High-resolution chromosome-level genome provides molecular insights into adaptive evolution in crabs

Zhang, Y.; Yuan, Y.; Zhang, M.; Yu, X.; Qiu, B.; Wu, F.; Tocher, D. R.; Zhang, J.; Ye, S.; Cui, W.; Leung, J. Y. S.; Ikhwanuddin, M.; Waqas, W.; Dildar, T.; Ma, H.

doi:10.1101/2024.06.24.600346

bioRxiv · 10.1101/2024.06.24.600346

High-resolution chromosome-level genome provides molecular insights into adaptive evolution in crabs

Zhang, Y.·Yuan, Y.·Zhang, M.·Yu, X.·Qiu, B.·Wu, F.·Tocher, D. R.·Zhang, J.·Ye, S.·Cui, W.·Leung, J. Y. S.·Ikhwanuddin, M.·Waqas, W.·Dildar, T.·Ma, H.

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Abstract

Crabs thrive in diverse ecosystems, from coral reefs to hydrothermal vents and terrestrial habitats. Here, we report a comprehensive genomic analysis of the mud crab 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. 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. Posttranscriptional regulation involving novel-miR1317 negatively regulates Abd-A levels. Furthermore, the fru genes potential role in ovarian development and the identification of novel-miRNA-35 as a regulator of Spfru2 add complexity to gene regulatory networks. Comparative functional analysis across Decapoda species reveals neofunctionalization of the elovl6 gene in the synthesis of long-chain polyunsaturated fatty acids (LC-PUFA), suggesting its importance in environmental adaptation. These findings contribute significantly to our understanding of crab adaptability and evolutionary dynamics, offering a robust foundation for future investigations.

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Zhang, Y., Yuan, Y., Zhang, M., Yu, X., Qiu, B., Wu, F., Tocher, D. R., Zhang, J., Ye, S., Cui, W., Leung, J. Y. S., Ikhwanuddin, M., Waqas, W., Dildar, T., Ma, H.. 2024-06-27. High-resolution chromosome-level genome provides molecular insights into adaptive evolution in crabs. https://doi.org/10.1101/2024.06.24.600346

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