Complete F-type Mitochondrial Genome Research Articles

The complete mitochondrial genome of freshwater mussel Pronodularia japanensis (Gonideinae, Unionidae, Unionida) from Tochigi Prefecture, Japan, and its phylogenetic analysis

We have sequenced the female-type (F-type) complete mitochondrial genome of Pronodularia japanensis (Gonideinae, Unionidae, Unionida, Bivalvia) from Tochigi Prefecture, Japan. The complete F-type mitochondrial genome (16,803 bp; LC505454) contains 13 protein-coding genes, 2 rRNA genes, and 22 tRNA genes. Molecular phylogenetic analyses using complete F-type mitochondrial genomes of 56 Unionida species revealed the phylogenetic position of P. japanensis in Unionidae. This study should be basic data to investigate the genetic diversity in this species.

The complete mitochondrial genome of freshwater mussel Nodularia douglasiae (Unionidae) from Lake Kasumigaura, Japan, and its phylogenetic analysis

We have sequenced the female type (F-type) mitochondrial genome of Nodularia douglasiae (Unioninae, Unionidae, Unionida, Bivalvia) from Lake Kasumigaura, Japan, and inferred the Unioninae phylogeny using complete mitochondrial genome sequences. The complete F-type mitochondrial genome (15,779 bp; LC496352) contains 13 protein-coding genes, 2 rRNA genes, and 22 tRNA genes. Molecular phylogenetic analyses using complete F-type mitochondrial genomes from 15 Unioninae species including N. douglasiae from China and Korea were performed. This study should be basic data to investigate the genetic diversity of freshwater mussel N. douglasiae.

Identification of complete F-type mitochondrial genome in Lamprotula scripta and Lamprotula caveata and analysis on DUI

Mitochondrial DNA is typically passed to offspring through maternal inheritance. However, in mussels, two kinds of mitochondrial DNA exist: F and M type, which are referred to as doubly uniparental inheritance (DUI). Studies have shown that DUI may be related to gender determination. In this study, we obtained the first complete F-type mitochondrial genome of Lamprotula scripta and Lamprotula caveata which were 16,250 bp and 16,641 bp in length, respectively, and had 13 protein coding genes (PCGs), 22 transfer RNAs, 2 ribosomal RNAs and 27 non-coding (NC) regions. The largest NC region of L. scripta was 639 bp and located between ND5 and tRNAGln. The largest NC of L. caveata was 1046 bp and also located between ND5 and tRNAGln. The overall AT content of L. scripta and L. caveata was 58.95% and 58.66%, respectively, which were lower than Lamprotula leai, Lamprotula gottschei and Lamprotula tortuosa. We next compared F and M mitochondrial genomic data on freshwater mussels and established a phylogenetic tree based on amino acid sequences of 13 PCGs and COII gene. Our results showed that F- and M-type mitochondria were significantly separated into two branches, and the basic structure of phylogenetic trees were divided into four distinct groups: Unioninae, Anodontini, Gonideinae and Ambleminae. Relatives of Gonideinae and Ambleminae were more closely related than Unioninae and Anodontini, indicating significant differences in mtDNA between the two mitogenome types. Moreover, we revealed that L. scripta and L. caveata are closely relatives, suggesting that they are both subordinates of the Gonideinae subfamily. Consequently, we speculate that the formation of DUI hinders their disappearance, which provides a basis for further studies into the mechanisms and genetic diversities of DUI formation.

The complete maternal mitochondrial genome of rare Chinese freshwater mussel Lepidodesma languilati (Bivalvia: Unionidae: Unioninae)

Lepidodesma languilati is considered threatened because of the influence of human activities in China. The complete F-type mitochondrial genome of L. languilati was determined in this study (GenBank accession no. KT381195). It is a 15 754-bp-long circular molecule that consists of 37 genes that are typically found in other invertebrates. The overall base composition of the entire sequence is as follows: A (39.1%), T (25.7%), C (23.4%), and G (11.8%). Except for cox1 (TTG), cob (ATT), nad1 (ATT), nad6 (ATA), nad4 (TTG), and atp8 (GTG), 7 of the 13 protein-coding genes initiate with orthodox ATG start codon. All the 13 protein-coding genes have complete termination codon TAA or TAG. Phylogenetic tree indicates that L. languilati belongs to Unioninae. The newly sequenced complete mitogenome can provide basic data for comparative studies on mitochondrial genomes of Unionidae. It could also lay the important theoretical foundation for phylogenetics, population genetics, germplasm resources protection, sustainable, and reasonable utilization.

