Genetic diversity and population structure of native, naturalized, and cultivated Salix purpurea

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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“…Loci with greater than 40% missing data were removed. Association with sex was performed using emmax [64] as described previously [18].…”

Section: Methodsmentioning

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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“…Loci associated with sex were identified using 60 nonclonal individuals from a naturalized population of S. purpurea [66]. GBS reads from each individual were aligned to the 94006v5 genome without Chr15Z using Bowtie2.…”

Section: Identification Of Sex-associated Locimentioning

confidence: 99%

A willow sex chromosome reveals convergent evolution of complex palindromic repeats

et al. 2020

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Background: Sex chromosomes have arisen independently in a wide variety of species, yet they share common characteristics, including the presence of suppressed recombination surrounding sex determination loci. Mammalian sex chromosomes contain multiple palindromic repeats across the non-recombining region that show sequence conservation through gene conversion and contain genes that are crucial for sexual reproduction. In plants, it is not clear if palindromic repeats play a role in maintaining sequence conservation in the absence of homologous recombination. Results: Here we present the first evidence of large palindromic structures in a plant sex chromosome, based on a highly contiguous assembly of the W chromosome of the dioecious shrub Salix purpurea. The W chromosome has an expanded number of genes due to transpositions from autosomes. It also contains two consecutive palindromes that span a region of 200 kb, with conspicuous 20-kb stretches of highly conserved sequences among the four arms that show evidence of gene conversion. Four genes in the palindrome are homologous to genes in the sex determination regions of the closely related genus Populus, which is located on a different chromosome. These genes show distinct, floral-biased expression patterns compared to paralogous copies on autosomes. Conclusion: The presence of palindromes in sex chromosomes of mammals and plants highlights the intrinsic importance of these features in adaptive evolution in the absence of recombination. Convergent evolution is driving both the independent establishment of sex chromosomes as well as their fine-scale sequence structure.

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“…There were 49 females and 29 males in the diversity panel, which were confirmed across years and experimental locations based on documented sex phenotypes in nursey beds. The diversity panel was not necessarily representative of the sex ratios in natural populations, since it was assembled from only a few selected individuals from multiple sites, rather than a thorough sampling of all individuals of a population (Gouker, et al ., 2019). There was significant departure from the expected 1: 1 segregation ratio of males and females in both the F1 and F 2 families.…”

Section: Resultsmentioning

confidence: 99%

“…Three populations of S. purpurea L. were used in this study: a diversity panel of unrelated natural accessions, an F 1 family, and an F 2 family generated by crossing F 1 individuals. The diversity panel contained 78 genotypes of S. purpurea natural accessions (Lin et al ., 2009, Gouker et al ., 2019) (Appendix S1). In July 2012, all genotypes were hand planted using 20-cm cuttings in a common garden design at three experimental sites (Appendix S2): Cornell AgriTech in Geneva, NY the Cornell Lake Erie Research and Extension Lab (CLEREL) in Portland, NY; and the West Virginia University (WVU) Agronomy Farm in Morgantown, WV.…”

Section: Methodsmentioning

confidence: 99%

Sexual dimorphism and sex ratio bias in the dioecious willowSalix purpureaL

Gouker

Carlson

Zou

et al. 2020

Preprint

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1Premise Sexual dimorphism in dioecious plant species is often not obvious or is 2 absent. Dioecious species populations also often exhibit deviations from expected sex ratios. 3Previous studies on members of the Salicaceae family have shown strong, partial, and no sexual 4 dimorphism. Some studies have shown sex-biased ratios in several Salix spp., however, S. 5 purpurea has never been examined for evidence of sexual dimorphism or for the presence of sex-6 ratio bias, and therefore a comprehensive phenotypic study is needed to fill this knowledge gap. 7 Methods This study examined a suite of morphological, phenological, physiological and wood 8 composition traits from multi-environment and multi-year replicated field trials in a diversity 9 panel of unrelated S. purpurea accessions and in full-sib F 1 and F 2 families produced through 1 0controlled cross pollinations to test for sexual dimorphism and sex ratio bias.

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Genetic diversity and population structure of native, naturalized, and cultivated Salix purpurea

Cited by 16 publications

References 74 publications

A Willow Sex Chromosome Reveals Convergent Evolution of Complex Palindromic Repeats

A Willow Sex Chromosome Reveals Convergent Evolution of Complex Palindromic Repeats

A willow sex chromosome reveals convergent evolution of complex palindromic repeats

Sexual dimorphism and sex ratio bias in the dioecious willowSalix purpureaL

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