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Mitochondrial DNA A DNA Mapp Seq Anal. 2018 May;29(4):511-524. doi: 10.1080/24701394.2017.1315567. Epub 2017 Apr 19.

Identifying selectively important amino acid positions associated with alternative habitat environments in fish mitochondrial genomes.

Xia JH1,2, Li HL1,2, Zhang Y1,2, Meng ZN1,2, Lin HR1,2.

Author information

1
a State Key Laboratory of Biocontrol, Institute of Aquatic Economic Animals, Sun Yat-Sen University , Guangzhou , PR China.
2
b Guangdong Provincial Key Laboratory for Aquatic Economic Animals, College of Life Sciences, Sun Yat-Sen University , Guangzhou , PR China.

Abstract

Fish species inhabitating seawater (SW) or freshwater (FW) habitats have to develop genetic adaptations to alternative environment factors, especially salinity. Functional consequences of the protein variations associated with habitat environments in fish mitochondrial genomes have not yet received much attention. We analyzed 829 complete fish mitochondrial genomes and compared the amino acid differences of 13 mitochondrial protein families between FW and SW fish groups. We identified 47 specificity determining sites (SDS) that associated with FW or SW environments from 12 mitochondrial protein families. Thirty-two (68%) of the SDS sites are hydrophobic, 13 (28%) are neutral, and the remaining sites are acidic or basic. Seven of those SDS from ND1, ND2 and ND5 were scored as probably damaging to the protein structures. Furthermore, phylogenetic tree based Bayes Empirical Bayes analysis also detected 63 positive sites associated with alternative habitat environments across ten mtDNA proteins. These signatures could be important for studying mitochondrial genetic variation relevant to fish physiology and ecology.

KEYWORDS:

Fish; habitat; mitochondria; protein sequence; selection; specificity determining sites

PMID:
28423967
DOI:
10.1080/24701394.2017.1315567
[Indexed for MEDLINE]

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