title: Complete mitochondrial genome sequence of the spinyhead croaker Collichthys lucidus (Perciformes, Sciaenidae) with phylogenetic considerations.
abstract: The complete mitochondrial genome of the spinyhead croaker Collichthys lucidus was determined using long-PCR and primer walking methods. It is a circular molecule of 16,451 bp in length with a standard set of 22 tRNAs, 2 rRNAs, 13 protein-coding genes as well as a non-coding control region in the same order as those of the other bony fishes. C. lucidus mitogenome exhibited a clear strand-specific bias in nucleotide composition, as evidence by a GC- skew of the H-strand of -0.319. The strand-specific bias was also reflected in the codon usage of genes oriented in opposite directions. All tRNA genes except for tRNA(                            Ser(AGY)) harbored the typical cloverleaf secondary structures and possessed anticodons that matched the vertebrate mitochondrial genetic code. Contrary to the typical structure of control region consistig of TAS, central, and CSB domains, there were no central conserved blocks available in C. lucidus mitogenome. Despite extensive studies based on both morphology and molecules, phylogenetic position of C. lucidus with Sciaenidae is still controversial. Our phylogenetic results provided more evidence to support previous morphological studies and consistently placed C. lucidus as a sister taxon to Collichthys niveatus, with both of these taxa forming the monophyletic Collichthys.
authors.affiliation: Fisheries College, Ocean University of China, Qingdao, 266003, China.
authors.forename: Jiao
authors.initials: J
authors.lastname: Cheng
authors.forename: Guo-Qiang
authors.initials: GQ
authors.lastname: Ma
authors.forename: Zhen-Qing
authors.initials: ZQ
authors.lastname: Miao
authors.forename: Bo-Nian
authors.initials: BN
authors.lastname: Shui
authors.forename: Tian-Xiang
authors.initials: TX
authors.lastname: Gao
mesh_terms: D000818:Animals; D001482:Base Composition / Q000235:genetics; D001483:Base Sequence; D003062:Codon / Q000235:genetics; D021901:DNA, Intergenic / Q000235:genetics; D004272:DNA, Mitochondrial / Q000235:genetics; D054629:Genome, Mitochondrial / Q000235:genetics*; D008969:Molecular Sequence Data; D009711:Nucleotides / Q000235:genetics; D016366:Open Reading Frames / Q000235:genetics; D010473:Perciformes / Q000235:genetics*; D010802:Phylogeny; D012335:RNA, Ribosomal / Q000235:genetics; D012343:RNA, Transfer / Q000235:genetics; D017422:Sequence Analysis, DNA
chemical_list: D003062:Codon; D021901:DNA, Intergenic; D004272:DNA, Mitochondrial; D009711:Nucleotides; D012335:RNA, Ribosomal; D012343:RNA, Transfer