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.
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ABSTRACT: In this study, the complete mitochondrial genome (mitogenome) sequence of Chinese bahaba was determined by long PCR and primer walking methods. The complete mitochondrial genome is 16,500 bp in length and contains 37 mitochondrial genes (13 protein-coding genes, 2 ribosomal RNA genes and 22 transfer RNA genes) as well as a control region (CR) as other bony fishes. Within the CR, we identified the extended termination-associated sequence domain, the central conserved sequence block domains (CSB-D, CSB-E and CSB-F) and the conserved sequence block domains (CSB-1, CSB-2 and CSB-3).Mitochondrial DNA 09/2012; · 1.70 Impact Factor
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ABSTRACT: Abstract Through primer walking method, the mitochondrial genome sequence of white croaker (Pennahia argentata) from Japanese coastal water was obtained in this study. The mitogenome length of Japanese white croaker was 16,486 bp. The genome contains 13 protein-coding genes, 2 ribosomal RNA genes, and 22 transfer RNA genes, a control region (CR) and a dominating non-coding region. The termination-associated sequence, the central conserved domain, and the conserved sequence blocks were identified in the control region. The origin of L-strand replication was located in a cluster of five tRNA genes between tRNA-Asn and tRNA-Cys.Mitochondrial DNA 04/2013; · 1.70 Impact Factor
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ABSTRACT: The complete mitochondrial genome is of great importance for better understanding the genome-level characteristics and phylogenetic relationships among related species. In the present study, we determined the complete mitochondrial genome DNA sequence of the mud crab (Scylla paramamosain) by 454 deep sequencing and sanger sequencing approaches. The complete genome DNA was 15, 824 bp in length and contained a typical set of 13 protein-coding genes, 22 transfer RNA (tRNA) genes, two ribosomal RNA (rRNA) genes and a putative control region (CR). Of 37 genes, twenty-three were encoded by the heavy strand (H-strand), while the other ones were encoded by light strand (L-strand). The gene order in the mitochondrial genome was largely identical to those obtained in most arthropods, although the relative position of gene tRNA(His) differed from other arthropods. Among 13 protein-coding genes, three (ATPase subunits 6 (ATP6), NADH dehydrogenase subunits 1 (ND1) and ND3) started with a rare start codon ATT, whereas, one gene cytochrome c oxidase subunit I (COI) ended with the incomplete stop codon TA. All 22 tRNAs could fold into a typical clover-leaf secondary structure, with the gene sizes ranging from 63 to 73 bp. The phylogenetic analysis based on 12 concatenated protein-coding genes showed that the molecular genetic relationship of 19 species of 11 genera was identical to the traditional taxonomy.Gene 02/2013; · 2.20 Impact Factor