Complete mitochondrial DNA sequence of the ark shell Scapharca broughtonii: an ultra-large metazoan mitochondrial genome.

The complete mitochondrial (mt) genome of the ark shell Scapharca broughtonii was determined using long PCR and a genome walking sequencing strategy with genus-specific primers. The S. broughtonii mt genome (GenBank accession number AB729113) contained 12 protein-coding genes (the atp8 gene is missing, as in most bivalves), 2 ribosomal RNA genes, and 42 transfer tRNA genes, in a length of 46,985 nucleotides for the size of mtDNA with only one copy of the heteroplasmic tandem repeat (HTR) unit. Moreover the S. broughtonii mt genome shows size variation; these genomes ranged in size from about 47 kb to about 50 kb because of variation in the number of repeat sequences in the non-coding region. The mt-genome of S. broughtonii is, to date, the longest reported metazoan mtDNA sequence. Sequence duplication in non-coding region and the formation of HTR arrays were two of the factors responsible for the ultra-large size of this mt genome. All the tRNA genes were found within the S. broughtonii mt genome, unlike the other bivalves usually lacking one or more tRNA genes. Twelve additional specimens were used to analyze the patterns of tandem repeat arrays by PCR amplification and agarose electrophoresis. Each of the 12 specimens displayed extensive heteroplasmy and had 8-10 length variants. The motifs of the HTR arrays are about 353-362 bp and the number of repeats ranges from 1 to 11.

Liu YG ，Kurokawa T ，Sekino M ，Tanabe T ，Watanabe K ... -  《-》

The complete mitochondrial DNA of Tegillarca granosa and comparative mitogenomic analyses of three Arcidae species.

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).

Sun S ，Kong L ，Yu H ，Li Q ... -  《-》

A unique tRNA gene family and a novel, highly expressed ORF in the mitochondrial genome of the silver-lip pearl oyster, Pinctada maxima (Bivalvia: Pteriidae).

Characteristics of mitochondrial (mt) DNA such as gene content and arrangement, as well as mt tRNA secondary structure, are frequently used in comparative genomic analyses because they provide valuable phylogenetic information. However, most analyses do not characterize the relationship of tRNA genes from the same mt genome and, in some cases, analyses overlook possible novel open reading frames (ORFs) when the 13 expected protein-coding genes are already annotated. In this study, we describe the sequence and characterization of the complete mt genome of the silver-lip pearl oyster, Pinctada maxima. The 16,994-bp mt genome contains the same 13 protein-coding genes (PCGs) and two ribosomal RNA genes typical of metazoans. The gene arrangement, however, is completely distinct from that of all other available bivalve mt genomes, and a unique tRNA gene family is observed in this genome. The unique tRNA gene family includes two trnS(-AGY) and trnQ genes, a trnM isomerism, but it lacks trnS(-CUN). We also report the first clear evidence of alloacceptor tRNA gene recruitment (trnP→trnS(-AGY)) in mollusks. In addition, a novel ORF (orfUR1) expressed at high levels is present in the mt genome of this pearl oyster. This gene contains a conserved domain, "Oxidored_q1_N", which is a member of Complex I and thus may play an important role in key biological functions. Because orfUR1 has a very similar nucleotide composition and codon bias to that of other genes in this genome, we hypothesize that this gene may have been moved to the mt genome via gene transfer from the nuclear genome at an early stage of speciation of P. maxima, or it may have evolved as a result of gene duplication, followed by rapid sequence divergence. Lastly, a 319-bp region was identified as the possible control region (CR) even though it does not correspond to the longest non-coding region in the genome. Unlike other studies of mt genomes, this study compares the evolutionary patterns of all available bivalve mt tRNA and atp8 genes.

Wu X ，Li X ，Li L ，Yu Z ... -  《-》

Complete mitochondrial DNA sequence of oyster Crassostrea hongkongensis-a case of "Tandem duplication-random loss" for genome rearrangement in Crassostrea?

Yu Z ，Wei Z ，Kong X ，Shi W ... -  《-》

The complete mitochondrial genome of the clam Mactra veneriformis (Bivalvia: Mactridae): has a unique non-coding region, missing atp8 and typical tRNA Ser.

Meng X ，Shen X ，Zhao N ，Tian M ，Liang M ，Hao J ，Cheng H ，Yan B ，Dong Z ，Zhu X ... -  《-》