Accordingly, it is an increasingly widespread practice to apply multiple data sets to a common group of taxa. One of the consequences of analyzing multiple data sets is that the phylogenies inferred may differ from each other in one or more details. This phylogenetic incongruence is not rare; to the contrary, it is almost the rule rather than the exception, being evident to varying degrees.
Sesame (Sesamum indicum L.) is one of the oldest and most nutritional oilseed crops, of which domestication history has been poorly understood. This study suggested that sesame has undergone domestication bottleneck during its use for a long time. In this investigation, the molecular analysis included 4.4 Mbp of the genomic DNA of sesame comprising stearoyl acyl desaturase (sad), fatty acid desaturase 2 (fad2) and omega 3 fatty acid desaturase (o3fad) genes in 99 accessions of four populations of sesame germplasm namely: wild species, landraces, improved cultivars and introgressed lines. Results indicated that the improved cultivars and landraces lost 46.6 and 36.7% of nucleotide diversity, respectively, which indicate that the genetic diversity of the crop had been eroded due to selection after domestication. However, there was no significant reduction in genetic diversity of improved cultivars compared with landraces, indicating that unique improved cultivars generated through crosses were of less frequency in this population. Moreover, introgressed lines retained only 17.77% (π) and 4.57% (θ) of landrace diversity. To evaluate the impact of selection across fatty acid biosynthetic pathway, individual nucleotide diversity at three major genes involved in the pathway was surveyed. The analysis between wild and improved cultivars supported positive selection in fad2 and o3fad loci. Though locus-to-locus sequence variation was observed, positive results with two most important loci supported selection after domestication. Reduced diversity in these critical quality governing genes in improved cultivars suggested that future sesame cultivation would benefit from the incorporation of alleles from sesame's wild relatives.
Many sessile colonial organisms intensively compete with conspecifics for growing space. This competition can result in either cooperative fusion or aggressive rejection between colonies, and some species have evolved highly polymorphic genetic systems that mediate the outcome of these interactions. Here we demonstrate the potential for interactions among close kin as the basis for the evolutionary maintenance of a genetically polymorphic allorecognition system in the colonial hydroid Hydractinia symbiolongicarpus, which lives on gastropod shells occupied by hermit crabs. Fusion between hydroids in the laboratory is restricted mainly to encounters between full siblings, whereas other encounters result in aggressive rejection. Natural selection acting on the costs or benefits of fusion between colonies could be responsible for the present maintenance of such a highly specific behavioral response, but only if encounters between fusible colonies still occur in contemporary populations. The large size of these hydroid populations and the mobility of the crabs should limit the potential for interactions among closely related hydroids on the same shell. However, RAPD polymorphisms among a large sample of hydroids from a population off the coast of Massachusetts indicate that genetically similar colonies are often found together on the same shell. Some genetic distances between colonies on the same shell were low relative to genetic distances between colonies on different shells or genetic distances between known full siblings from laboratory matings. We conservatively estimate that 2-18% of co-occurring colonies may be full sibling pairs. These observations suggest that encounters between genetically similar hydroids are common, despite the mobile nature of their habitat, and these encounters may provide frequent opportunities for natural selection to influence the evolution of cooperative and agonistic behaviors and their polymorphic genetic basis.
The majority of flowering plant species are hermaphrodites and possess flowers in which the male and female organs are in close proximity. Despite this proximity, outcrossing is favored in a large number of these species because of the action of self-incompatibility (SI) systems that permit the pistil to reject self-pollen. The chapter discusses the nature of the male component, the putative ligand for the S-locus receptor-like kinase (SRK) receptor. This is important with regard to the mechanism of SI because it would provide a means of testing the hypothesis that the members of the receptor tyrosine kinase (RLK) superfamily function as receptors. A major advantage of the SI system is that the male component of the SI response is predicted to be encoded by a gene located at the S locus. A combination of biochemical and map-based approaches will lead to the identification of this gene in the near future.
S-allele diversity in Solanum carolinense was surveyed in two natural populations, located in Tennessee and North Carolina, with a molecular assay to determine the genotype of individual plants. A total of 13 different S-alleles were identified and sequenced. There is high overlap between the two populations sampled, with 10 alleles shared in common, one allele found only in Tennessee, and two found only in North Carolina. The number of alleles in this species appears to be extremely low compared with other species with gametophytic self-incompatibility. Sequence comparisons show that most alleles are extremely different one from another in their primary sequence and a phylogenetic analysis indicates extensive trans-specific evolution of S-lineages. In addition, some alleles appear to be derived much more recently. The implications of these observations are discussed in the light of recent theoretical results on S-allele population diversity and persistence.
