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Compared to organelle genomes, the nuclear genome comprises a vast reservoir of genes that potentially harbor phylogenetic signal. Despite the valuable data that sequencing projects of model systems offer, relatively few single-copy nuclear genes are being used in systematics. In part this is due to the challenges inherent in generating orthologous...
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... to the large number of comparisons obtained by BLAST (38,883), the first step in selection of candidate genes was to restrict our searches to those that obey the following constraint parameters: 1) percent identity between 90 % and 100 %; 2) length of alignment 600 bp; 3) E = 0; 4) presence in at least two Asteraceae tribes (Fig. 2). Using these constraints, nine candidate genes were selected for the next step (Table 2 and Appendix 1 in the Supplementary material) and compared by an on-line BLAST using both "blastn" and "blastx" search options. The former was used to find potentially homologous genomic sequences (i.e., including exons and introns) in other ...
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... genomic sequences (i.e., including exons and introns) in other angiosperms, and the latter to estimate which protein (if any known) is similar to each candidate, allowing us to do a preliminary characterization and comparison to Arabidopsis thaliana, the closest organism to Asteraceae which genome has been completely sequenced and assembled (Fig. ...
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... in alignment) of ~ 22 nucleotides length and located ~ 200 nucleotides of exon sequence apart from each other, and 2) sequence representation in alignment of at least 3 different Asteraceae tribes. Finally, primers for five candidates that met these criteria (Table 3 and Appendix 2 in the Supplementary material) were designed and tested by PCR (Fig. ...
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... (i.e., multiple fragments of different sizes depending on the sample) or failed to amplify; thus, they were excluded for the next step. For each of the remaining five candidates we selected the best primer combination (Appendix 3 in the Supplementary material) in terms of amplification simplicity and pattern obtained (1-3 neat bands per sample), (Fig. ...
Citations
... Single-copy nuclear genes (SCNGs), characterized by bi-parental inheritance, higher evolutionary rates, and numerous unlinked loci (Alvarez et al., 2008;Hojjati et al., 2019), offer significant potential for addressing issues related to hybridization and incomplete lineage sorting, potentially reconciling discrepancies among plastome genes (Small et al., 2004;Doyle, 2022). However, the recovery of SCNGs in this study was constrained (Table 2), possibly due to low sequencing coverage. ...
Dioscorea nipponica Makino, a perennial twining herb with medicinal importance, has a disjunctive distribution in the Sino-Japanese Floristic Region. It has a long history in traditional Chinese medicine, with demonstrated efficacy against various health conditions. However, the limited genomic data and knowledge of genetic variation have hindered its comprehensive exploration, utilization and conservation. In this study, we undertook low-coverage whole genome sequencing of diverse D. nipponica accessions to develop both plastome (including whole plastome sequences, plastome-derived SSRs and plastome-divergent hotspots) and nuclear genomic resources (including polymorphic nuclear SSRs and single-copy nuclear genes), as well as elucidate the intraspecific phylogeny of this species. Our research revealed 639 plastome-derived SSRs and highlighted six key mutational hotspots (namely CDS ycf1, IGS trnL-rpl32, IGS trnE-trnT, IGS rps16-trnQ, Intron 1 of clpP, and Intron trnG) within these accessions. Besides, three IGS regions (i.e., ndhD-cssA, trnL-rpl32, trnD-trnY), and the intron rps16 were identified as potential markers for distinguishing D. nipponica from its closely related species. In parallel, we successfully developed 988 high-quality candidate polymorphic nuclear SSRs and identified 17 single-copy nuclear genes for D. nipponica, all of which empower us to conduct in-depth investigations into phylogenetics and population genetics of this species. Although our phylogenetic analyses, based on plastome sequences and single-copy nuclear genes revealed cytonuclear discordance within D. nipponica, both findings challenged the current subspecies classification. In summary, this study developed a wealth of genomic resources for D. nipponica and enhanced our understanding of the intraspecific phylogeny of this species, offering valuable insights that can be instrumental in the conservation and strategic utilization of this economically significant plant.
