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

NandhaGopal SoundharaPandiyan; Carlton Ranjith Wilson Alphonse; Subramoniam Thanumalaya; Samuel Gnana Prakash Vincent; Rajaretinam Rajesh Kannan

doi:10.1007/s13205-024-04121-4

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

3 Biotech. 2024 Nov;14(11):276. doi: 10.1007/s13205-024-04121-4. Epub 2024 Oct 23.

Authors

NandhaGopal SoundharaPandiyan¹, Carlton Ranjith Wilson Alphonse¹, Subramoniam Thanumalaya², Samuel Gnana Prakash Vincent³, Rajaretinam Rajesh Kannan⁴

Affiliations

¹ Centre for Molecular and Nanomedical Sciences, Centre for Nanoscience and Nanotechnology, School of Bio and Chemical Engineering, Sathyabama Institute of Science and Technology, Chennai, Tamil Nadu 600119 India.
² Department of Zoology, Madras University, Chennai, Tamil Nadu 600 025 India.
³ Centre for Marine Science and Technology, Manonmaniam Sundaranar University, Tirunelveli, 672 012 India.
⁴ Department of Biotechnology, Sharda School of Engineering and Technology, Sharda University, Plot No, 32, 34, Knowledge Park III, Greater Noida, Uttar Pradesh 201306 India.

PMID: 39464522
PMCID: PMC11499489 (available on 2025-11-01)
DOI: 10.1007/s13205-024-04121-4

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.

Keywords: Atyidae; Caridina pseudogracilirostris; Comparative genomics; Crustacean genome; NGS; Orthofinder.

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