De nova assembly, annotation and comparative genomics study on the draft genome of Indian brackish water shrimp Caridina pseudogracilirostris

Abstract

Abstract The caridean shrimp Caridina pseudogracilirostris (order-Decapoda, family-Atyidae) is commonly found in the brackish waters of the southwestern coastal regions of peninsular India. The draft genome sequencing of this shrimp was carried out by Illumina NovaSeq6000 platform. We obtained a draft genome assembly of C. pseudogracilirostris (1.3 Gbp; 6,03,962 scaffolds; scaffold N50 = 2641 bp; 35.71% GC, 52.8% BUSCO completeness). It revealed that 24.60% of the genomic sequences are repetitive and has high proportion of simple sequence repeats (SSR) spanning 7.26% of the entire genome. Other major repeat classes found are Retroelements (3.19%), LINEs (2.37%) and L2/CR1/Rex (1.05%). A total of 14101 genes were identified with AUGUSTUS. The predicted genes were functionally annotated using EggNOG-mapper and the genes containing database hits were sorted based on the biological processes using Panther database. Genes associated with developmental process (31), cellular process (30), immune system process, (20) and reproductive process (24) were further analyzed in pathway commons and narrowed down into genes involved in regulatory pathways. We have conducted a comparative study with 15 crustacean species using OrthoFinder. It provided the phylogenetic species tree and a total of 7396 orthogroups were identified. C. pseudogracilirostris has shown only 3.7% orthologous genes.