In marine species, high dispersal is often associated with only mild genetic differentiation over large spatial scales. Despite this generalization, there are numerous reasons for the accumulation of genetic differences between,large, semi-isolated marine populations. A suite of well-known evolutionary mechanisms can operate within and between populations to result in genetic divergence, and these mechanisms may well be augmented by newly discovered genetic processes. This variety of mechanisms for genetic divergence is paralleled by great diversity in the types of reproductive isolation shown by recently diverged marine species. Differences in spawning time, mate recognition, environmental tolerance, and gamete compatibility have all been implicated in marine speciation events. There is substantial evidence for rapid evolution of reproductive isolation in strictly allopatric populations (e.g. across the Isthmus of Panama). Evidence for the action of selection in increasing reproductive isolation in sympatric populations is fragmentary. Although a great deal of information is available on population genetics, reproductive isolation, and cryptic or sibling species in marine environments, the influence of particular genetic changes on reproductive isolation is poorly understood for marine (or terrestrial) taxa. For a few systems, like the co-evolution of gamete recognition proteins, changes in a small number of genes may give rise to reproductive isolation. Such studies show how a focus on the physiology, ecology, or sensory biology of reproductive isolation can help uncover the genetic changes associated with speciation and can also help provide a link between the genetics of population divergence and the speciation process.
▪ Abstract Trans-species polymorphism (TSP) is the occurrence of similar alleles in related species. Excluding instances in which the similarity arose by convergent evolution, TSP is generated by the passage of alleles from ancestral to descendant species. Closely related, recently diverged species, such as those of the Lake Victoria cichlid flock, may share neutral alleles, but long-lasting TSPs occur only in genetic systems evolving under balancing selection. Two such systems have been studied extensively, the major histocompatibility complex (Mhc) of jawed vertebrates and the self-incompatibility (SI) system of flowering plants. Allelic lineages that diverged many millions of years ago and passed through numerous speciation events have been described in both systems. The lineages may differ at up to 50% of their coding sites, both synonymous and nonsynonymous. The differences arise by the process of incorporation of mutations, which is different from the process of fixation. TSP, on the one hand, compl...
The application of genomic approaches to marine biota has profoundly altered our understanding of life in the oceans, especially regarding concepts of adaptation, speciation and evolution. The avalanche of genomic data has provided an unbiased view of marine biology that has never been seen before. In particular, comparative and metagenomic approaches with microbes from different biogeochemical marine provinces provided the first insights into how they acquire and discard genes as needed, even across kingdom boundaries, in response to their environment. These data clearly reveal that marine microbes have remarkable abilities to change their genomes according to both environmental stresses and biotic interactions. Thus, it is most likely that the flux of energy and matter in the marine system is reflected by the presence or absence of genes and proteins in marine organisms, which could provide novel tools to understand biogeochemical processes of global significance. However, the challenge is to put the reductionistic knowledge gained by genomics and metagenomics into the larger contexts of cellular systems and ecosystems to identify emergent properties that could not have been predicted by breaking down the whole into its individual parts.
Abstract In gametophytic self-incompatibility, the S-locus encodes an S-protein whose expression results in successful pollination only when the pollen allele differs from both maternal alleles. Analysis of nucleotide and amino acid sequences of a number of S-alleles has revealed extraordinary allelic sequence divergence and an excess of interspecific shared polymorphism. Population genetic theory and analysis of the distribution of the number of shared polymorphic sites verifies that the sequence diversity is consistent with the alleles being extraordinarily old. Theory also predicts that S-alleles will exhibit less population structuring in a subdivided population than will a neutral locus, and data are being collected to test this. Self-incompatibility must involve two features - a pollen component that specifies the identity of the pollen and a pistil component that recognizes and elicits a response to self-pollen. The S-locus clearly determines the pistil component, but lack of expression of S in pollen leaves open the possibility that there may be another pollen factor. Experiments with transgenic plants have demonstrated that the S-protein expression in the pistil is necessary and sufficient to determine the pistil phenotype. However, several lines of evidence suggest that the degree of elimination of self-pollen in plants with gametophytic self-incompatibility depends on additional genetic factors besides the S-locus. Modifiers may affect self-incompatibility by affecting either the pollen component, the pistil component or both. Population genetic models that test the consequences of modification of these two components are reviewed and extended. Conditions for invasion of reduced degree of self-incompatibility depend in part on the level of inbreeding depression.
