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The complete mitochondrial genome of the Chinese hook snout carp Opsariichthys bidens (Actinopterygii : Cyprinifonnes) and an altemative pattem of mitogenomic evolution in vertebrate
Wang, Xuzhen; Wang, Jun; He, Shunping; Mayden, Richard L.; He, SP, Chinese Acad Sci, Inst Hydrobiol, Lab Fish Phylogenet & Biogeog, Wuhan 430072, Peoples R China
2007-09-01
Source PublicationGENE
ISSN0378-1119
Volume399Issue:1Pages:11-19
AbstractThe complete mitochondrial genome sequence of the Chinese hook snout carp, Opsariichthys bidens, was newly determined using the long and accurate polymerase chain reaction method. The 16,611-nucleotide mitogenome contains 13 protein-coding genes, two rRNA genes (12S, 16S) 22 tRNA genes, and a noncoding control region. We use these data and homologous sequence data from multiple other ostariophysan fishes in a phylogenetic evaluation to test hypothesis pertaining to codon usage pattern of O. bidens mitochondrial protein genes as well as to re-examine the ostariophysan phylogeny. The mitochondrial genome of O. bidens reveals an alternative pattern of vertebrate mitochondrial evolution. For the mitochondrial protein genes of O. bidens, the most frequently used codon generally ends with either A or C, with C preferred over A for most fourfold degenerate codon families; the relative synonymous codon usage of G-ending codons is greatly elevated in all categories. The codon usage pattern of O. bidens mitochondrial protein genes is remarkably different from the general pattern found previously in the relatively closely 9 related zebrafish and most other vertebrate mitochondria. Nucleotide bias at third codon positions is the main cause of codon bias in the mitochondrial protein genes of O. bidens, as it is biased particularly in favor of C over A. Bayesian analysis of 12 concatenated mitochondrial protein sequences for O. bidens and 46 other teleostean taxa supports the monophyly of Cypriniformes and Otophysi and results in a robust estimate of the otophysan phylogeny. (C) 2007 Published by Elsevier B.V.; The complete mitochondrial genome sequence of the Chinese hook snout carp, Opsariichthys bidens, was newly determined using the long and accurate polymerase chain reaction method. The 16,611-nucleotide mitogenome contains 13 protein-coding genes, two rRNA genes (12S, 16S) 22 tRNA genes, and a noncoding control region. We use these data and homologous sequence data from multiple other ostariophysan fishes in a phylogenetic evaluation to test hypothesis pertaining to codon usage pattern of O. bidens mitochondrial protein genes as well as to re-examine the ostariophysan phylogeny. The mitochondrial genome of O. bidens reveals an alternative pattern of vertebrate mitochondrial evolution. For the mitochondrial protein genes of O. bidens, the most frequently used codon generally ends with either A or C, with C preferred over A for most fourfold degenerate codon families; the relative synonymous codon usage of G-ending codons is greatly elevated in all categories. The codon usage pattern of O. bidens mitochondrial protein genes is remarkably different from the general pattern found previously in the relatively closely 9 related zebrafish and most other vertebrate mitochondria. Nucleotide bias at third codon positions is the main cause of codon bias in the mitochondrial protein genes of O. bidens, as it is biased particularly in favor of C over A. Bayesian analysis of 12 concatenated mitochondrial protein sequences for O. bidens and 46 other teleostean taxa supports the monophyly of Cypriniformes and Otophysi and results in a robust estimate of the otophysan phylogeny. (C) 2007 Published by Elsevier B.V.
SubtypeArticle
KeywordCyprinidae Ostariophysi Mitochondrial Genome Evolution
DepartmentChinese Acad Sci, Inst Hydrobiol, Lab Fish Phylogenet & Biogeog, Wuhan 430072, Peoples R China; Chinese Acad Sci, Bijing Inst Genom, Beijing Proteom Inst, Beijing 101300, Peoples R China; Univ So Denmark, Dept Biochem & Mol Biol, DK-5230 Odense, Denmark; Univ Aarhus, Inst Human Genet, DK-8000 Aarhus, Denmark; St Louis Univ, Dept Biol, St Louis, MO 63103 USA
Subject AreaGenetics & Heredity
DOI10.1016/j.gene.2007.04.019
WOS HeadingsScience & Technology ; Life Sciences & Biomedicine
Indexed BySCI
Language英语
WOS Research AreaGenetics & Heredity
WOS SubjectGenetics & Heredity
WOS IDWOS:000248882500002
WOS KeywordHIGHER-LEVEL RELATIONSHIPS ; LONGER DNA-SEQUENCES ; TRANSFER-RNA GENES ; OSTARIOPHYSAN FISHES ; BONY FISHES ; ORGANIZATION ; PHYLOGENY ; TELEOSTEI ; PERSPECTIVE ; ORDER
Citation statistics
Cited Times:48[WOS]   [WOS Record]     [Related Records in WOS]
Document Type期刊论文
Identifierhttp://ir.ihb.ac.cn/handle/152342/8470
Collection期刊论文
Corresponding AuthorHe, SP, Chinese Acad Sci, Inst Hydrobiol, Lab Fish Phylogenet & Biogeog, Wuhan 430072, Peoples R China
Affiliation1.Chinese Acad Sci, Inst Hydrobiol, Lab Fish Phylogenet & Biogeog, Wuhan 430072, Peoples R China
2.Chinese Acad Sci, Bijing Inst Genom, Beijing Proteom Inst, Beijing 101300, Peoples R China
3.Univ So Denmark, Dept Biochem & Mol Biol, DK-5230 Odense, Denmark
4.Univ Aarhus, Inst Human Genet, DK-8000 Aarhus, Denmark
5.St Louis Univ, Dept Biol, St Louis, MO 63103 USA
Recommended Citation
GB/T 7714
Wang, Xuzhen,Wang, Jun,He, Shunping,et al. The complete mitochondrial genome of the Chinese hook snout carp Opsariichthys bidens (Actinopterygii : Cyprinifonnes) and an altemative pattem of mitogenomic evolution in vertebrate[J]. GENE,2007,399(1):11-19.
APA Wang, Xuzhen,Wang, Jun,He, Shunping,Mayden, Richard L.,&He, SP, Chinese Acad Sci, Inst Hydrobiol, Lab Fish Phylogenet & Biogeog, Wuhan 430072, Peoples R China.(2007).The complete mitochondrial genome of the Chinese hook snout carp Opsariichthys bidens (Actinopterygii : Cyprinifonnes) and an altemative pattem of mitogenomic evolution in vertebrate.GENE,399(1),11-19.
MLA Wang, Xuzhen,et al."The complete mitochondrial genome of the Chinese hook snout carp Opsariichthys bidens (Actinopterygii : Cyprinifonnes) and an altemative pattem of mitogenomic evolution in vertebrate".GENE 399.1(2007):11-19.
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