Guangdong Provincial Key Laboratory of Marine Biotechnology, Shantou University, 243 Daxue Road, Shantou, 515063, China.
International Joint Research Center for the Development and Utilization of Important Mariculture Varieties Surrounding the South China Sea Region, Shantou University, Shantou, China.
BMC Biol. 2024 Nov 7;22(1):255. doi: 10.1186/s12915-024-02054-1.
Evolutionary adaptation drives organismal adjustments to environmental pressures, exemplified in the diverse morphological and ecological adaptations seen in Decapoda crustaceans, particularly brachyuran crabs. Crabs thrive in diverse ecosystems, from coral reefs to hydrothermal vents and terrestrial habitats. Despite their ecological importance, the genetic mechanisms underpinning their developmental processes, reproductive strategies, and nutrient acquisition remain poorly understood.
Here, we report a comprehensive genomic analysis of the green mud crab Scylla paramamosain using ultralong sequencing technologies, achieving a high-quality chromosome-level assembly. The refined 1.21 Gb genome, with an impressive contig N50 of 11.45 Mb, offers a valuable genomic resource. The genome exhibits 33,662 protein-coding genes, enriched in various pathways related to development and environmental adaptation. Gene family analysis shows expansion in development-related pathways and contraction in metabolic pathways, indicating niche adaptations. Notably, investigation into Hox gene regulation sheds light on their role in pleopod development, with the Abd-A gene identified as a linchpin. Post-transcriptional regulation involving novel-miR1317 negatively regulates Abd-A levels. Furthermore, the potential role of fru gene in ovarian development and the identification of novel-miR35 as a regulator of Spfru2 add complexity to gene regulatory networks. Comparative functional analysis across Decapoda species reveals neo-functionalization of the elovl6 gene in the synthesis of long-chain polyunsaturated fatty acids (LC-PUFA), suggesting its importance in environmental adaptation.
Our findings shed light on various aspects of crab biology, including genome sequencing, assembly, and annotation, as well as gene family expansion, contraction, and regulatory mechanisms governing crucial developmental processes such as metamorphosis, reproductive strategies, and fatty acid metabolism.
进化适应驱动生物体对环境压力进行调整，这在十足目甲壳动物中表现得尤为明显，尤其是短尾亚目螃蟹。螃蟹在从珊瑚礁到热液喷口和陆地栖息地等各种生态系统中繁衍生息。尽管它们具有重要的生态意义，但支撑其发育过程、繁殖策略和营养获取的遗传机制仍知之甚少。
本研究利用超长测序技术对拟穴青蟹 Scylla paramamosain 进行了全面的基因组分析，获得了高质量的染色体水平组装。经过优化的 1.21Gb 基因组，具有令人印象深刻的 11.45Mb 的 contig N50，为研究提供了有价值的基因组资源。该基因组包含 33662 个蛋白质编码基因，这些基因在与发育和环境适应相关的各种途径中富集。基因家族分析表明，与发育相关的途径发生扩张，而代谢途径发生收缩，表明生态位的适应。值得注意的是，对 Hox 基因调控的研究揭示了它们在腹肢发育中的作用，其中 Abd-A 基因被确定为关键基因。涉及新型-miR1317 的转录后调控负调控 Abd-A 水平。此外，fru 基因在卵巢发育中的潜在作用以及新型-miR35 作为 Spfru2 调节剂的鉴定，增加了基因调控网络的复杂性。对十足目物种的比较功能分析揭示了 elovl6 基因在长链多不饱和脂肪酸（LC-PUFA）合成中的新功能化，表明其在环境适应中的重要性。
本研究结果揭示了螃蟹生物学的各个方面，包括基因组测序、组装和注释，以及基因家族的扩张、收缩和调控机制，这些机制控制着变态、繁殖策略和脂肪酸代谢等关键发育过程。
