The complete mitochondrial genome of the clamMactra veneriformis(Bivalvia: Mactridae): Has a unique non-coding region, missingatp8and typicaltRNA^Ser

Abstract

Mactra veneriformis (Bivalvia: Mactridae) is one commonly cultured bivalve species in the western Pacific Ocean. In the current study, the complete mitrochondrial DNA (mtDNA) of the clam M. veneriformis was determined. The M. veneriformis mt genome is 16,854 bp in length and encodes 34 genes on the same strand, including 12 protein-coding genes (PCGs), 2 ribosomal RNA genes and 20 transfer RNA genes. The length of 12 PCGs is 11,358 bp, which accounts for 67.4% in whole mt genome. The proportion is similar to other clams' mt genomes and within those of bivalves mt genomes. Gene order (which is the same as that of RZ C. antiquata) of M. veneriformis mt genome is compared with that of other veneroids. Compared with the typical gene content of animal mt genomes, atp8 and two tRNA(Ser) genes are missing in the mt genome. All non-coding regions are 1978 bp in length, among them the longest one is speculated as the control region, which is located between the tRNA(His) and tRNA(Arg). The secondary largest non-coding region (NCR(664)) between the tRNA(Gln) and tRNA(Thr) in the M. veneriformis mt genome contains one section of tandem repeats (125 nt × 5.2 or 249 nt × 2.6). The tandem repeats account for 97.89% (650/664) of the NCR(664), which is a unique characteristic of the M. veneriformis mt non-coding regions compared with those of other veneroids.

Comparative analysis of the complete mitochondrial genomes in two limpets from Lottiidae (Gastropoda: Patellogastropoda): rare irregular gene rearrangement within Gastropoda

“…The control region (CR) is the largest non-coding region; it usually presents a high AT content and is therefore also known as the A + T rich region 29 . It is an essential element involved in mitochondrial genome replication and transcription initiation 30 .…”

“…In conclusion, there are significant differences in the intergenic spacers and overlapping nucleotides of the two species, and these species of limpets also present large variations compared with other families (e.g., Nacellidae, Acmaeidae and Patellidae) [24][25][26][27][28] . The control region (CR) is the largest non-coding region; it usually presents a high AT content and is therefore also known as the A + T rich region 29 . It is an essential element involved in mitochondrial genome replication and transcription initiation 30 .…”

Comparative mitogenomic analysis reveals cryptic species: A case study in Mactridae (Mollusca: Bivalvia)

“…Mactridae includes 348 recognized species distributed in the world, but only two mitochondrial genomes (M. veneriformis and Coelomactra antiquata) have been reported recently (Meng et al, 2013a;Meng et al, 2012;Meng et al, 2013c). Mitochondrial genome of the commercially important M. chinensis has not been reported.…”

“…In addition to the mitochondrial genome sequence of M. chinensis from this study, the three recent reported mitochondrial genomes from Mactra veneriformis and Coelomactra antiquata (two genomes from the latter with specimens from Ri Zhao, Shandong Province in northern China and Zhang Zhou, Fujian Province in southern China) (Meng et al, 2013a;Meng et al, 2012;Meng et al, 2013c) were included in the phylogenetic analysis which includes a total of 25 bivalve mitochondrial genomes.…”

Confounding by linkage disequilibrium

“…One possible way to control for the effects of mitochondrial variants in genome-wide association study is to type diagnostic mitochondrial polymorphisms to allow for the mitochondrial haplogroup membership to be inferred and used as a covariate. 42 …”