Comparative genomic analysis of mitochondrial protein-coding genes in Veneroida clams: Analysis of superfamily-specific genomic and evolutionary features.
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.
Department of Animal Life Science, Kangwon National University, Chuncheon 200-701, Republic of Korea.
Jae Yeon
JY
Hwang
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.
Chang-Kyu
CK
Lee
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.
Heebal
H
Kim
Biotechnology Research Division, National Fisheries Research and Development Institute, Busan 619-705, Republic of Korea.
Bo-Hye
BH
Nam
Biotechnology Research Division, National Fisheries Research and Development Institute, Busan 619-705, Republic of Korea.
Cheul Min
CM
An
Biotechnology Research Division, National Fisheries Research and Development Institute, Busan 619-705, Republic of Korea.
Jung Youn
JY
Park
Department of Animal Life System, Kangwon National University, Chuncheon 200-701, Republic of Korea.
Kyu-Hyun
KH
Park
Graduate School of International Agricultural Technology/GBST, Seoul National University, Pyeongchang 232-916, Republic of Korea.
Chul-Sung
CS
Huh
Department of Animal Life Science, Kangwon National University, Chuncheon 200-701, Republic of Korea. Electronic address: itanimal@kangwon.ac.kr.
Eun Bae
EB
Kim
D000818:Animals; D005075:Biological Evolution; D049872:Bivalvia / Q000235:genetics*; D004272:DNA, Mitochondrial / Q000235:genetics; D005786:Gene Expression Regulation / Q000502:physiology*; D016678:Genome; D024101:Mitochondrial Proteins / Q000235:genetics / Q000378:metabolism*; D005810:Multigene Family
D004272:DNA, Mitochondrial; D024101:Mitochondrial Proteins
Mitochondrial DNA; Superfamilly; Veneroida; dN/dS