... Hence, it seemed that these markers would hold the greatest promise for future studies aimed at identifying, conserving, and sustainably utilizing D. futschauensis and its close relatives. Unlike plastome sequence with a high level of conservation, generally uniparental inheritance and absence of recombination [49], single-copy nuclear genes (SCNGs) have bi-parental inheritance, a higher rate of evolution, and a large number of multiple unlinked loci [50,51]. Given these attributes, the use of multiple unlinked SCNGs is more likely to deal with hybridization and incomplete lineage sorting events, and may solve incongruences between organelle genes [52,53]. ...
Dioscorea futschauensis Uline ex R. Knuth, a perennial climbing herb belonging to the Stenophora section of the genus Dioscorea L. (Dioscoreaceae), originates from Southeast China and is highly regarded for its medicinal properties. Despite its medicinal significance, the absence of genomic information has impeded the effective utilization and conservation of this species. Here, we conducted genome survey sequencing of D. futschauensis to unveil its genomic characteristics and identify species-specific genomic markers, including whole plastome sequence, plastome-divergent hotspots, single-copy nuclear genes and polymorphic nuclear SSRs. The genome of D. futschauen-sis was approximated to be 1392.76 Mb in length, accompanied by a substantial heterozygosity rate of 1.75% and a repeat content of 67.43%. Comparative plastome analysis illuminated the conserved genome structure and gene content within D. futschauensis, and revealed four highly divergent hotspots (atpF intron, psbA-matK, matK-rps16, and rrn16-trnI) that could serve as molecular markers for D. futschauensis and its closely related species. Furthermore, more than 200 single-copy nuclear genes and 78 polymorphic nuclear SSRs were identified within D. futschauensis. Overall, the comprehensive genomic information and abundant genetic resources provided herein will not only facilitate extended research in the realms of population genetics, phylogenetics and conservation biology of D. futschauensis, but also hold considerable value for its cultivation and molecular breeding applications.
... The enrichment of 28 gene functions revealed that equal codon usage frequency is contributed to the plants' evolution. Although the single-copy genes mined using whole-genome all-by-all blast were used to construct the phylogenetic tree, it needs more accurate and longer protein-coding genes and is limited by species relationships (Wu et al., 2006;AÁ lvarez et al., 2008). The species tree inferred here with 28 gene trees can also illustrate a true phylogenetic relationship, thus these 28 specific genes can contribute to the evolution and classification of the rosid species. ...
... Due to the limitations inherent in cpDNA and ITS markers and because of the phylogenetic potential of single-copy nuclear genes, they are increasingly being used in systematic studies. Some of the principal advantages of single-copy nuclear genes are (1) bi-parental inheritance; (2) co-occurrence of introns and exons within the same gene, yielding characters that evolve at different rates, and thus can provide phylogenetic data at different levels; and (3) a large number of independent markers (Alvarez et al. 2008, Li et al. 2017. Furthermore, SCNGs are ideal for detecting hybridization, introgression, and ancient allo-polyploidization events, whereas ITS region markers, which undergo concerted evolution, appear to be less reliable for detecting ancient hybridization and, especially, introgression events (Adams, Miller and Low, 2016;Duarte et al. 2010). ...
