Active Miniature Transposons From a Plant Genome and Its Nonrecombining Y Chromosome

Institute of Evolutionary Biology, Ashworth Laboratories, University of Edinburgh, Edinburgh, EH9 3JT, United Kingdom.
Genetics (Impact Factor: 5.96). 03/2008; 178(2):1085-92. DOI: 10.1534/genetics.107.081745
Source: PubMed


Mechanisms involved in eroding fitness of evolving Y chromosomes have been the focus of much theoretical and empirical work. Evolving Y chromosomes are expected to accumulate transposable elements (TEs), but it is not known whether such accumulation contributes to their genetic degeneration. Among TEs, miniature inverted-repeat transposable elements are nonautonomous DNA transposons, often inserted in introns and untranslated regions of genes. Thus, if they invade Y-linked genes and selection against their insertion is ineffective, they could contribute to genetic degeneration of evolving Y chromosomes. Here, we examine the population dynamics of active MITEs in the young Y chromosomes of the plant Silene latifolia and compare their distribution with those in recombining genomic regions. To isolate active MITEs, we developed a straightforward approach on the basis of the assumption that recent transposon insertions or excisions create singleton or low-frequency size polymorphisms that can be detected in alleles from natural populations. Transposon display was then used to infer the distribution of MITE insertion frequencies. The overall frequency spectrum showed an excess of singleton and low-frequency insertions, which suggests that these elements are readily removed from recombining chromosomes. In contrast, insertions on the Y chromosomes were present at high frequencies. Their potential contribution to Y degeneration is discussed.