Chalcone synthase (CHS) is a small multigene family with at least four members (CHS-A, B, C and PS) in common morning glory Ipomoea purpurea ROTH. The chalcone synthase enzyme performs the initial condensation reaction that results in the 15-carbon three-ring structure that is the backbone of flavonoid biosynthesis. The biochemical pathway that commences with CHS is important in plant disease defence, pigment biosynthesis and UV protection. Accordingly, it is of substantial interest to characterize levels and patterns of molecular diversity for genes that encode this important enzyme. We report the sequence of 19 CHS-A alleles from Mexican and American populations of common morning glory. American populations of this annual self-compatible vine are believed to have been introduced from Mexico, where the species is native. Individual plants were sampled from populations of common morning glory throughout Mexico and the south-eastern USA. Four American alleles were sequenced and these, together with one allele from Mexico City, were identical in primary nucleotide sequence. These data suggest a restricted origin for the American population, probably as a consequence of selection for domestication by pre-Columbian peoples. Additionally the Mitontic (Chiapas, Mexico) population is significantly more homogeneous than expected by chance indicating that this population may also have experienced a recent population bottleneck. Estimates of nucleotide diversity from the Mexican CHS-A alleles were high. We present evidence that these estimates may, in part, result from low to moderate levels of interlocus recombination/gene conversion. We also present evidence that the ancient duplication of the CHS gene family, preceding the origin of the genus Ipomoea, was associated with heterogeneity in the rate of substitution between the resulting gene family members. The group of gene family members whose sequences possess a signature amino acid of the closely related Stilbene synthase exhibit a significantly faster proportional rate of nonsynonymous substitution.
The multi-allelic self-incompatibility polymorphisms in angiosperms have long interested geneticists and population geneticists, but the limits of classical genetic resolution were reached many years ago. In recent years, new progress has been made by molecular genetic approaches. Intriguing similarities to and differences from the fungal systems are emerging. The polymorphism at these loci is now known to be even more baroque than appeared from classical genetic studies. Alleles differ so much at the level of both the DNA and protein sequence that they would be difficult to recognise as products of the same locus, were it not for the presence of certain conserved regions. Despite the successes of the recent work, the locus responsible for the specificity of the incompatibility reaction in pollen, and the mechanism of self-incompatibility, remain elusive.
Comparison of numbers of synonymous and nonsynonymous substitutions is useful for understanding mechanisms of molecular evolution.
In this paper, I examine the statistical properties of six methods of estimating numbers of synonymous and nonsynonymous substitutions.
The six methods are Miyata and Yasunaga’s (MY) method; Nei and Gojobori’s (NG) method; Li, Wu and Luo’s (LWL) method; Pamilo,
Bianchi and Li’s (PBL) method; and Ina’s (Ina) two methods. When the transition/transversion bias at the mutation level is
strong, the numbers of synonymous and nonsynonymous substitutions are estimated more accurately by the PBL and Ina methods
than by the NG, MY and LWL methods. When the nucleotide-frequency bias is strong and distantly related sequences are compared,
all the six methods give underestimates of the number of synonymous substitutions. The concept of synonymous and nonsynonymous
categories is also useful for analysis of DNA polymorphism data.
A complex picture of S-loci is beginning to emerge from recent studies of the S-locus of RNase-based gametophytic self-incompatibility displayed by the Rosaceae, Solanaceae, and Scrophulariaceae, and of
the S-locus of the type of sporophytic self-incompatibility displayed by the Brassicaceae. It now appears that not only do these
S-loci contain two separate genes, one controlling pollen function and the other controlling pistil function in self-incompatibility
interactions, but also many other genes whose functions are largely unknown. The implications of these recent findings for
the study of the mechanisms of self-incompatibililty interactions and evolution of the self-incompatibility systems are discussed.
Natural selection is the force driving evolution and therefore much effort has been invested in the deciphering and understanding
of the main mechanisms underlying such a force. Because of the main implications of identifying selective processes in proteins
and the perspectives for defining functional/structural amino acid sites in protein structures, many models have been devised
in order to search for shifts in the selective constraints throughout evolution. However, most of these models suffer from
simplistic assumptions that deem results inconclusive or ambiguous. In this chapter we discuss the importance of natural selection
in the emergence and generation of evolutionary novelties and the many different approaches built to identify the forces shaping
the evolution of proteins. We also highlight the fact that, despite the plethora of new mathematical/statistical methods to
identify selection at the molecular level, much remains to be done to build more realistic models. Molecular coevolution is
among the most promising approaches to tackle the simplistic assumptions of linearity of protein sequence evolution but the
field in this respect remains in its infancy. Here we discuss in depth the marriage between the linear sequence analysis of
selection and the three-dimensionality of proteins through coevolutionary analyses and urge researchers to account for amino
acid dependencies when looking for Darwin thoughts swamped in a sea of neutral evolution and pre-existing finite mutational
and fitness landscape.
