College of Fisheries, Hubei Provincial Engineering Laboratory for Pond Aquaculture, Huazhong Agricultural University, Wuhan, 430070, China.
Aquaculture and Genetic Breeding Laboratory, Freshwater Fisheries Research Institute of Fujian, Fuzhou, 350002, China.
Genome Biol. 2021 Jul 12;22(1):203. doi: 10.1186/s13059-021-02430-y.
The origin of sex chromosomes requires the establishment of recombination suppression between the proto-sex chromosomes. In many fish species, the sex chromosome pair is homomorphic with a recent origin, providing species for studying how and why recombination suppression evolved in the initial stages of sex chromosome differentiation, but this requires accurate sequence assembly of the X and Y (or Z and W) chromosomes, which may be difficult if they are recently diverged.
Here we produce a haplotype-resolved genome assembly of zig-zag eel (Mastacembelus armatus), an aquaculture fish, at the chromosomal scale. The diploid assembly is nearly gap-free, and in most chromosomes, we resolve the centromeric and subtelomeric heterochromatic sequences. In particular, the Y chromosome, including its highly repetitive short arm, has zero gaps. Using resequencing data, we identify a ~7 Mb fully sex-linked region (SLR), spanning the sex chromosome centromere and almost entirely embedded in the pericentromeric heterochromatin. The SLRs on the X and Y chromosomes are almost identical in sequence and gene content, but both are repetitive and heterochromatic, consistent with zero or low recombination. We further identify an HMG-domain containing gene HMGN6 in the SLR as a candidate sex-determining gene that is expressed at the onset of testis development.
Our study supports the idea that preexisting regions of low recombination, such as pericentromeric regions, can give rise to SLR in the absence of structural variations between the proto-sex chromosomes.
性染色体的起源需要在原性染色体之间建立重组抑制。在许多鱼类物种中，性染色体对是同形的，起源较近，为研究重组抑制在性染色体分化的初始阶段是如何以及为何进化提供了物种，但这需要对 X 和 Y（或 Z 和 W）染色体进行准确的序列组装，如果它们最近才分化，这可能很困难。
在这里，我们以染色体规模对养殖鳗鱼（Mastacembelus armatus）进行了单倍型解析基因组组装。该二倍体组装几乎没有间隙，并且在大多数染色体中，我们解析了着丝粒和端粒异染色质序列。特别是，Y 染色体，包括其高度重复的短臂，没有间隙。使用重测序数据，我们确定了一个约 7 Mb 的完全性连锁区（SLR），跨越性染色体着丝粒，几乎完全嵌入着丝粒异染色质中。X 和 Y 染色体上的 SLR 在序列和基因组成上几乎相同，但两者均重复且异染色质化，表明重组率为零或很低。我们进一步在 SLR 中鉴定出一个含有 HMG 结构域的基因 HMGN6，作为候选性别决定基因，该基因在睾丸发育开始时表达。
我们的研究支持这样的观点，即预先存在的低重组区域，如着丝粒区域，可以在原性染色体之间没有结构变异的情况下产生 SLR。
