Genome sequencing of Caridina pseudogracilirostris and its comparative analysis with malacostracan crustaceans.

Abstract

The Caridina pseudogracilirostris is commonly found in the brackish waters of the southwestern coastal regions of India. This study provides a comprehensive genomic investigation of the shrimp species C. pseudogracilirostris, offering insights into its genetic makeup, evolutionary dynamics, and functional annotations. The genomic DNA was isolated from tissue samples, sequenced using next-generation sequencing (NGS), and stored in the National Center for Biotechnology Information (NCBI) Sequence Read Archive (SRA) database (Accession No: PRJNA847710). De novo sequencing indicated a genome size of 1.31 Gbp with a low heterozygosity of about 0.81%. Repeat masking and annotation revealed that repeated elements constitute 24.60% of the genome, with simple sequence repeats (SSRs) accounting for 7.26%. Gene prediction identified 14,101 genes, with functional annotations indicating involvement in critical biological processes such as development, cellular function, immunological responses, and reproduction. Furthermore, phylogenetic analysis revealed genomic links among Malacostraca species, indicating gene duplication as a strategy for genetic diversity and adaptation. C. pseudogracilirostris has 1,856 duplicated genes, reflecting a distinct genomic architecture and evolutionary strategy within the Malacostraca branch. These findings enhance our understanding of the genetic characteristics and evolutionary relationships of C. pseudogracilirostris, providing significant insights into the overall evolutionary dynamics of the Malacostraca group.

Supplementary information: The online version contains supplementary material available at 10.1007/s13205-024-04121-4.