cDNA clones for an S-allele, designated S5, of the self-incompatibility locus (S-locus) of Lycopersicon peruvianum have been isolated by probing a pistil cDNA library with cDNAs for S-alleles of Petunia inflata and Solanum chacoense. The longest S5-cDNA is 869 bp and contains an open reading frame of 217 amino acids. An alignment of the deduced amino acid sequence of S5-protein with that of the 18 S-proteins from five other solanaceous species is presented. Sequence comparison further refines the primary structural features of the S-proteins previously revealed from comparison of subsets of these sequences. Based on this comparison and evidence presented elsewhere, it is proposed that accumulation of point mutations, and not intragenic recombination, is responsible for the generation of new allelic specificities.
Apple (Malus × domestica Borkh.) is a typical Rosaceae species that exhibits gametophytic self-incompatibility (GSI) controlled by polymorphic S-alleles. In this study, the S-alleles of wild Malus species were amplified, sequenced and compared using polymerase chain reaction (PCR) technology. 21 S-alleles were identified in 27 wild Malus species. The results indicated that the overwhelming majority of S-alleles between wild Malus species and cultivars shared identical sequences. Simultaneously, five new S alleles (designated S
48
–S
52
) were identified in wild Malus species. There are the S
48
-RNase in M. angustifolia (Ation) Michaux, S
49
-RNase in M. orientalis Uglitzk. Ex Juz. and M. sylvestris (L.) Mill., S
50
-RNase in M. tschonoskii (Maxim.) C.K. Schneid. and M. sieversii (Ldb.) Roem., S
51
-RNase in M. komarovii (Sarg.) Rehd. and M. kansuensis (Batal.) C. K. Schneid., S
52
-RNase in M. manshurica (Maxim.) V. Komorov wild Malus species. Additionally, an S
1
-RNase was cloned in wild Malus prunifolia var. ringo, which have the same open reading frame as Malus × domestica cv. Fuji, but lacked whole intron.
KeywordsDetermination and identification–
S-Genotypes–
S-RNase–Wild Malus species
Since Darwinian times considerable knowledge has accumulated on the distribution, physiology and genetics of self-incompatibility
(SI) in higher plants. In the second half of this century the first attempts were made to identify the biochemical bases of
SI. These included thediscovery that cutinase enables pollen tube penetration at the surface* of the stigma in Cruciferae, sorting of segregation pollen S-phenotypes by serological techniques, a lock-and-key model of the SI reaction, the first detection
and characterisation of SI proteins and the discovery of the role of the tapetum in the determination of pollen phenotypes
in homomorphic sporophytic SI. This pioneering work was followed by a worldwide effort to identify and understand the cellular
and molecular processes which lead to the recognition and rejection of SI pollen. The present review article summarizes briefly
the current state of knowledge in areas essential for the understanding and exploitation of SI and outlines new information
that has become available during recent years.
Recent genetic analyses have demonstrated that self-incompatibility in flowering plants derives from the coordinated expression of a system of loci. To address the selective mechanisms through which a genetic system of this kind evolves, I present a three-locus model for the origin of gametophytic self-incompatibility. Conventional models assume that a single locus encodes all physiological effects associated with self-incompatibility and that the viability of offspring depends only on whether they were derived by selfing or outcrossing. My model explicitly represents the genetic determination of offspring viability by a locus subject to symmetrically overdominant selection. Initially, the level of expression of the proto-S locus is insufficient to induce self-incompatibility. Weak gametophytic self-incompatibility arises upon the introduction of a rare allele at an unlinked modifier locus which enhances the expression of the proto-S locus. While conventional models predict that the origin of self-incompatibility requires at least two- to threefold levels of inbreeding depression, I find that the comparatively low levels of inbreeding depression generated by a single overdominant locus can ensure the invasion of an enhancer of self-incompatibility under sufficiently high rates of receipt of self-pollen. Associations among components of the incompatibility system promote the origin of self-incompatibility. Enhancement of heterozygosity at the initially neutral proto-S locus improves offspring viability through associative overdominance. Further, the modifier that enhances the expression of self-incompatibility develops a direct association with heterozygosity at the overdominant viability locus. These results suggest that the evolutionary processes by which incompatibility systems originate may differ significantly from those associated with their breakdown. The genetic mechanism explored here may apply to the evolution of other systems that restrict reproduction, including maternal-fetal incompatibility in mammals.
