Table6_Deciphering male influence in gynogenetic Pengze crucian carp (Carassius auratus var. pengsenensis): insights from Nanopore sequencing of structural variations.XLSX

In this study, we investigate gynogenetic reproduction in Pengze Crucian Carp (Carassius auratus var. pengsenensis) using third-generation Nanopore sequencing to uncover structural variations (SVs) in offspring. Our objective was to understand the role of male genetic material in gynogenesis by examining the genomes of both parents and their offspring. We discovered a notable number of male-specific structural variations (MSSVs): 1,195 to 1,709 MSSVs in homologous offspring, accounting for approximately 0.52%–0.60% of their detected SVs, and 236 to 350 MSSVs in heterologous offspring, making up about 0.10%–0.13%. These results highlight the significant influence of male genetic material on the genetic composition of offspring, particularly in homologous pairs, challenging the traditional view of asexual reproduction. The gene annotation of MSSVs revealed their presence in critical gene regions, indicating potential functional impacts. Specifically, we found 5 MSSVs in the exonic regions of protein-coding genes in homologous offspring, suggesting possible direct effects on protein structure and function. Validation of an MSSV in the exonic region of the polyunsaturated fatty acid 5-lipoxygenase gene confirmed male genetic material transmission in some offspring. This study underscores the importance of further research on the genetic diversity and gynogenesis mechanisms, providing valuable insights for reproductive biology, aquaculture, and fostering innovation in biological research and aquaculture practices.

本研究以彭泽鲫（Carassius auratus var. pengsenensis）为实验材料，利用第三代纳米孔测序（third-generation Nanopore sequencing）技术对其子代的结构变异（structural variations, SVs）进行解析，旨在通过分析亲本及其子代的基因组，阐明雄性遗传物质在雌核发育（gynogenetic reproduction）过程中的作用。本研究共检测到大量雄性特异性结构变异（male-specific structural variations, MSSVs）：同源子代（homologous offspring）中存在1195至1709个MSSVs，约占其检测到的结构变异总量的0.52%~0.60%；异源子代（heterologous offspring）中则存在236至350个MSSVs，占比约为0.10%~0.13%。上述结果表明，雄性遗传物质对子代的遗传组成具有显著影响，尤其在同源子代群体中更为突出，这一发现挑战了传统的无性生殖认知。对MSSVs进行基因注释（gene annotation）后发现，这些变异位点位于关键基因区域，提示其可能产生功能性影响。具体而言，我们在同源子代的蛋白质编码基因（protein-coding genes）外显子区域（exonic regions）中发现了5个MSSVs，表明这些变异可能对蛋白质的结构与功能产生直接作用。针对多不饱和脂肪酸5-脂氧合酶基因（polyunsaturated fatty acid 5-lipoxygenase gene）外显子区域的一处MSSVs进行验证后，证实部分子代中确实存在雄性遗传物质的传递。本研究强调了针对遗传多样性与雌核发育机制开展深入研究的重要性，可为生殖生物学、水产养殖领域提供宝贵的研究视角，并有望推动生物研究与水产养殖实践的创新发展。