Abstract
AbstractExopalaemon carinicauda, a eurythermal and euryhaline shrimp, contributes one third of the total biomass production of polyculture ponds in eastern China and is considered as a potential ideal experimental animal for research on crustaceans. We conducted a high-quality chromosome-level genome assembly of E. carinicauda combining PacBio HiFi and Hi-C sequencing data. The total assembly size was 5.86 Gb, with a contig N50 of 235.52 kb and a scaffold N50 of 138.24 Mb. Approximately 95.29% of the assembled sequences were anchored onto 45 pseudochromosomes. BUSCO analysis revealed that 92.89% of 1,013 single-copy genes were highly conserved orthologs. A total of 44, 288 protein-coding genes were predicted, of which 70.53% were functionally annotated. Given its high heterozygosity (2.62%) and large proportion of repeat sequences (71.49%), it is one of the most complex genome assemblies. This chromosome-scale genome will be a valuable resource for future molecular breeding and functional genomics research on E. carinicauda.
Publisher
Springer Science and Business Media LLC
Reference57 articles.
1. World Register of Marine Species https://www.marinespecies.org (2024).
2. Zhang, Q., Zhang, C., Yu, Y. & Li, F. Analysis of genetic diversity and population structure of the ridgetail white prawn Exopalaemon carinicauda in China. Aquacult Rep. 27, 101369 (2022).
3. Li, J. et al. Genome survey and high-resolution backcross genetic linkage map construction of the ridgetail white prawn Exopalaemon carinicauda applications to QTL mapping of growth traits. Bmc Genomics. 20, 598 (2019).
4. Ge, Q., Li, Z., Li, J., Wang, J. & Li, J. Effects of acute salinity stress on the survival and prophenoloxidase system of Exopalaemon carinicauda. Acta Oceanol Sin. 39, 57–64 (2020).
5. Wang, X., Yan, B., Ma, S. & Dong, S. Study on The Biology and Cultural Ecology of Exopalaemon carinicauda. Shandong Fisheries. 22, 21–24 (2005).