Self-incompatibility (SI), a genetically controlled mechanism to prevent inbreeding in plants, offers a relatively simple model system for studying the interactions between plant cells or between a plant cell and the secreted product or products of another cell. Examples of two major types of SI, gametophytic and sporophytic, have been studied by cloning cDNAs corresponding to glycoproteins of the female tissues that segregate with particular variants encoded by the putative S locus. These secreted glycoproteins are envisaged to interact with the currently undescribed pollen component to cause arrest of pollen tube growth.
Certain major-histocompatibility-complex (MHC) loci are highly polymorphic, and the mechanism of maintenance of this polymorphism remains controversial. Recent studies of the pattern of nucleotide substitution at MHC loci have produced strong evidence that this polymorphism is maintained mainly by positive Darwinian selection that operates on the antigen recognition site (ARS) of the MHC molecule. The ARS of the class I MHC consists of three subregions: (1) the binding cleft, (2) T-cell-receptor-directed residues, and (3) outward-directed residues. Here we report that the rate of nonsynonymous nucleotide substitution is much higher in the binding cleft than in the other ARS subregions. Furthermore, nonsynonymous nucleotide substitutions that result in a change of residue side-chain charge occur significantly more frequently than expected by chance. We conclude that the main target of positive selection on the class I MHC molecules is the binding cleft of the ARS and that this selection acts primarily to promote diversity among alleles with respect to the pattern of residue side-chain charges (charge profile) in the binding cleft. These results provide additional support for the hypothesis that MHC polymorphism is maintained by overdominant selection relating to antigen-binding capacity and thus to disease resistance.
Different alleles undergoing strong symmetric balancing selection show a simple genealogical structure (allelic genealogy), similar to the gene genealogy described by the coalescence process for a sample of neutral genes randomly drawn from a panmictic population at equilibrium. The only difference between the two genealogies lies in the different time scales. An approximate scaling factor for allelic genealogy relative to that of neutral gene genealogy is [square root of S/(2M)].[In[S/(16 pi M2)]]-3/2, where M = Nu and S = 2Ns (N, effective population size; u, mutation rate to selected alleles per locus per generation; s, selection coefficient). The larger the value of square root of S/M (greater than or equal to 100), the larger the scaling factor. These findings, supported by simulation results, allow one to apply the theoretical results of the coalescence process directly to the allelic genealogy. Combined with the trans-species evolution of the major histocompatibility complex polymorphism for which balancing selection is believed to be responsible, allelic genealogy predicts that the number of breeding individuals in the human population could not be as small as 50-100 at any time of its evolutionary history. The analysis appears to contradict the founder principle as being important in recent mammalian evolution.
To explain the long-term persistence of polymorphic alleles (trans-specific polymorphism) at the major histocompatibility complex (MHC) loci in rodents and primates, a computer simulation study was conducted about the coalescence time of different alleles sampled under various forms of selection. At the same time, average heterozygosity, the number of alleles in a sample, and the rate of codon substitution were examined to explain the mechanism of maintenance of polymorphism at the MHC loci. The results obtained are as follows. (1) The coalescence time for neutral alleles is too short to explain the trans-specific polymorphism at the MHC loci. (2) Under overdominant selection, the coalescence time can be tens of millions of years, depending on the parameter values used. The average heterozygosity and the number of alleles observed are also high enough to explain MHC polymorphism. (3) The pathogen adaptation model proposed by Snell is incapable of explaining MHC polymorphism, since the coalescence time for this model is too short and the expected heterozygosity and the expected number of alleles are too small. (4) From the mathematical point of view, the minority advantage model of frequency-dependent selection is capable of explaining a high degree of polymorphism and trans-specific polymorphism. (5) The molecular mimicry hypothesis also gives a sufficiently long coalescence time when the mutation rate is low in the host but very high in the parasite. However, the expected heterozygosity and the expected number of alleles tend to be too small. (6) Consideration of the molecular mechanism of the function of MHC molecules and other biological observations suggest that the most important factor for the maintenance of MHC polymorphism is overdominant selection. However, some experiments are necessary to distinguish between the overdominance and frequency-dependent selection hypotheses.
Three alleles of the self-incompatibility gene of Nicotiana alata have been cloned and sequenced. A comparison of the sequences shows a surprisingly low level of homology (56%) and the presence of defined regions of homology and variability. The homologous regions include the N-terminal sequence, most of the cysteine residues and glycosylation sites, as well as other blocks throughout the sequence. We interpret these conserved regions as "framework" and nonconserved regions as "hypervariable," following the terminology used to describe analogous regions in the IgG supergene family. The low level of overall homology forms the basis of a general method for isolating S-allele-specific cDNAs. Allele-specific antibodies can be generated using synthetic peptides corresponding to one of the variable regions. When applied to sections of the pistil, these antibodies label the intercellular matrix in the stigma and transmitting tissue of the style and the cell walls in the epidermis of the placenta. HindIII digestion of genomic DNA generates a characteristic pattern of S-gene fragments for each genotype. These restriction fragment length polymorphisms can be used to assign S-genotype to progeny arising from breeding experiments.
