Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Key Laboratory of Aquatic Science of Chongqing, School of Life Sciences, Southwest University, Chongqing, China.
MOE Laboratory of Biosystems Homeostasis & Protection, Life Sciences Institute, Zhejiang University, Hangzhou, China.
Mol Ecol Resour. 2021 Feb;21(2):543-560. doi: 10.1111/1755-0998.13273. Epub 2020 Nov 3.
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.
罗非鱼是最常被养殖的鱼类之一，在食品行业中被称为“水禽”。尼罗罗非鱼和蓝罗非鱼自大约 500 万年前分化以来，其性染色体系统经历了非常近期的转变，使它们成为阐明性染色体转变的分子和进化机制的理想模型。对它们的性别决定途径的研究对于在水产养殖中开发遗传性别控制也至关重要。我们在这里报告了尼罗罗非鱼和蓝罗非鱼的新基因组，这些基因组整合了长读测序和染色质构象数据。这两个近乎完整的基因组将超过 97%的序列锚定到连锁群（LG）中，并组装了大多数复杂的重复区域，包括端粒、着丝粒和 rDNA 簇。特别是，我们推断在慈鲷和罗非鱼的祖先中，LG3 分别发生了两次重复扩张事件。由此产生的大片异染色质区域集中在 LG3 的一端，包含 mRNA 和小 RNA 基因的串联阵列，其中我们在蓝罗非鱼中鉴定出一个候选雌性决定基因 Paics。Paics 在早期性腺发生过程中在性腺中表现出单核苷酸变异、拷贝数和表达模式的雌性特异性。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，并表明重复内容的不均匀分布会影响局部重组率，这可能使某些染色体更有可能成为性染色体。
