Characterization of whole mitochondrial genome Amyda cartilaginea from Dharmasraya, West Sumatera

Abstract

Previous data of the whole mitochondrial genome of soft-shelled turtle that it’s available in a public repository: Dogania subplana, Pelochelys cantorii, Chitra indica, Trionyx triunguis, Apalone spinifera, Rafetus swinhoei, and Pelodiscus sinensis. The first two species have natural distribution in Indonesia. Amyda cartilaginea is a species of soft-shelled turtle that is abundant in Indonesia. However, the whole mitochondrial genome data of A. cartilaginea is not available. This study aims to characterize the partial mitochondrial genome and analyze the phylogenetic position of A. cartilaginea. We reported almost complete mitochondrial genome of A. cartilaginea that caught from Batanghari river in Dharmasraya District, West Sumatera. The amplification of mitochondrial DNA fragments was performed using several primers designed following mitochondrial gene organization and sequence of D. subplana (Accession No AF366350). We sequenced half of the whole mitochondrial genome (7757 bp, 48%). The gene organization of the mitochondrial genome of A. cartilaginea was identic with D. subplana and P. cantorii. The phylogenetic tree analysis based on 16SrRNA revealed that the position of A. cartilaginea clustered with another soft-shelled turtle. Further study is needed to make a complete sequence of the mitochondrial genome of A. cartilaginea, with special focus on the control region to be applied to sustainable wild population management.