Complete mitochondrial genome of the sandfish Holothuria scabra (Holothuroidea, Holothuriidae)

Abstract

The complete mitochondrial genome (mitogenome) sequence of Holothuria scabra, an economically and ecologically important tropical sea cucumber, was first sequenced and annotated. The mitochondrial DNA is 15,779 bp in length and contains 13 protein-coding genes (PCGs), 2 rRNA genes, 22 tRNA genes, and a 456 bp putative control region, of which gene order is identical to the echinoderm ground pattern. Comparative analyses between H. scabra and other holothurians revealed three new findings: (1) the mitogenome of H. scabra is highly compact having five regions with overlapping genes and least intergenic nucleotides among the sequenced holothurians, only accounting for 3.58% of its mitogenome; (2) the genus Holothuria mitogenomes show a pattern of high interspecies divergence at the 13 PCGs, and the genetic p-distance reaches 25.68% between H. scabra and H. forskali; (3) the incomplete stop codon T of cox2 shared with H. forskali may be a common feature in the genus Holothuria.

Keywords:

• Incomplete stop codon
• interspecies divergence
• intergenic region
• mitochondrial DNA

Declaration of interest

This study was funded by the Key Projects in the National Science & Technology Pillar Program during the 12th Five-year Plan Period (2012BAD18B03 and 2011BAD13B02), Guangdong Province Program (2012B091100272 and 2012B061500012), and the Science & Technology Promoting Projects for Oceanic & Fishery in Guangdong Province (A201100D01 and A201101D02). The authors report that they have no conflicts of interest and are solely responsible for the content and writing of the article.