title: The complete mitochondrial DNA of Tegillarca granosa and comparative mitogenomic analyses of three Arcidae species.
abstract: To better understand the characteristics and the evolutionary dynamics of mt genomes in Arcidae, the complete mitochondrial genome of Tegillarca granosa was firstly determined and compared with other two Arcidae species (Scapharca broughtonii and Scapharca kagoshimensis). The complete mitochondrial genome of T. granosa was 31,589 bp in length, including 12 protein-coding genes, 2 rRNA genes and 23 tRNA genes, and a major non-coding region. Three tandem repeat fragments were identified in the major non-coding region and the tandem repeat motifs of these fragments can be folded into stem-loop structures. The mitochondrial genome of the three species has several common features such as the AT content, the arrangement of the protein-coding genes, the codon usage of the protein-coding genes and AT/GC skew. However, a high level of variability is presented in the size of the genome, the number of tRNA genes and the length of non-coding sequences in the three mitogenomes. According to the phylogenetic analyses, these mitogenome-level characters are correlated with their phylogenetic relationships. It is the absence of the duplicated tRNAs and large non-coding sequences that are responsible for the length divergence of mitogenomes between T. granosa and other two Arcidae species. The phylogenetic analyses were conducted based on 12 partitioned protein genes, which support the relationship at the family level: (((Pectinidae+Ostreidae)+Mytilidae)+Arcidae).
authors.affiliation: Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao 266003, China.
authors.forename: Shao'e
authors.initials: S
authors.lastname: Sun
authors.affiliation: Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao 266003, China. Electronic address: klfaly@ouc.edu.cn.
authors.forename: Lingfeng
authors.initials: L
authors.lastname: Kong
authors.affiliation: Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao 266003, China.
authors.forename: Hong
authors.initials: H
authors.lastname: Yu
authors.affiliation: Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao 266003, China.
authors.forename: Qi
authors.initials: Q
authors.lastname: Li
mesh_terms: D000818:Animals; D049893:Arcidae / Q000235:genetics*; D001482:Base Composition; D001483:Base Sequence; D002874:Chromosome Mapping; D004272:DNA, Mitochondrial / Q000235:genetics*; D054629:Genome, Mitochondrial / Q000235:genetics*; D008928:Mitochondria / Q000235:genetics*; D008969:Molecular Sequence Data; D016366:Open Reading Frames; D010802:Phylogeny; D012335:RNA, Ribosomal / Q000235:genetics; D012343:RNA, Transfer / Q000235:genetics; D016415:Sequence Alignment; D017422:Sequence Analysis, DNA; D020080:Tandem Repeat Sequences / Q000235:genetics
chemical_list: D004272:DNA, Mitochondrial; D012335:RNA, Ribosomal; D012343:RNA, Transfer
keywords: Arcidae; Comparative analysis; Mitochondrial genome; Phylogenetic relationships