Gap-free X and Y chromosome assemblies of Salix arbutifolia reveal an evolutionary change from male to female heterogamety in willows, without a change in the position of the sex-determining locus

Yi Wang; Guang-Nan Gong; Yuan Wang; Ren-Gang Zhang; Elvira Hörandl; Zhi-Xiang Zhang; Deborah Charlesworth; Li He

doi:10.1111/nph.19744

Gap-free X and Y chromosome assemblies of Salix arbutifolia reveal an evolutionary change from male to female heterogamety in willows, without a change in the position of the sex-determining locus

New Phytol. 2024 Apr 6. doi: 10.1111/nph.19744. Online ahead of print.

Authors

Yi Wang^{1

2}, Guang-Nan Gong¹, Yuan Wang¹, Ren-Gang Zhang³, Elvira Hörandl⁴, Zhi-Xiang Zhang², Deborah Charlesworth⁵, Li He¹

Affiliations

¹ Eastern China Conservation Centre for Wild Endangered Plant Resources, Shanghai Chenshan Botanical Garden, Shanghai, 201602, China.
² Laboratory of Systematic Evolution and Biogeography of Woody Plants, School of Ecology and Nature Conservation, Beijing Forestry University, Beijing, 100091, China.
³ Yunnan Key Laboratory for Integrative Conservation of Plant Species with Extremely Small Populations, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, Yunnan, China.
⁴ Department of Systematics, Biodiversity and Evolution of Plants (with Herbarium), University of Goettingen, 37073, Göttingen, Germany.
⁵ Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, EH9 3FL, UK.

PMID: 38581199
DOI: 10.1111/nph.19744

Abstract

In the Vetrix clade of Salix, a genus of woody flowering plants, sex determination involves chromosome 15, but an XY system has changed to a ZW system. We studied the detailed genetic changes involved. We used genome sequencing, with chromosome conformation capture (Hi-C) and PacBio HiFi reads to assemble chromosome level gap-free X and Y of Salix arbutifolia, and distinguished the haplotypes in the 15X- and 15Y-linked regions, to study the evolutionary history of the sex-linked regions (SLRs). Our sequencing revealed heteromorphism of the X and Y haplotypes of the SLR, with the X-linked region being considerably larger than the corresponding Y region, mainly due to accumulated repetitive sequences and gene duplications. The phylogenies of single-copy orthogroups within the SLRs indicate that S. arbutifolia and Salix purpurea share an ancestral SLR within a repeat-rich region near the chromosome 15 centromere. During the change in heterogamety, the X-linked region changed to a W-linked one, while the Z was derived from the Y.

Keywords: Salix arbutifolia; evolutionary strata; heteromorphism; inversion; pericentromeric regions; sex chromosome turnovers.

Abstract

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