Tilapias are one of the most farmed fishes that are coined as “aquatic chicken” by the food industry. Nile tilapia and blue tilapia exhibit very recent transition of sex chromosome systems since their divergence approximately five million years ago, making them a great model for elucidating the molecular and evolutionary mechanisms of sex chromosome turnovers. Studies of their sex‐determining pathways are also critical for developing genetic sex control in aquaculture. We report here the newly produced genomes of Nile tilapia and blue tilapia that integrate long‐read sequencing and chromatin conformation data. The two nearly complete genomes have anchored over 97% of the sequences into linkage groups (LGs), and assembled majorities of complex repetitive regions including telomeres, centromeres and rDNA clusters. In particular, we inferred two episodes of repeat expansion at LG3 respectively in the ancestor of cichlids and that of tilapias. The consequential large heterochromatic region concentrated at one end of LG3 comprises tandem arrays of mRNA and small RNA genes, among which we have identified a candidate female determining gene Paics in blue tilapia. Paics shows female‐specific patterns of single‐nucleotide variants, copy numbers and expression patterns in gonads during early gonadogenesis. Our work provides a very important genomic resource for functional studies of cichlids, and suggested that unequal distribution of repeat content that impacts the local recombination rate might make some chromosomes more likely to become sex chromosomes.

中文翻译：

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两种罗非鱼的高质量染色体水平基因组揭示了它们重复序列和性染色体的进化

罗非鱼是养殖最多的鱼类之一，被食品行业称为“水生鸡”。尼罗罗非鱼和蓝罗非鱼表现出自大约 500 万年前发生分歧以来性染色体系统的最新转变，使它们成为阐明性染色体转换的分子和进化机制的绝佳模型。研究它们的性别决定途径对于在水产养殖中发展遗传性别控制也至关重要。我们在此报告整合了长读长测序和染色质构象数据的尼罗罗非鱼和蓝罗非鱼的新基因组。这两个近乎完整的基因组已将超过 97% 的序列锚定到连锁群 (LGs) 中，并组装了大部分复杂的重复区域，包括端粒、着丝粒和 rDNA 簇。特别是，我们分别在慈鲷的祖先和罗非鱼的祖先中推断出 LG3 处的两次重复扩增。位于 LG3 一端的大异染色质区域包含 mRNA 和小 RNA 基因的串联阵列，其中我们已经确定了一个候选的女性决定基因蓝罗非鱼中的Paics。Paics显示了性腺发生早期性腺中单核苷酸变异的女性特异性模式、拷贝数和表达模式。我们的工作为慈鲷的功能研究提供了一个非常重要的基因组资源，并表明影响局部重组率的重复内容分布不均可能使某些染色体更有可能成为性染色体。