Complete maternal mitochondrial genome of freshwater mussel Aculamprotula tientsinensis (Bivalvia: Unionidae: Unioninae)

Aculamprotula tientsinensis is a rare and endemic species of freshwater mussel in China. This study firstly determined the complete F-type mitochondrial genome of A. tientsinensis. The circle genome (15 695 bp) comprises 13 protein-coding genes, 22 tRNA genes, 2 rRNA genes, 1 FORF gene. Except for cob, nad5 and nad6, the remaining protein-coding genes initiate with the orthodox start codon (ATG, ATA, ATT). There are 26 non-coding regions in the mitogenome of A. tientsinensis, ranging in size from 1 to 229 bp. The base composition of the genome is A (37.83%), G (12.69%), T (25.43%) and C (24.06%). Gene order is identical to other female species of Unionidae but for Gonideinae. The phylogenetic analyses of Unionidae indicate that A. tientsinensis is closely related to A. tortuosa and A. coreana, which belong to Unioninae. The complete mitogenome can deepen comparative and evolutionary genomics of Unionidae and be more comprehensive to parse the genetic relationship between the species and the ownership beyond species.

The complete F-type mitochondrial genome of Chinese freshwater mussel Anodonta euscaphys

Anodonta euscaphys is the endemic species of freshwater mussel in China. The complete F-type mitochondrial genome of the A. euscaphys is amplified and analyzed in this study. It is 15,741 bp in length. The base composition of the genome with A + T bias is 64.78%. There are 24 noncoding regions found throughout the mitogenome of A. euscaphys, ranging in size from 3 to 302 bp, the largest of which was between ND2 and tRNAGlu. The phylogenetic tree based on 22 mitogenome, including 16 F-type freshwater mussels, 2 M-type freshwater mussels and 4 marine mussels were analyzed in our study, the results showed that the F-type and the M-type of the freshwater mussels were clustered respectively, the A. euscaphys was clustered with Anodonta family species firstly, and it was the closest to the Anodonta arcaeformis in our analysis.

The F-type complete mitochondrial genome of Chinese freshwater mussels Cuneopsis pisciculus

The complete F-type mitochondrial genome of Cuneopsis pisciculus was first determined in this research. This circular genome (15,907 bp in size) contained 13 protein-coding genes, 22 tRNA genes and 2rRNA genes. The protein-coding genes initiated with orthodox ATG or ATA start codon. Twenty-five non-coding regions were found throughout the mitochondrial genome of C. pisciculus, ranging in size from 1 to 326 bp. The maximum was between tRNAGln and gene ND5 (326 bp).

Complete F-type mitochondrial genome of freshwater mussels Unio douglasiae

The complete F-type mitochondrial genome of Unio douglasiae is reported for the first time in this research. It is 15,767 bp in size and contains 13 protein-coding genes, 22 tRNA genes, and 2 rRNA genes. Except for COI, ND2, CYTB, ND1, ND6, ND4L, ATP8 with ATA start codon, and ND4 with ATT start codon, the remaining protein-coding genes initiate with the orthodox ATG start codon. There are 25 noncoding regions found throughout the mitogenome of Unio douglasiae, ranging in the size from 1 to 312 bp, the largest of which is between tRNAGlu and ND2 (312 bp).

The complete F-type mitochondrial genome of Chinese Anodonta arcaeformis (Bivalvia: Unionidae: Anodontinae)

Anodonta arcaeformis is a Chinese common species. The complete F-type mitochondrial genome was first determined. The complete genome is 15,672 bp in length, with AT content 64.59%. All the 37 typical animal mitochondrial genes were identified, including 13 protein coding genes, 22 tRNA genes and 2 rRNA genes. And a novel FORF (277 bp, 92aa) was found between tRNAGlu and ND2, which was considered to be involved in sex determination. The putative control region (270 bp) is located between ND5 and tRNAGln, with an A + T content of 70.07%. The gene order is identical to other species of Unionidae female mitochondrial except Gonideinae.