Previous studies of nrDNA (nuclear DNA) of Juniperus seravschanica indicated its nuclear DNA (ITS) was from an ancestor of J. polycarpos. However, analysis of cpDNA (chloroplast DNA) suggested the taxon had derived its chloroplast from an ancestor of J. foetidissima. That study has been viewed as putative, because the ITS region is sometimes unreliable for the detection of ancestral hybrids due to concerted evolution and lineage sorting. The recent availability of several single copy nuclear genes (SCNGs) with primers specifically designed for Juniperus presented an opportunity to fully investigate this case of putative chloroplast capture. Three phylogenetic analyses using five SCNGs (LHCA4, maldehy, myb, CnAIP3 and 4CL), ITS region, and four cpDNAs (petN-psbM, trnD-trnT, trnL-trnF and trnS-trnG) were performed on J. seravschanica, as well as other members of the J. excelsa complex: J. excelsa, J. polycarpos, and J. p. var. turcomanica. Analyses revealed incongruence between SCNGs, ITS region and cpDNA showing that J. seravschanica contains an ancestral J. foetidissima/ J. thruifera cp genome. In addition, the phylogenies indicate that the J. excelsa complex is composed of three distinct clades at the species level: J. excelsa, J. polycarpos and J. seravschanica and two varieties of J. polycarpos: J. p. var. polycarpos and J. p. var. turcomanica.
... In particular, short internodes in phylogenetic trees, where lineages split in quick succession, are difficult to resolve [1]. Plastid and nuclear ribosomal DNA loci (nrDNA) have predominantly been used in phylogenetic studies of flowering plants [2][3][4][5][6][7]. However, their applicability for resolving shallow divergences is limited by several characteristics. ...
... The biparental inheritance of nuclear markers facilitates the identification of possible hybridization and polyploidization events, and when used in concert with plastid markers the directionally of hybridization can be inferred [9,10,[14][15][16][17][18][19]. When present in low-or single-copy, nuclear markers are a highly valuable source of putative orthologous loci, that are increasingly being accessed in plant phylogenomics [7,9,10,15,[19][20][21][22][23][24][25][26][27][28][29][30][31][32][33][34]. For a long time in plant phylogenetics, data and technology were unavailable or at least limited to explore and broadly screen the nuclear genome. ...
Identifying orthologous molecular markers that potentially resolve relationships at and below species level has been a major challenge in molecular phylogenetics over the past decade. Non-coding regions of nuclear low- or single-copy markers are a vast and promising source of data providing information for shallow-scale phylogenetics. Taking advantage of public transcriptome data from the One Thousand Plant Project (1KP), we developed a genome-scale mining strategy for recovering potentially orthologous single-copy markers to address low-scale phylogenetics. Our marker design targeted the amplification of intron-rich nuclear single-copy regions from genomic DNA. As a case study we used Hydrangea section Cornidia, one of the most recently diverged lineages within Hydrangeaceae (Cornales), for comparing the performance of three of these nuclear markers to other "fast" evolving plastid markers.
Our data mining and filtering process retrieved 73 putative nuclear single-copy genes which are potentially useful for resolving phylogenetic relationships at a range of divergence depths within Cornales. The three assessed nuclear markers showed considerably more phylogenetic signal for shallow evolutionary depths than conventional plastid markers. Phylogenetic signal in plastid markers increased less markedly towards deeper evolutionary divergences. Potential phylogenetic noise introduced by nuclear markers was lower than their respective phylogenetic signal across all evolutionary depths. In contrast, plastid markers showed higher probabilities for introducing phylogenetic noise than signal at the deepest evolutionary divergences within the tribe Hydrangeeae (Hydrangeaceae).
While nuclear single-copy markers are highly informative for shallow evolutionary depths without introducing phylogenetic noise, plastid markers might be more appropriate for resolving deeper-level divergences such as the backbone relationships of the Hydrangeaceae family and deeper, at which non-coding parts of nuclear markers could potentially introduce noise due to elevated rates of evolution. The herein developed and demonstrated transcriptome based mining strategy has a great potential for the design of novel and highly informative nuclear markers for a range of plant groups and evolutionary scales.
... Single or low copy nuclear markers are increasingly used for phylogenetics in angiosperms (Christelova et al. 2011;Zhang et al. 2012;Naumann et al. 2013), and specifically in Asteraceae ( Alvarez et al. 2008;Krak et al. 2012), because they have the advantage (compared to markers such as ITS) that the cooccurrence of introns and exons provides information at different evolutionary levels and a huge number of markers is available ( Alvarez et al. 2008). Low copy nuclear genes also suffer less homoplasy than ITS (Alvarez & Wendel 2003). ...