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Available from: Roberta Bergero, Oct 05, 2015
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    • "The reduction in effective population size need not be very great. For example, X chromosomes in mammals and plants have a lower recombination frequency than the autosomes, because X chromosomes recombine only in females, and, in mammals and papaya, this chromosome has a detectably higher repetitive content than the genome-wide average (reviewed in Bergero et al. 2008). Transposable element heterozygosity is known to reduce recombination in maize (Dooner and Martinez-Férez 1997; Fu et al. 2002; Dooner and He 2008), and transposable elements are abundant in S. latifolia (Cermak et al. 2008; Macas et al. 2008), whose haploid genome size is similar to that of maize (Grover et al. 2008). "
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    ABSTRACT: The existence of sexually antagonistic polymorphism is widely considered the most likely explanation for the evolution of suppressed recombination of sex chromosome pairs. This explanation is largely untested empirically, and no such polymorphisms have been identified, other than in fish, where no evidence directly implicates these genes in events causing loss of recombination. We tested for the presence of loci with sexually antagonistic (SA) polymorphism in the plant Silene latifolia, which is dioecious (with separate male and female individuals) and has a pair of highly heteromorphic sex chromosomes, with XY males. Suppressed recombination between much of the Y and X sex chromosomes evolved in several steps, and the results in Bergero et al. (2013) show that it is still ongoing in the recombining or pseudo-autosomal, regions (PARs) of these chromosomes. We used molecular evolutionary approaches to test for the footprints of SA polymorphisms, based on sequence diversity levels in S. latifolia PAR genes identified by genetic mapping. Nucleotide diversity is high for at least four of six PAR genes identified, and our data suggest the existence of polymorphisms maintained by balancing selection in this genome region, since molecular evolutionary (HKA) tests exclude an elevated mutation rate, and other tests also suggest balancing selection. The presence of sexually antagonistic alleles at a locus or loci in the PAR is suggested by the very different X and Y chromosome allele frequencies for at least one PAR gene.
    Genetics 06/2013; 194(3). DOI:10.1534/genetics.113.152397 · 5.96 Impact Factor
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    • "A systematic study of repetitive DNA in S. latifolia showed that Copia retroelements are probably the most abundant DNA element on the Y chromosome [28]. The first active MITE (miniature inverted-repeat transposable element) elements in S. latifolia were described by Bergero et al. [29]. "
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    ABSTRACT: Genome size evolution is a complex process influenced by polyploidization, satellite DNA accumulation, and expansion of retroelements. How this process could be affected by different reproductive strategies is still poorly understood. We analyzed differences in the number and distribution of major repetitive DNA elements in two closely related species, Silene latifolia and S. vulgaris. Both species are diploid and possess the same chromosome number (2n = 24), but differ in their genome size and mode of reproduction. The dioecious S. latifolia (1C = 2.70 pg DNA) possesses sex chromosomes and its genome is 2.5× larger than that of the gynodioecious S. vulgaris (1C = 1.13 pg DNA), which does not possess sex chromosomes. We discovered that the genome of S. latifolia is larger mainly due to the expansion of Ogre retrotransposons. Surprisingly, the centromeric STAR-C and TR1 tandem repeats were found to be more abundant in S. vulgaris, the species with the smaller genome. We further examined the distribution of major repetitive sequences in related species in the Caryophyllaceae family. The results of FISH (fluorescence in situ hybridization) on mitotic chromosomes with the Retand element indicate that large rearrangements occurred during the evolution of the Caryophyllaceae family. Our data demonstrate that the evolution of genome size in the genus Silene is accompanied by the expansion of different repetitive elements with specific patterns in the dioecious species possessing the sex chromosomes.
    PLoS ONE 02/2012; 7(2):e31898. DOI:10.1371/journal.pone.0031898 · 3.23 Impact Factor
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    • "The ligation reaction involved incubating the sample for 30 min at 16°C followed by 10 min of 37°C for 12 cycles. Preselective and selective amplications were performed as described by Bergero et al. (2008). Amplied products were run on an Applied Biosystems 3730 Genetic Analyzer and visualized in the software program Genographer (Amundsen and Warnke, 2005; Benham et al., 1999). "
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    ABSTRACT: T AGROSTIS consists of between 150 and 200 species (Harvey, 2007). Creeping bentgrass (Agrostis stolonifera L.) is the most widely utilized cool-season turf species for highly man-aged playing surfaces such as golf course greens, tees, and fairways (Turgeon, 1996). Creeping bentgrass is a highly outcrossing allo-tetraploid (2n = 4x = 28). The other Agrostis species commonly used as turf are A. canina L. (2n = 2x = 14), A. capillaris L. (2n = 4x = 28), A. gigantea Roth. (2n = 2x = 42), and A. castellana Boiss. and Reut. (2n = 6x = 42). The quality of creeping bentgrass is adversely aected by heat, wear, soil compaction, and a number of fungal pathogenic diseases such as dollar spot (caused by Sclero-tinia homoeocarpa F.T. Benn.), brown patch (caused by Rhizocto-nia solani Kühn), and anthracnose (caused by Colletotrichum cereale Manns). Agrostis breeding programs work to develop improved biotic and abiotic stress tolerant germplasm while maintaining ABSTRACT Creeping bentgrass (Agrostis stolonifera L.) is an important species to the turfgrass industry because of its adaptation for use in high quality turf stands such as golf course putting greens, tees, and fairways. Creeping bentgrass is a highly outcrossing allotetraploid, making genetic marker development difcult. Genetic markers anchored to miniature inverted-repeat transposable ele-ments (MITEs) were developed in Agrostis that could be used in genetic linkage mapping, quan-titative trait loci studies, or diversity analyses. The FindMITE software program identied 495 candi-date MITEs from 16,122 Agrostis DNA sequences. There was evidence of transposition in 79 of the candidate MITEs based on MITE insertional poly-morphisms. Genetic markers were developed by MITE-display, a modied amplied fragment length polymorphism technique that anchors amplied fragments to MITEs. Four MITE-display primer combinations were tested on a creeping bentgrass experimental mapping population and 139 polymorphic markers were developed with a polymorphic information content of 0.33. Twenty-eight of the polymorphic genetic markers seg-regated normally. MITE-display genetic markers are a new class of genetic markers for studies of the Agrostis genome. These genetic markers tar-get transposable elements and provide an easy method of identifying allelic variation between Agrostis accessions that may be used for diver-sity studies or genetic linkage map development.
    Crop Science 01/2011; 51. DOI:10.2135/cropsci2010.04.0215 · 1.58 Impact Factor
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