Statistical tests for detecting gene conversion are described for a sample of homologous DNA sequences. The tests are based on imbalances in the distribution of segments on which some pair of sequences agrees. The methods automatically control for variable mutation rates along the genome and do not depend on a priori choices of potentially monophyletic subsets of the sample. The tests show strong evidence for multiple intragenic conversion events at two loci in Escherichia coli. The gnd locus in E. coli shows a highly significant excess of maximal segments of length 70-200 bp, which suggests conversion events of that size. The data also indicate that the rate of these short conversion events might be of the order of neutral mutation rate. There is also evidence for correlated mutation in adjacent codon positions. The same tests applied to a locus in an RNA virus were negative.
Multiple sequence alignment can be a useful technique for studying molecular evolution and analyzing sequence-structure relationships. Until recently, it has been impractical to apply dynamic programming, the most widely accepted method for producing pairwise alignments, to comparisons of more than three sequences. We describe the design and application of a tool for multiple alignment of amino acid sequences that implements a new algorithm that greatly reduces the computational demands of dynamic programming. This tool is able to align in reasonable time as many as eight sequences the length of an average protein.
The genetic code is degenerate, but alternative synonymous codons are generally not used with equal frequency. Since the pioneering work of Grantham'a group (1, 2) it has been apparent that genes from one species often share similarities incodon frequency; under the “genome hypothesis” (1, 2) there is a species-specific pattern to codon usage.
However, it has become clear that in most species there are also considerable differences among genes (3–7). Multivariate analyses have revealed that in each species so far examined there is a single major trend in codon usage among genes, usually from highly biased to more nearly even usage of synonymous codons. Thus, to represent the codon usage pattern of an organism it is not sufficient to sum over all genes (8), as this conceals the underlying heterogeneity. Rather, it is necessary to describe the trend among genes seen in that species. We illustrate these trends for six species where codon usage has been examined in detail, by presenting the pooled codon usage for the 10% of genes at either end of the major trend (Table 1).
Closely-related organisms have similar patterns of codon usage, and so the six species in Table 1 are representative of wider groups. For example, with respect to codon usage, Salmonella typhimurlum closely resembles E. coli (9), while all mammalian species so far examined (principally mouse, rat and cow) largely resemble humans (4, 8).
Concentrations of prostaglandins of the E and F series were estimated by radioimmunoassay in cerebrospinal fluid (CSF) of 30 febrile patients (infants and adults) and of 19 afebrile, adult patients. In CSF of all feverish patients with meningitis, pneumonia, or pyelonephritis, concentrations of prostaglandins of the E series were about twice higher than those of the afebrile subjects. In contrast, concentrations of prostaglandins of the F series remained largely unchanged during fever.
In accord with the results of animal experiments prostaglandins of the E series seem to act as mediators of fever during infectious diseases also in man.
U. maydis is a fungal pathogen of corn with two forms: one is yeast-like and nonpathogenic; the other is filamentous and pathogenic. The b locus, with 25 different alleles, regulates this dimorphism: any combination of two different alleles triggers pathogenic development, whereas the presence of identical alleles results in the yeast-like form. We have cloned four b alleles (b1, b2, b3, and b4) and show that the b locus contains a single open reading frame (ORF) of 410 amino acids with a variable N-terminal region and a highly conserved C-terminal region (60% and 93% identity, respectively). Mutational analysis confirms that this ORF is responsible for b activity. The b polypeptides appear to be DNA binding proteins because they contain a motif related to the homeodomain in their constant region. We propose that combinatorial interactions between b polypeptides generate regulatory proteins that determine the developmental program of the fungus.
We investigated the structure and expression of three S-alleles of Petunia hybrida in self-incompatible varieties and in a pseudo-self-compatible line in which the self-incompatibility response is defective. Comparison of derived amino acid sequences from different gametophytic S-alleles revealed a pattern of sequence conservation and variability that was highly nonrandom. In self-incompatible varieties, petunia S-locus mRNA accumulates preferentially in styles during the transition from bud self-compatibility to self-incompatibility. S-Allele sequences homologous to the cloned S1 allele were present in a pseudo-self-compatible variety, and were expressed at levels indistinguishable from those observed in a self-incompatible line homozygous for the S1 allele. Taken together, our data indicate that (1) limited sequence differences may confer allelic specificity, (2) S-locus mRNAs accumulate in a precise organ-specific pattern during floral development, and (3) the ability to inhibit the growth of incompatible pollen tubes appears to require a threshold accumulation of the stylar gene product, along with the participation of as yet undefined pollen gene products.