... Single or low copy nuclear markers are increasingly used for phylogenetics in angiosperms (Christelova et al. 2011;Zhang et al. 2012;Naumann et al. 2013), and specifically in Asteraceae ( Alvarez et al. 2008;Krak et al. 2012), because they have the advantage (compared to markers such as ITS) that the cooccurrence of introns and exons provides information at different evolutionary levels and a huge number of markers is available ( Alvarez et al. 2008). Low copy nuclear genes also suffer less homoplasy than ITS (Alvarez & Wendel 2003). ...
Plant genome size evolution is a very dynamic process: the ancestral genome of the angiosperms has most likely been small which led to a tendency towards genome increase during evolution. However, findings in several Angiosperm lineages also demonstrate mechanisms that also led to genome size contraction. Recent molecular investigations on the Asteraceae genus Crepis suggest that several genomic reduction events have occurred during the evolution of the genus. This study focuses on the Mediterranean Crepis sect. Neglectoides. It includes three species with some of the smallest genomes whithin the whole genus. Crepis neglecta has the largest genome in sect. Neglectoides, which is approximately twice the size of that of the other two species, Crepis cretica and Crepis hellenica. Whereas C. cretica and C. hellencia are more closely related to each other than to C. neglecta the karyotypes of the latter species and C. cretica are similar while that of C. hellenica differs considerably. The karyotypic organisation of the three species is investigated with fluorescence-in-situ-hybridisation and studied in a molecular phylogenetic framework based on the nuclear markers Actin, CHR12, CPN60B, GPCR1, and XTH23. Our findings further corroborate the occurrence of genome size contraction in Crepis and suggest that the difference in genome size between C. neglecta and C. cretica is mostly due to the elimination of dispersed repetitive elements whereas chromosomal reorganisation was involved in the karyotype formation of C. hellenica. This article is protected by copyright. All rights reserved.
This article is protected by copyright. All rights reserved.
... Single or low copy nuclear markers are increasingly used for phylogenetics in angiosperms (Christelova et al. 2011;Zhang et al. 2012;Naumann et al. 2013), and specifically in Asteraceae ( Alvarez et al. 2008;Krak et al. 2012), because they have the advantage (compared to markers such as ITS) that the cooccurrence of introns and exons provides information at different evolutionary levels and a huge number of markers is available ( Alvarez et al. 2008). Low copy nuclear genes also suffer less homoplasy than ITS (Alvarez & Wendel 2003). ...
... Single or low copy nuclear markers are increasingly used for phylogenetics in angiosperms (Christelova et al. 2011;Zhang et al. 2012;Naumann et al. 2013), and specifically in Asteraceae ( Alvarez et al. 2008;Krak et al. 2012), because they have the advantage (compared to markers such as ITS) that the cooccurrence of introns and exons provides information at different evolutionary levels and a huge number of markers is available ( Alvarez et al. 2008). Low copy nuclear genes also suffer less homoplasy than ITS (Alvarez & Wendel 2003). ...
Plant genome size evolution is a very dynamic process: the ancestral genome of angiosperms
was initially most likely small, which led to a tendency towards genome
increase during evolution. However, findings in several angiosperm lineages demonstrate
mechanisms that also led to genome size contraction. Recent molecular investigations
on the Asteraceae genus Crepis suggest that several genomic reduction events
have occurred during the evolution of the genus. This study focuses on the Mediterranean
Crepis sect. Neglectoides, which includes three species with some of the smallest
genomes within the whole genus. Crepis neglecta has the largest genome in sect. Neglectoides,
approximately twice the size of the two species Crepis cretica and Crepis
hellenica. Whereas C. cretica and C. hellencia are more closely related to each other
than to C. neglecta the karyotypes of the latter species and C. cretica are similar, while
that of C. hellenica differs considerably. Here, the karyotypic organisation of the three
species is investigated with fluorescence in-situ hybridisation and studied in a molecular
phylogenetic framework based on the nuclear markers Actin, CHR12, CPN60B,
GPCR1 and XTH23. Our findings further corroborate the occurrence of genome size
contraction in Crepis, and suggest that the difference in genome size between C. neglecta
