Mitochondrial DNA Markers for PCR-Based Phylogenetic Analysis of Ark Shells

Tomomi Tanaka,Futoshi Aranishi

doi:10.4236/ojms.2013.34021

Abstract

Arcidae species are commercially important bivalves in Japan and are commonly referred to as bloody ark due to their red blood. They have thick shells with distinct radiating ribs, and the numbers of these ribs are important morphological features for species discrimination. However, some Arcidae species are morphologically indistinguishable, with a similar number of the ribs in adults and deficient rib formation, particularly among juveniles. Thus, we developed a reliable molecular marker to genetically discriminate between 7 Arcidae species belonging to Scapharca, Anadara, and Tegillarca based on species-specific polymorphic segments of mitochondrial DNA. PCR amplification of partial COI, 16S rRNA, 12S rRNA, and Cyt b genes was performed on 7 species using 8 primer sets. Only the set of Scapharca-specific forward primer and universal reverse primer for the partial COI gene successfully yielded single PCR products from all 7 species examined. Thus, nucleotide sequences of 481 bp portion of these PCR products were determined, and the degrees of nucleotide substitutions ranged from 0.4% between S. broughtonii and T. granosa to 20.2% between S. satowi and A. antiquata. In addition, a phylogenetic tree showed significant differences between 7 species, with higher bootstrap support than 69.

Highlights

Ark shells are a group of bivalves, in which red blood cells circulate through open blood-vascular systems, and hemoglobin pigment in both blood and tissue cells colors the body red [1]
We developed a reliable molecular marker to genetically discriminate between 7 Arcidae species belonging to Scapharca, Anadara, and Tegillarca based on species-specific polymorphic segments of mitochondrial DNA
Universal primer pairs developed for PCR amplification of the mitochondrial DNA (mtDNA) 16S rRNA, 12S rRNA, and cytochrome b (Cyt b) genes were examined

Summary

Introduction

Ark shells are a group of bivalves, in which red blood cells circulate through open blood-vascular systems, and hemoglobin pigment in both blood and tissue cells colors the body red [1]. 200 species of ark shells have been classified into the family Arcidae [2] and widely distributed globally in shallow tropical and temperate seas [3]. Scapharca, Anadara, and Tegillarca have been actively collected for food throughout Asia [5]. Shell surfaces are sculptured by radial ribs and covered with thick velvety periostracum [6]. These morphological features are important indicator of species identification, the radial ribs are often similar between species (Table 1). Morphologically identification of sympatrically related species is difficult, because their radial ribs are similar in number and change with maturity. Genetic markers are required for accurate ark shells identification

Methods

Results

Conclusion