A Willow Sex Chromosome Reveals Convergent Evolution of Complex Palindromic Repeats

Abstract

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].

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

“…These results may be caused by the lack and/or mis-assembly of SDRs in the reference genome, especially when the genome from a homozygous (XX or ZZ) individual was used as reference, the reads from Y- or W-specific regions of hemizygous (XY or ZW) individuals may be misaligned to homologous sequences on autosomes and led to false associations. Similar phenomena were also observed in the sex association analysis of P. trichocarpa , P. balsamifera and S. purpurea , which may lead to an inaccurate localization of SDRs in assemblies (Geraldes et al , 2015; Zhou et al , 2020). The high sequence similarity between these sex-associated regions and the SDRs we finally established strongly supports this possibility (Figs.…”

“…3B ), which led us to speculate that this element may be the main driving force for gene replication during the evolution of SDRs in P. euphratica and P. alba . However, we failed to detect the same pattern in S. purpurea , in which multiple Copia LTR-RTs were predicted instead of the Helitron elements (Zhou et al , 2020). This implies that poplar and willow may have different SDR turnover mechanisms, which requires further evidence from more species to confirm.…”

“…More interesting, we also identified three copies of the gene encoding a type A cytokinin response regulator ( RR ) in the W-specific region ( Fig. 3A ), the ortholog of which has also been identified to be associated with sex determination in poplar and willow (Geraldes et al , 2015; Bräutigam et al , 2017; Melnikova et al , 2019; Zhou et al , 2020). Very little sequence differences were found among these three copies, and combined with the fact that the ortholog of the RR gene is located at the distal end of chromosome 19 in P. trichocarpa and P. euphratica ( Fig.…”

“…This family includes two sister genera, Populus and Salix , which are composed exclusively of dioecious species (Peto, 1938; Zhang et al , 2018; Li et al , 2019). Previous studies in multiple Salix species have consistently mapped the sex determination regions (SDRs) to chromosome 15, and proposed a ZW system in which females are the heterogametic sex (Pucholt et al , 2015, 2017; Hou et al , 2015; Chen et al , 2016; Zhou et al , 2018, 2020). However, an XY system was recently identified on chromosome 7 in S. nigra (Sanderson et al , 2020).…”

“…Thus far, the only SDR that has been assembled in Populus is that of P. trichocarpa and P. deltoides , and it appears to be much smaller than those observed in Salix (Geraldes et al , 2015; Xue et al , 2020). Our recent study on the W chromosome of S. purpurea showed intriguing palindromic structures, in which four copies of the gene encoding a type A cytokinin response regulator ( RR ) were identified (Zhou et al , 2020). Interestingly, the ortholog of this gene has also been reported to be associated with sex in Populus from section Tacamahaca (Geraldes et al , 2015; Bräutigam et al , 2017; Melnikova et al , 2019), which increases the possibility that this gene is an excellent candidate for a common sex determination mechanism in the Salicaceae.…”