Sequences of 11 alleles of the gametophytic self-incompatibility locus (S locus) from three species of the Solanaceae family have recently been determined. Pairwise comparisons of these alleles reveal two unexpected observations: (i) amino acid sequence similarity can be as low as 40% within species and (ii) some interspecific similarities are higher than intraspecific similarities. The gene genealogy clearly illustrates this unusual pattern of relationships. The data suggest that some of the polymorphism at the S locus existed prior to the divergence of these species and has been maintained to the present. In support of this hypothesis, the number of shared polymorphic sites was found to exceed the number found in simulations with independent accumulation of mutations. Strictly neutral evolution is exceedingly unlikely to maintain the polymorphism for such a long time. The allele multiplicity and extreme age of the alleles is consistent with Wright's classic one-locus population genetic model of gametophytic self-incompatibility. Similarities between the plant S locus and the mammalian major histocompatibility complex are discussed.
We have isolated and sequenced cDNAs for S2- and S3-alleles of the self-incompatibility locus (S-locus) in Solanum chacoense Bitt., a wild potato species displaying gametophytic self-incompatibility. The S2- and S3-alleles encode pistil-specific proteins of 30 kDa and 31 kDa, respectively, which were previously identified based on cosegregation with their respective alleles in genetic crosses. The amino acid sequence homology between the S2- and S3-proteins is 41.5%. This high degree of sequence variability between alleles is a distinctive feature of the S-gene system. Of the 31 amino acid residues which were previously found to be conserved among three Nicotiana alata S-proteins (S2, S3, and S6) and two fungal ribonucleases (RNase T2 and RNase Rh), 27 are also conserved in the S2- and S3-proteins of S. chacoense. These residues include two histidines implicated in the active site of the RNase T2, six cysteines, four of which form disulfide bonds in RNase T2, and hydrophobic residues which might form the core structure of the protein. The finding that these residues are conserved among S-proteins with very divergent sequences suggests a functional role for the ribonuclease activity of the S-protein in gametophytic self-incompatibility.
The mating-type alleles A and a of Neurospora crassa control mating in the sexual cycle and function in establishing heterokaryon
incompatibility in the vegetative cycle. The A and a alleles were cloned, and they were shown to encode both the sexual functions
and vegetative incompatibility. The mating-type clones contain nonhomologous DNA segments that are flanked by common DNA sequences.
Neurospora crassa and all heterothallic and pseudohomothallic Neurospora species contain a single copy of one mating-type
sequence or the other within each haploid genome. The six known self-fertile homothallic isolates contain an A homolog, but
only one species also contains a homologous sequences. Homothallism in these species is not due to mating-type switching,
as it is in Saccharomyces cerevisiae.
The estimation of the amount of evolutionary divergence that has taken place between two DNA coding sequences depends strongly on the degree of constraint on amino acid replacements. If amino acid replacements are relatively unconstrained, the individual nucleotide is the appropriate unit of analysis and the method of Tajima and Nei can be used. If amino acid replacements are constrained, however, this method is shown to be inapplicable. For sequences with strong amino acid constraints, a method is outlined analogous to the Tajima and Nei method using codons as the unit of analysis. Only synonymous substitutions are used. Codon usage data can be employed to estimate the necessary parameters of the calculation, or a priori models of substitution may be employed. Sequences with significant but intermediate constraints on amino acid replacements are, in principle, unanalyzable.
The major histocompatibility complex (MHC) loci are known to be highly polymorphic in humans, mice and certain other mammals, with heterozygosity as high as 80-90% (ref. 1). Four different hypotheses have been proposed to explain this high degree of polymorphism: (1) a high mutation rate, (2) gene conversion or interlocus genetic exchange, (3) over dominant selection and (4) frequency-dependent selection. In an attempt to establish which of these hypotheses is correct, we examined the pattern of nucleotide substitution between polymorphic alleles in the region of the antigen recognition site (ARS) and other regions of human and mouse class I MHC genes. The results indicate that in ARS the rate of nonsynonymous (amino acid altering) substitution is significantly higher than that of synonymous substitution in both humans and mice, whereas in other regions the reverse is true. This observation, together with a theoretical study and other considerations, supports the hypothesis of overdominant selection (heterozygote advantage).
