Impact of Repetitive Elements on the Y Chromosome Formation in Plants

Hobza, Roman; Čegan, Radim; Jesionek, Wojciech; Kejnovský, Eduard; Vyskot, Boris; Kubát, Zdeněk

doi:10.3390/genes8110302

Cited by 44 publications

(35 citation statements)

References 76 publications

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“…These results suggest that the SDRs of these two species were established relatively recently, which is a common feature of the sex chromosomes of the Salicaceae species studied so far (Geraldes et al , 2015; Pucholt et al , 2017; Zhou et al , 2018, 2020). Along with this, our results also suggest that the Y and W chromosomes have expanded in content, a pattern that is common in young sex chromosomes of plants (Hobza et al , 2015, 2017). Moreover, our results simultaneously showed that the Salicaceae exhibit an extremely fast rate of sex-chromosome turnover.…”

Section: Discussionsupporting

confidence: 81%

A general model to explain repeated turnovers of sex determination in the Salicaceae

Yang

Zhang

Wang

et al. 2020

Preprint

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0Dioecy, the presence of separate sexes on distinct individuals, has evolved repeatedly 3 1 in multiple plant lineages. However, the specific mechanisms through which sex 3 2 systems evolve and their commonalities among plant species remain poorly 3 3 understood. With both XY and ZW sex systems, the family Salicaceae provides a 3 4 system to uncover the evolutionary forces driving sex chromosome turnovers. In this 3 5 study, we performed a genome-wide association study to characterize sex 3 6 determination in two Populus species, P. euphratica and P. alba. Our results reveal an 3 7XY system of sex determination on chromosome 14 of P. euphratica, and a ZW 3 8 system on chromosome 19 of P. alba. We further assembled the corresponding sex 3 9 determination regions, and found that their sex chromosome turnovers may be driven 4 0 by the repeated translocations of a Helitron-like transposon. During the translocation, 4 1 this factor may have captured partial or intact sequences that are orthologous to a 4 2 type-A cytokinin response regulator gene. Based on results from this and other 4 3recently published studies, we hypothesize that this gene may act as a master regulator 4 4 of sex determination for the entire family. We propose a general model to explain how 4 5 the XY and ZW sex systems in this family can be determined by the same RR gene. 6Our study provides new insights into the diversification of incipient sex chromosome 4 7 in flowering plants by showing how transposition and rearrangement of a single gene 4 8 can control sex in both XY and ZW systems. 4 9 5 0

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Section: Discussionsupporting

confidence: 81%

A general model to explain repeated turnovers of sex determination in the Salicaceae

Yang

Zhang

Wang

et al. 2020

Preprint

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“…These translocations and other structural rearrangements may also suppress recombination and cause linkage between autosomal and sex-linked genes [2]. In plants, the large sizes of young Y chromosomes have been attributed to the accumulation of retrotransposons (reviewed in [29]).…”

Section: Discussionmentioning

confidence: 99%

A Willow Sex Chromosome Reveals Convergent Evolution of Complex Palindromic Repeats

Zhou

Macaya‐Sanz

Carlson

et al. 2019

Preprint

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1 Background 2 Sex chromosomes in a wide variety of species share common characteristics, including the 3 presence of suppressed recombination surrounding sex determination loci. They have arisen 4 independently in numerous lineages, providing a conclusive example of convergent evolution. 5Mammalian sex chromosomes contain multiple palindromic repeats across the non-recombining 6 region that facilitate sequence conservation through gene conversion, and contain genes that are 7 crucial for sexual reproduction. Plant sex chromosomes are less well understood, and in 8 particular it is not clear how coding sequence conservation is maintained in the absence of 9 homologous recombination. 10 Results 11 Here we present the first evidence of large palindromic structures in a plant sex chromosome, 12 based on a highly contiguous assembly of the W chromosome of the dioecious shrub Salix 13 purpurea. Two consecutive palindromes span over a region of 200 kb, with conspicuous 20 kb 14 stretches of highly conserved sequences among the four arms. The closely-related species S. 15 suchowensis also has two copies of a portion of the palindrome arm and provides strong 16 evidence for gene conversion. Four genes in the palindrome are homologous to genes in the SDR 17 of the closely-related genus Populus, which is located on a different chromosome. These genes 18 show distinct, floral-biased expression patterns compared to paralogous copies on autosomes.19 Conclusion 20The presence of palindromic structures in sex chromosomes of mammals and plants highlights 21 the intrinsic importance of these features in adaptive evolution in the absence of recombination. 22Convergent evolution is driving both the independent establishment of sex chromosomes as well 23 as their fine-scale sequence structure. 24 26 103 297 kb in length lacked mapped markers and could not be placed unambiguously. 104Location of the SDR 105 We repeated sex association analysis with our new assembly with Chr15Z removed. 106Among 54,959 tested SNPs, all 105 significantly sex-associated SNPs were present only on 107 Chr15W (Fig. 1a; Additional File 2: Figure S2a-c), and markers from PARs and other scaffolds 108 in the main genome did not show any sex association (Additional File 2: Figure S2a). The eight 109 top-ranking sex-associated markers were distributed from 7.66 Mb to 8.66 Mb. Sex-associated 110 markers were primarily heterozygous in females and homozygous in males, confirming our 111 previously-reported observation of ZW sex determination in S. purpurea [18].

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“…Peichel, personal communication; see also Chalopin, Volff, Galiana, Anderson, & Schartl, 2015;Hobza et al, 2017). As a definitive validation of our model, it would be worthwhile to determine the number of alignment sites of DNA segments representative of our HIDRs in a future Y chromosome assembly.…”

Section: Hidr Snpsmentioning

confidence: 99%

Widespread intersex differentiation across the stickleback genome – The signature of sexually antagonistic selection?

et al. 2019

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Females and males within a species commonly have distinct reproductive roles, and the associated traits may be under perpetual divergent natural selection between the sexes if their sex‐specific control has not yet evolved. Here, we explore whether such sexually antagonistic selection can be detected based on the magnitude of differentiation between the sexes across genome‐wide genetic polymorphisms by whole‐genome sequencing of large pools of female and male threespine stickleback fish. We find numerous autosomal genome regions exhibiting intersex allele frequency differences beyond the range plausible under pure sampling stochasticity. Alternative sequence alignment strategies rule out that these high‐differentiation regions represent sex chromosome segments misassembled into the autosomes. Instead, comparing allele frequencies and sequence read depth between the sexes reveals that regions of high intersex differentiation arise because autosomal chromosome segments got copied into the male‐specific sex chromosome (Y), where they acquired new mutations. Because the Y chromosome is missing in the stickleback reference genome, sequence reads derived from DNA copies on the Y chromosome still align to the original homologous regions on the autosomes. We argue that this phenomenon hampers the identification of sexually antagonistic selection within a genome, and can lead to spurious conclusions from population genomic analyses when the underlying samples differ in sex ratios. Because the hemizygous sex chromosome sequence (Y or W) is not represented in most reference genomes, these problems may apply broadly.

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Impact of Repetitive Elements on the Y Chromosome Formation in Plants

Cited by 44 publications

References 76 publications

A general model to explain repeated turnovers of sex determination in the Salicaceae

A general model to explain repeated turnovers of sex determination in the Salicaceae

A Willow Sex Chromosome Reveals Convergent Evolution of Complex Palindromic Repeats

Widespread intersex differentiation across the stickleback genome – The signature of sexually antagonistic selection?

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