and C. cretica is mostly due to elimination of dispersed repetitive elements,
whereas chromosomal reorganisation was involved in the karyotype formation of
C. hellenica.
INTRODUCTION
It is assumed that the very early ancestors of recent flowering
plants had very small genome sizes (Soltis et al. 2003), and it
had been suggested that genome size evolution in plants was
unidirectional towards larger genomes (Bennetzen & Kellogg
1997), e.g. through transposon bursts, for example in the maize
genome (SanMiguel et al. 1998) or the genome of Arabidopsis
lyrata (L.) O’Kane & Al-Shehbaz (He et al. 2012). However,
more and more evidence has accumulated that the opposite
event, genome size contraction, is rather common in plant genome
evolution (reviewed in Grover et al. 2008). Apart from allopolyploidisation,
transposable elements and, in particular,
retrotransposons are major players in both genome expansion
and contraction (SanMiguel et al. 1998; Dart et al. 2004; Liu
et al. 2007; Hawkins et al. 2009; Renny-Byfield et al. 2011; He
et al. 2012).
The Asterales is the species-richest order of the dicotyledonous
flowering plants and includes the large Asteraceae family of
about
... The use of multiple nuclear loci has become increasingly standardized in phylogenetic reconstruction, owing to the increased power of such data sets to improve our understanding of basic processes of interest to biologists, such as character evolution, historical biogeography, and hybridization ( Sang, 2002 ;Álvarez et al., 2008 ). The absence of multiple independent loci in a phylogenetic study (including solely organellar approaches) inherently precludes the ability to discover differing phylogenetic histories among genomic segments. ...
• Premise of the study: The use of multiple genetic regions from the nuclear genome, including low-copy markers, has long been recognized as essential to robust phylogenetic construction, addressing gene tree incongruence, and allowing increased resolution to test current taxonomy and resolve basic hypotheses about character evolution, biogeography, and other organismal traits of interest to biologists. Heuchera, the largest genus of Saxifragaceae endemic to North America, has presented an unusually difficult case for systematists with limited sampling in previous molecular studies. We used morphological and multilocus molecular phylogenetic data to test the monophyly of Heuchera, better resolve hypotheses of relationships, and test hypotheses of character evolution, biogeography, and diversification rates.
• Methods: Phylogenetic relationships were inferred using sequences from six nuclear loci and 39 morphological characters using concatenation and coalescent analysis. Ancestral state reconstruction, diversification, and correlated evolution of morphological traits were performed using parsimony, BiSSE, and Pagel’s method, respectively.
• Key results: The concatenation and species tree analyses gave confident support to the monophyly of Heuchera and suggested several well-supported subclades. The addition of morphological data significantly improved support numbers. Ancestral character reconstruction suggested frequent homoplasy and reversal of floral characters and a complex biogeographical history.
• Conclusions: Heuchera is a natural genus; however, the current subgeneric classification is artificial and requires revision. Biogeographic reconstructions suggest a Pacific Northwest origin for the genus; morphological shifts in stamen exsertion and hypanthium length are hypothesized to have driven diversification in Heuchera in concert with possible pollinator shifts.