Two simple methods for estimating the numbers of synonymous and nonsynonymous nucleotide substitutions are presented. Although they give no weights to different types of codon substitutions, these methods give essentially the same results as those obtained by Miyata and Yasunaga's and by Li et al.'s methods. Computer simulation indicates that estimates of synonymous substitutions obtained by the two methods are quite accurate unless the number of nucleotide substitutions per site is very large. It is shown that all available methods tend to give an underestimate of the number of nonsynonymous substitutions when the number is large.
A new method called the neighbor-joining method is proposed for reconstructing phylogenetic trees from evolutionary distance data. The principle of this method is to find pairs of operational taxonomic units (OTUs [= neighbors]) that minimize the total branch length at each stage of clustering of OTUs starting with a starlike tree. The branch lengths as well as the topology of a parsimonious tree can quickly be obtained by using this method. Using computer simulation, we studied the efficiency of this method in obtaining the correct unrooted tree in comparison with that of five other tree-making methods: the unweighted pair group method of analysis, Farris's method, Sattath and Tversky's method, Li's method, and Tateno et al.'s modified Farris method. The new, neighbor-joining method and Sattath and Tversky's method are shown to be generally better than the other methods.
Simple but exact statistical tests for detecting a cluster of associated nucleotide changes in DNA are presented. The tests are based on the linear distribution of a set of s sites among a total of n sites, where the s sites may be the variable sites, sites of insertion/deletion, or categorized in some other way. These tests are especially useful for detecting gene conversion and intragenic recombination in a sample of DNA sequences. In this case, the sites of interest are those that correspond to particular ways of splitting the sequences into two groups (e.g., sequences A and D vs. sequences B, C, and E-J). Each such split is termed a phylogenetic partition. Application of these methods to a well-documented case of gene conversion in human gamma-globin genes shows that sites corresponding to two of the three observed partitions are significantly clustered, whereas application to hominoid mitochondrial DNA sequences--among which no recombination is expected to occur--shows no evidence of such clustering. This indicates that clustering of partition-specific sites is largely due to intragenic recombination or gene conversion. Alternative hypotheses explaining the observed clustering of sites, such as biased selection or mutation, are discussed.
A new method is proposed for estimating the number of synonymous and nonsynonymous nucleotide substitutions between homologous genes. In this method, a nucleotide site is classified as nondegenerate, twofold degenerate, or fourfold degenerate, depending on how often nucleotide substitutions will result in amino acid replacement; nucleotide changes are classified as either transitional or transversional, and changes between codons are assumed to occur with different probabilities, which are determined by their relative frequencies among more than 3,000 changes in mammalian genes. The method is applied to a large number of mammalian genes. The rate of nonsynonymous substitution is extremely variable among genes; it ranges from 0.004 X 10(-9) (histone H4) to 2.80 X 10(-9) (interferon gamma), with a mean of 0.88 X 10(-9) substitutions per nonsynonymous site per year. The rate of synonymous substitution is also variable among genes; the highest rate is three to four times higher than the lowest one, with a mean of 4.7 X 10(-9) substitutions per synonymous site per year. The rate of nucleotide substitution is lowest at nondegenerate sites (the average being 0.94 X 10(-9), intermediate at twofold degenerate sites (2.26 X 10(-9)). and highest at fourfold degenerate sites (4.2 X 10(-9)). The implication of our results for the mechanisms of DNA evolution and that of the relative likelihood of codon interchanges in parsimonious phylogenetic reconstruction are discussed.
Mathematical properties of the overdominance model with mutation and random genetic drift are studied by using the method of stochastic differential equations (Itô and McKean 1974). It is shown that overdominant selection is very powerful in increasing the mean heterozygosity as compared with neutral mutations, and if 2Ns (N = effective population size; s = selective disadvantage for homozygotes) is larger than 10, a very low mutation rate is sufficient to explain the observed level of allozyme polymorphism. The distribution of heterozygosity for overdominant genes is considerably different from that of neutral mutations, and if the ratio of selection coefficient (s) to mutation rate (nu) is large and the mean heterozygosity (h) is lower than 0.2, single-locus heterozygosity is either approximately 0 or 0.5. If h increases further, however, heterozygosity shows a multiple-peak distribution. Reflecting this type of distribution, the relationship between the mean and variance of heterozygosity is considerably different from that for neutral genes. When s/v is large, the proportion of polymorphic loci increases approximately linearly with mean heterozygosity. The distribution of allele frequencies is also drastically different from that of neutral genes, and generally shows a peak at the intermediate gene frequency. Implications of these results on the maintenance of allozyme polymorphism are discussed.
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