Unraveling the Complete Mitochondrial Genome of (Purple Zebra Shrimp) (Crustacea: Decapoda) Provides Insights Into Its Phylogenetic Relationships and Gene Order Rearrangements

Overview

Journal Ecol Evol

Date 2024 Nov 22

PMID 39575143

Authors

Sofia Priyadarsani Das

Yu-Kai Kao

Huu-The Nguyen

Yu-Ru Lin

Zhen-Hao Liao

Yeh-Fang Hu

Fan-Hua Nan

Affiliations

Soon will be listed here.

Abstract

Understanding the functions of mitochondrial genomes is crucial for studies related to the evolution of genomes, phylogenomics, and species identification. For the first time, complete mitogenome of a non-snapping shrimp has been successfully sequenced and characterized from Taiwan that belongs to the Decapoda order, Crustacea class, and Caridea infraorder. This study involved analysis of nucleotide composition, codon usage, gene ordering, evolutionary selection pressure, and comparative mitogenomics. The mitogenome of is 16,605 base pairs in length and consists of standard set of 37 genes found in metazoans. The gene rearrangements in the mitochondrial genome of this species shows extensive rearrangements comparing to the typical pattern found in pancrustaceans mitogenomes. Therefore, it could be concluded that gene rearrangements most likely happen only in the caridea infraorder. The current investigation discovered transposition of the tRNA and rRNA genes along with reversal in strands in the tRNAs. No other Alpheidae mitochondrial genome that has been investigated thus far has revealed this pattern. All 13 protein coding genes in the mitochondrial genomes of superfamily Alphoidea exhibited Ka/Ks values lower than 1, according to the ratios of nonsynonymous and synonymous substitutions rates. This suggests that a strong purifying selection had taken place. The maximum likelihood tree consisting of 46 mitogenomes of infraorder Caridea along with outgroups, revealed the existence of in the family Alpheidae and it formed a monophyletic group along with Palaemonoidea and Alpheoidea superfamily.

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