Department of Genetics, Evolution & Environment, University College London, London, UK.
Department of Biochemistry and Biophysics, National Bioinformatics Infrastructure Sweden, Science for Life Laboratory, Stockholm University, Stockholm, Sweden.
BMC Biol. 2020 Jun 30;18(1):78. doi: 10.1186/s12915-020-00808-1.
Sex chromosomes have evolved independently multiple times in eukaryotes and are therefore considered a prime example of convergent genome evolution. Sex chromosomes are known to emerge after recombination is halted between a homologous pair of chromosomes, and this leads to a range of non-adaptive modifications causing gradual degeneration and gene loss on the sex-limited chromosome. However, the proximal causes of recombination suppression and the pace at which degeneration subsequently occurs remain unclear.
Here, we use long- and short-read single-molecule sequencing approaches to assemble and annotate a draft genome of the basket willow, Salix viminalis, a species with a female heterogametic system at the earliest stages of sex chromosome emergence. Our single-molecule approach allowed us to phase the emerging Z and W haplotypes in a female, and we detected very low levels of Z/W single-nucleotide divergence in the non-recombining region. Linked-read sequencing of the same female and an additional male (ZZ) revealed the presence of two evolutionary strata supported by both divergence between the Z and W haplotypes and by haplotype phylogenetic trees. Gene order is still largely conserved between the Z and W homologs, although the W-linked region contains genes involved in cytokinin signaling regulation that are not syntenic with the Z homolog. Furthermore, we find no support across multiple lines of evidence for inversions, which have long been assumed to halt recombination between the sex chromosomes.
Our data suggest that selection against recombination is a more gradual process at the earliest stages of sex chromosome formation than would be expected from an inversion and may result instead from the accumulation of transposable elements. Our results present a cohesive understanding of the earliest genomic consequences of recombination suppression as well as valuable insights into the initial stages of sex chromosome formation and regulation of sex differentiation.
性染色体在真核生物中已经独立进化了多次，因此被认为是趋同进化基因组的一个主要范例。性染色体的出现是由于同源染色体对之间的重组停止，从而导致一系列非适应性修饰，导致性限染色体逐渐退化和基因丢失。然而，重组抑制的近端原因和随后退化的速度仍不清楚。
在这里，我们使用长读长和短读长单分子测序方法来组装和注释篮子柳（Salix viminalis）的草图基因组，篮子柳是一种在性染色体出现的早期阶段具有雌性异配性系统的物种。我们的单分子方法使我们能够对雌性中出现的 Z 和 W 单倍型进行相位划分，并在非重组区域检测到非常低水平的 Z/W 单核苷酸差异。对同一雌性和另一个雄性（ZZ）的连锁读取测序揭示了存在两个进化层，这两个进化层既支持 Z 和 W 单倍型之间的分歧，也支持单倍型系统发育树。尽管 W 连锁区域包含与 Z 同源物不成对的细胞分裂素信号调节相关的基因，但 Z 和 W 同源物之间的基因顺序仍然在很大程度上保持不变。此外，我们没有发现多个证据支持倒位，倒位长期以来一直被认为会阻止性染色体之间的重组。
我们的数据表明，与倒位相比，在性染色体形成的早期阶段，对重组的选择是一个更渐进的过程，而不是由转座元件的积累引起的。我们的结果提供了对重组抑制的最早基因组后果的综合理解，以及对性染色体形成和性别分化调控的初始阶段的有价值的见解。
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