Complete F-type mitochondrial genome of freshwater mussel Lanceolaria glayana

Lanceolaria glayana is widely distributed in China as a common species of freshwater pearl mussel. The complete F-type mitochondrial genome of L. glayana was firstly reported by this research. This circle genome (15,736 bp in size) contains 13 protein-coding genes, 22 tRNA genes, 2rRNA genes. Most of the protein-coding genes initiated with the orthodox ATG start codon while COI and ND4 were corresponding to ATA start codon. Further, 28 non-coding regions were found throughout the mitogenome of L. glayana, ranging from 1 to 310 bp. The maximum is between ND5 and tRNA Gln (310 bp), which is longer than the control region sequences (about 280 bp) of freshwater mussels from Poland and South Korea.

Complete F-type mitochondrial genome of Chinese freshwater mussels Lamprotula gottschei

Lamprotula gottschei (Von Martens, 1894) is one of the freshwater pearl mussels which have great meaning on economy in China. The complete F-type mitochondrial genome of L. gottschei was firstly determined. This circle genome (15,915 bp in size) comprises 13 protein-coding genes, 22 tRNA genes, 2 rRNA genes, except for COI, CYTB, ND4, ND6 and ND4L, with ATA start codon, the remaining protein-coding genes initiated with the orthodox ATG start codon. There were 25 non-coding regions found throughout the mitogenome of L. gottschei, ranging in size from 1 to 305 bp, the largest of which is between ND2 and tRNAGln (305 bp), and is longer than the control region sequences (about 280bp) of freshwater mussels from Poland and South Korea. Strictly maternal inheritance (SMI) of mitochondrial DNA (mtDNA) is the standard rule in nearly all anisogamic organisms (SMI), (Roze et al., 2005; White et al., 2008). However, bivalves of the marine family Mytilidae and Veneroida as well as the freshwater family Unionidae possess two independently inheritance mode of mitochondrial DNA (mtDNA) (Boyle & Etter, 2013), which involves maternal (F) and paternal (M) transmission routes concomitant with highly divergent gender-associated mtDNA genomes. This system of mtDNA transmission was called doubly uniparental inheritance (DUI) (Zouros, 2000).

The complete F-type mitochondrial genome of threatened Chinese freshwater mussel Solenaia oleivora (Bivalvia: Unionidae: Gonideinae)

The freshwater mussel Solenaia oleivora is considered threatened due to anthropogenic habitat modification and pollution. The complete F-type mitochondrial genome (mitogenome) of S. oleivora was first determined (GenBank accession no. KF296320). The length of this mitogenome is 16,392 bp with an AT content of 59.9%. There are 37 typical animal mitochondrial genes and a putative control region. Within the control region, 5 tandem repeats of a 106 bp element were identified. The gene order rearrangement of cox2-rrnS in F-type mitogenome compared to that of other freshwater mussels, is not unique for S. oleivora, but is shared with all other available freshwater mussels in the subfamily Gonideinae. The complete mitogenome can provide a basic data for the further studies on molecular taxonomy, phylogenetic analyses and conservation genetics.

Complete F-type mitochondrial genome of Chinese freshwater mussel Lamprotula tortuosa

Lamprotula tortuosa is the endemic species of freshwater pearl mussel in China. The complete F-type mitochondrial genome of L. tortuosa was first determined. This circle genome (15,722 bp in size) comprises 13 protein-coding genes, 22 tRNA genes, 2 rRNA genes, except for COI, CYTB, ND6, and ND4L, with TTG, ATT, ATT, and ATA start codon, respectively; the remaining protein-coding genes initiated with the orthodox ATG start codon. There were 25 noncoding regions found throughout the mitogenome of L. tortuosa, ranging in size from 1 to 241 bp, the largest of which is between ND5 and tRNAGln (241 bp), but is shorter than the control region sequences(about 280 bp) of freshwater mussels from Poland and South Korea.