... Taxon and character sampling for molecular analyses -We sequenced three nuclear (internal transcribed spacer: ITS, external transcribed spacer: ETS, chalcone synthase: CHS) and three plastid ( rpl32-trn L, psb A -trn H, and ndh F -rpl32 ) DNA regions for multiple accessions of Adenostyles representing all species and subspecies ( Wagenitz, 1983 ;Dillenberger and Kadereit, 2012 ) and almost the entire distribution range ( Fig. 1 ; see also Meusel and Jäger, 1992 ) of the genus (Appendix 1). CHS is a nuclear coding region without introns belonging to a gene family of CHS and CHS-like genes ( Helariutta et al., 1996 ;Álvarez et al., 2008 ). The taxa (and number of accessions) included were as follows: 1. Adenostyles alliariae (14); 2. A. alpina (= A. glabra (Miller) DC.) with subsp. ...
Unlabelled:
•
Premise of the study:
Heterogeneity of edaphic conditions plays a large role in driving the diversification of many plant groups. In the Alps and other European high mountains, many closely related calcicole and calcifuge plant taxa exist. To better understand patterns and processes of edaphic differentiation, the phylogeny of the edaphically variable genus Adenostyles was studied. The genus contains three species, of which A. alpina has five subspecies. Each species and subspecies is largely confined to either calcareous or noncalcareous substrates. •
Methods:
We analyzed the phylogeny of Adenostyles using DNA sequences of nrITS, nrETS, nuclear chalcone synthase, and three plastid markers (rpl32-trnL, psbA-trnH, and ndhF-rpl32) from 45 in-group and five out-group samples. The phylogeny was used to reconstruct ancestral edaphic associations and distribution areas. •
Key results:
Within Adenostyles alpina, the shifts of edaphic association from calcicole to calcifuge in subsp. briquetii (Corsica) and in a clade of subsp. macrocephala (southernmost Italy) plus subsp. pyrenaica (Pyrenees) coincide with dispersal events. •
Conclusions:
We conclude that colonization of areas with novel edaphic conditions via dispersal can trigger shifts of edaphic association. Accordingly, edaphic niche shifts can result from chance events.
... and GenBank database. CHS region was amplified using primers developed by Alvarez et al. [40], previously reported as single-copy genes. Six regions, A25, A27, B12, D10, D13, D22, were amplified using primers developed by Chapman et al. [41], which were universally applicable to the Asteraceae family. ...
Background
Understanding demographic histories, such as divergence time, patterns of gene flow, and population size changes, in ecologically diverging lineages provide implications for the process and maintenance of population differentiation by ecological adaptation. This study addressed the demographic histories in two independently derived lineages of flood-resistant riparian plants and their non-riparian relatives [Ainsliaea linearis (riparian) and A. apiculata (non-riparian); A. oblonga (riparian) and A. macroclinidioides (non-riparian); Asteraceae] using an isolation-with-migration (IM) model based on variation at 10 nuclear DNA loci.
Results
The highest posterior probabilities of the divergence time parameters were estimated to be ca. 25,000 years ago for A. linearis and A. apiculata and ca. 9000 years ago for A. oblonga and A. macroclinidioides, although the confidence intervals of the parameters had broad ranges. The likelihood ratio tests detected evidence of historical gene flow between both riparian/non-riparian species pairs. The riparian populations showed lower levels of genetic diversity and a significant reduction in effective population sizes compared to the non-riparian populations and their ancestral populations.
Conclusions
This study showed the recent origins of flood-resistant riparian plants, which are remarkable examples of plant ecological adaptation. The recent divergence and genetic signatures of historical gene flow among riparian/non-riparian species implied that they underwent morphological and ecological differentiation within short evolutionary timescales and have maintained their species boundaries in the face of gene flow. Comparative analyses of adaptive divergence in two sets of riparian/non-riparian lineages suggested that strong natural selection by flooding had frequently reduced the genetic diversity and size of riparian populations through genetic drift, possibly leading to fixation of adaptive traits in riparian populations. The two sets of riparian/non-riparian lineages showed contrasting patterns of gene flow and genetic differentiation, implying that each lineage showed different degrees of reproductive isolation and that they had experienced unique evolutionary and demographic histories in the process of adaptive divergence.
