Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Southwest University School of Life Sciences, No. 2 Tiansheng Road, Beibei, Chongqing 400715, China.
Department of Evolutionary Genetics, Leibniz-Institute for Zoo and Wildlife Research, Alfred-Kowalke-Straße 17, 10315 Berlin, Germany.
Gigascience. 2020 Aug 1;9(8). doi: 10.1093/gigascience/giaa092.
The western mosquitofish (Gambusia affinis) is a sexually dimorphic poeciliid fish known for its worldwide biological invasion and therefore an important research model for studying invasion biology. This organism may also be used as a suitable model to explore sex chromosome evolution and reproductive development in terms of differentiation of ZW sex chromosomes, ovoviviparity, and specialization of reproductive organs. However, there is a lack of high-quality genomic data for the female G. affinis; hence, this study aimed to generate a chromosome-level genome assembly for it.
The chromosome-level genome assembly was constructed using Oxford nanopore sequencing, BioNano, and Hi-C technology. G. affinis genomic DNA sequences containing 217 contigs with an N50 length of 12.9 Mb and 125 scaffolds with an N50 length of 26.5 Mb were obtained by Oxford nanopore and BioNano, respectively, and the 113 scaffolds (90.4% of scaffolds containing 97.9% nucleotide bases) were assembled into 24 chromosomes (pseudo-chromosomes) by Hi-C. The Z and W chromosomes of G. affinis were identified by comparative genomic analysis of female and male G. affinis, and the mechanism of differentiation of the Z and W chromosomes was explored. Combined with transcriptome data from 6 tissues, a total of 23,997 protein-coding genes were predicted and 23,737 (98.9%) genes were functionally annotated.
The high-quality female G. affinis reference genome provides a valuable omics resource for future studies of comparative genomics and functional genomics to explore the evolution of Z and W chromosomes and the reproductive developmental biology of G. affinis.
西方食蚊鱼（Gambusia affinis）是一种具有性二态性的花鳉鱼，以其在全球范围内的生物入侵而闻名，因此是研究入侵生物学的重要研究模型。就 ZW 性染色体的分化、卵胎生和生殖器官的特化而言，该生物也可能被用作探索性染色体进化和生殖发育的合适模型。然而，雌性 G. affinis 的高质量基因组数据缺乏；因此，本研究旨在为其生成染色体水平的基因组组装。
使用牛津纳米孔测序、BioNano 和 Hi-C 技术构建了染色体水平的基因组组装。通过牛津纳米孔和 BioNano 分别获得了包含 217 个 contig 的 G. affinis 基因组 DNA 序列，N50 长度为 12.9Mb，以及包含 125 个 scaffold 的 G. affinis 基因组 DNA 序列，N50 长度为 26.5Mb，通过 Hi-C 将 113 个 scaffold（包含 97.9%核苷酸的 90.4%的 scaffold）组装成 24 条染色体（假染色体）。通过雌雄 G. affinis 的比较基因组分析鉴定了 G. affinis 的 Z 和 W 染色体，并探讨了 Z 和 W 染色体分化的机制。结合来自 6 种组织的转录组数据，共预测了 23997 个蛋白质编码基因，其中 23737 个（98.9%）基因被功能注释。
高质量的雌性 G. affinis 参考基因组为比较基因组学和功能基因组学的未来研究提供了有价值的组学资源，以探索 Z 和 W 染色体的进化以及 G. affinis 的生殖发育生物学。
