黄魟基因组组装及比较基因组学

Genome assembly and comparative genomics of Hemitrygon bennettii

  • 摘要:
    目的 针对黄魟因栖息地退化、过度兼捕致种群下降的濒危现状,为其保护遗传学研究提供数据支撑,同时为基因组学及生物演化相关研究的深入开展提供基础框架。
    方法 采用高通量测序与生物信息学方法,组装并注释黄魟全基因组序列,结合14种软骨鱼类开展比较基因组分析,解析其系统发育及演化历史。
    结果 黄魟基因组大小预估为4 018.13 Mb,重复序列比例和杂合率分别为65.38%;基于有参组装策略获得基因组序列全长3 198.64 Mb,scaffold N50为136.64 Mb,BUSCO完整性97.0%;注释分析共识别出57.50%的重复序列,以LINE元件为主,注释蛋白编码基因27 151个。系统发育分析显示黄魟与赤魟亲缘关系最近,约在430万年前分化,二者染色体呈高度共线性;扩张基因家族主要与染色质稳定、核小体组装相关,正选择基因富集于染色质重塑、DNA修复、脂质代谢及信号转导通路。
    结论 本研究组装获得黄魟基因组及注释信息,并解析其基因组特征与适应演化模式。研究结果为黄魟种群遗传多样性评估、保护基因组学研究提供重要数据基础,也为软骨鱼类比较基因组学与演化机制研究提供参考,对科学制定黄魟种群保护与恢复策略具有重要理论价值。

     

    Abstract: Bennett's Stingray (Hemitrygon bennettii), an ovoviviparous benthic cartilaginous fish belonging to the family Dasyatidae, plays an important role in maintaining marine ecological balance and has certain medicinal value. However, its population has declined sharply due to marine environmental degradation and bycatch, and it has been listed as a vulnerable species by the IUCN. At present, systematic research on H. bennettii at the molecular genetic level is relatively lacking, which limits the in-depth analysis of its conservation genetics and adaptive mechanisms.In this study, high-throughput sequencing technology was used to obtain the whole-genome sequencing data of H. bennettii, and bioinformatics methods were employed for genome assembly, annotation and comparative genomic analysis. The results showed that the estimated genome size of H. bennettii was about 4 061.75 Mb, with a heterozygosity rate of 0.81% and a repeat sequence ratio of 65.38%. After updated assembly, the total genome length was 3 198.64 Mb, with a Scaffold N50 of 136.64 Mb and a BUSCO completeness of 97.02%, indicating high continuity and completeness. A total of 25 890 protein-coding genes and 7 401 non-coding RNA (ncRNA) genes were annotated, and the total length of repetitive sequences accounted for 57.50% of the genome, with LINE transposons as the dominant type.Comparative genomic analysis with 14 other cartilaginous fish species showed that H. bennettii was most closely related to red stingray (Hemitrygon akajei), with a divergence time of about 4.3 million years ago. A total of 25 unique gene families were identified in H. bennettii, including 5 significantly expanded and 1 875 significantly contracted gene families. The expanded gene families were mainly enriched in chromatin structure and gene expression regulation, while the contracted ones were related to immune response and signal transduction. In addition, 50 positively selected genes were detected, which were significantly enriched in lipid metabolism and chromatin regulation pathways, revealing the adaptive evolutionary characteristics of H. bennettii to benthic life.This study reports the high-quality reference genome of H. bennettii for the first time, providing key basic data and a research framework for subsequent studies on conservation genomics, population genetics and adaptive evolution of H. bennettii, and also providing an important supplement for the genomic research of Dasyatidae fishes in Myliobatiformes.

     

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