Wrasses are dominant components of major coral reef systems. Among wrasses, Cheilinus undulatus is an endangered species with high economic and ecological value that exhibits sex reversal of females to males, while sexual selection occurs in breeding aggregations. However, the molecular-associated mechanism underlying this remains unclear. Opsin gene diversification is regarded as a potent force in sexual selection. Here we present a genome assembly of C. undulatus, using Illumina, Nanopore and Hi-C sequencing. The 1.17 Gb genome was generated from 328 contigs with an N50 length of 16.5 Mb and anchored to 24 chromosomes. In total, 22,218 genes were functionally annotated, and 96.36% of BUSCO genes were fully represented. Transcriptomic analyses showed that 96.79% of the predicted genes were expressed. Transposons were most abundant, accounting for 39.88% of the genome, with low divergence, owing to their evolution with close species ~60.53 million years ago. In total, 567/1,826 gene families were expanded and contracted in the reconstructed phylogeny, respectively. Forty-six genes were under positive selection. Comparative genomic analyses with other fish revealed expansion of opsin SWS2B, LWS1 and Rh2. The elevated duplicates of SWS2B were generated by gene conversions via transposition of transposons followed by nonallelic homologous recombination. Amino acid substitutions of opsin paralogues occurred at key tuning sites, causing a spectral shift in maximal absorbance of visual pigment to capture functional changes. Among these opsin genes, SWS2B-3 and 4 and Rh1 are expressed in the retina. The genome sequence of C. undulatus provides valuable resources for future investigation of the conservation, evolution and behaviour of fishes.

中文翻译：

---

濒危驼头濑鱼 Cheilinus undulatus 的染色体水平基因组组装：对鱼类视蛋白基因扩增的洞察

濑鱼是主要珊瑚礁系统的主要组成部分。在隆头鱼中，Cheilinus undulatus是一种具有较高经济和生态价值的濒危物种，表现出雌性与雄性的性别逆转，而性选择则发生在繁殖聚集中。然而，其背后的分子相关机制仍不清楚。视蛋白基因多样化被认为是性选择的强大力量。在这里，我们展示了C的基因组组装。波状，使用 Illumina、Nanopore 和 Hi-C 测序。1.17 Gb 基因组由 328 个重叠群生成，N50 长度为 16.5 Mb，并锚定在 24 条染色体上。总共有22,218个基因被功能注释，96.36%的BUSCO基因被完全代表。转录组学分析表明，96.79% 的预测基因得到表达。转座子是最丰富的，占基因组的 39.88%，由于它们在大约 6053 万年前与近亲物种进化，因此差异很小。在重建的系统发育中，总共有 567/1,826 个基因家族分别被扩展和收缩。46 个基因处于阳性选择之下。与其他鱼类的比较基因组分析揭示了视蛋白SWS2B、LWS1和Rh2 的扩增. SWS2B的升高重复是通过转座子转座和非等位基因同源重组的基因转换产生的。视蛋白旁系物的氨基酸取代发生在关键的调谐位点，导致视觉色素的最大吸光度发生光谱变化以捕捉功能变化。在这些视蛋白基因中，SWS2B - 3和4以及Rh1在视网膜中表达。C的基因组序列。undulatus为未来调查鱼类的保护、进化和行为提供了宝贵的资源。