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Mar Genomics. 2015 Dec;24 Pt 3:329-34. doi: 10.1016/j.margen.2015.08.004. Epub 2015 Sep 4.

Comparative genomic analysis of mitochondrial protein-coding genes in Veneroida clams: Analysis of superfamily-specific genomic and evolutionary features.

Author information

1
Department of Animal Life Science, Kangwon National University, Chuncheon 200-701, Republic of Korea.
2
Department of Agricultural Biotechnology, Animal Biotechnology Major, Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul 151-921 Republic of Korea; Institute of Green Bio Science and Technology, Seoul National University, Kangwon-do 232-916, Republic of Korea.
3
Biotechnology Research Division, National Fisheries Research and Development Institute, Busan 619-705, Republic of Korea.
4
Department of Animal Life System, Kangwon National University, Chuncheon 200-701, Republic of Korea.
5
Graduate School of International Agricultural Technology/GBST, Seoul National University, Pyeongchang 232-916, Republic of Korea.
6
Department of Animal Life Science, Kangwon National University, Chuncheon 200-701, Republic of Korea. Electronic address: itanimal@kangwon.ac.kr.

Abstract

Veneroida is the largest order of bivalves, and these clams are commercially important in Asian countries. Although numerous studies have focused on the genomic characters of individual species or genera in Veneroida, superfamily-specific genomic characters have not been determined. In this study, we performed a comparative genomic analysis of 12 mitochondrial protein coding genes (PCGs) from 25 clams in six Veneroida superfamilies to determine genomic and evolutionary features of each superfamily. Length and distribution of nucleotides encoding the PCGs were too variable to define superfamily-specific genomic characters. Phylogenetic analysis revealed that PCGs are suitable for classification of species in three superfamilies: Cardioidea, Mactroidea, and Veneroidea. However, one species classified in Tellinoidea, Sinonovacula constricta, was evolutionarily closer to Solenoidea clams than Tellinoidea clams. dN/dS analysis showed that positively selected sites in NADH dehydrogenase subunit, nd4 and subunit of ATP synthase, atp6 were present in Mactroidea. Differences in selected sites in the nd4 and atp6 could be caused by superfamily-level differences in sodium transport or ATP synthesis functions, respectively. These differences in selected sites in NADH may have conferred these animals, which have low motility and do not generally move, with increased flexibility to maintain homeostasis in the face of osmotic pressure. Our study provides insight into evolutionary traits as well as facilitates identification of veneroids.

KEYWORDS:

Mitochondrial DNA; Superfamilly; Veneroida; dN/dS

PMID:
26343338
DOI:
10.1016/j.margen.2015.08.004
[Indexed for MEDLINE]

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