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Comparative Genomic Analysis of Caridina pseudogracilirostris and Model Organisms: Insights into Phylogenetic Relationships and Gene Evolution

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NandhaGopal SoundharaPandiyan, Rajesh Kannan Rajaretinam
» doi: 10.31838/ecb/2023.12.si6.309


To compare Caridina pseudogracilirostris with other model organisms based on orthologous features and understand the evolutionary changes by identifying conserved genes and gene families. Methods: Total protein sequences of eleven different species (Caenorhabditis elegans, Danio rerio, Daphnia pulex, Drosophila melanogaster, Dugesia japonica, Gallus gallus, Hydra vulgaris, Mus musculus, Strongylocentrotus purpuratus, Xenopus laevis), including C. pseudogracilirostris were retrieved from NCBI. The orthology and comparative genomics were performed using orthofinder tool which uses Diamond, MCL, mafft and FastTree algorithms. Findings: A total of 5,62,515 (75.9%) genes were involved in ortho-groups representing conserved genes/gene families across different species. C. pseudogracilirostris has a total of 14,101 genes out of which 9,843 (69.8%) were identified to be in orthologues with other species. This analysis revealed that C. pseudogracilirostris have a close relationship with D. japonica, and had unique rapidly evolving conserved protein families like Trypsin-like protease try-5, Acyl-CoA synthetase 7, Receptor-type tyrosine-protein phosphatase dep-1, Probable vesicular glutamate transporter eat-4, and Receptor-type guanylate cyclase gcy-25. Conclusion and Novelty: Comparing the genomes of C. pseudogracilirostris with other model organisms provided information on its relationship and rapidly evolving conserved protein families across different species. We herewith first report that C. pseudogracilirostris can be used as a potential model system to study environmental pollution, climate change, and metabolism pathways based on the conserved protein sequence.

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