Browse
Submit Data
Databases
API
Help

Dataset Information

29 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

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

ABSTRACT: 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.

SUBMITTER: Fukata Y

PROVIDER: S-EPMC7707249 | biostudies-literature | 2019 Oct

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Publications

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

Fukata Yohei Y Iigo Masayuki M

Mitochondrial DNA. Part B, Resources 20191011 2

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. ...[more]

PMID: 33366052

Similar Datasets

The complete mitochondrial genome of a freshwater mussel Nodularia douglasiae (Bivalvia: Unionidae).

Project description:The circular F-type mitochondrial genome (15,761?bp) was completely sequenced for a Korean freshwater mussel Nodularia douglasiae (synonym Unio douglasiae; Unionidae, Unionida, Bivalvia). It contains 13 PCGs, two rRNA genes, and 22 tRNA genes, as generally shown in metazoan mitochondrial genomes. Its gene order is identical to that of F-type mitochondrial genomes observed in other freshwater mussels. With nucleotide and amino acid sequences of the complete F-type mitochondrial genomes obtained from 38 unionid species reported so far, phylogenetic analyses were done and discussed. The present study may give valuable helps to explore genetic diversity and population structures of other freshwater mussels as well as N. douglasiae.

| S-EPMC7800389 | biostudies-literature

Complete mitochondrial genome of a Korean endemic freshwater mussel Nodularia breviconcha (Bivalvia: Unionidae).

Project description:Mitochondrial genome sequences were first determined and analyzed for a Korean endemic freshwater mussel Nodularia breviconcha (synonym Nodularia douglasiae sinuolatus; Unionidae, Unionida, Bivalvia). The complete mitochondrial genome was 15,741 bp in length, including 13 protein-coding genes (PCGs), 22 tRNA genes, and 2 rRNA genes. The overall GC content of mitochondrial genome for N. breviconcha was 34.3%. Phylogenetic analysis of 18 species within the family Unionidae suggested that Nodularia douglasiae is the most closely related to N. breviconcha. Our study will provide baseline, but important information for future research on ecological and genetic/genomic characteristics of this species.

| S-EPMC7808371 | biostudies-literature

Complete female-transmitted mitochondrial genomes of two freshwater mussels from the Lake Biwa system in Japan: Nodularia douglasiae and N. nipponensis.

Project description:We determined the complete mitochondrial sequences of female-transmitted (F) mitogenomes of two unionid specimens from the Lake Biwa system, Japan. Their gene contents and orders agreed with those of the typical F mitogenome of freshwater mussels. Molecular phylogenetic analysis using 20 previously identified partial COI and seven (five previously identified and two newly determined) whole mitogenome sequences revealed that one of the two mitogenomes was that of Nodularia douglasiae, while the other was N. nipponensis.

| S-EPMC8078931 | biostudies-literature

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

Project description: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.

| S-EPMC7510832 | biostudies-literature

F-type complete mitochondrial genomes of two Hyriposis species, H. schlegelii and H. cumingii (Bivalvia; Unionoida; Unionidae) from Lake Kasumigaura, Japan, and its phylogenetic analysis.

Project description:We have sequenced the female type (F-type) complete mitochondrial genomes of two Hyriposis species, H. schlegelii and H. cumingii (Gonideinae, Unionidae, Unionida, Bivalvia) from Lake Kasumigaura, Japan, and inferred the Unioninae phylogeny. Complete mitochondrial genomes (H. schlegelii, 15,954 bp, LC498622; H. cumingii, 15,961 bp, LC498621) contain 13 protein-coding genes (PCGs), 2 rRNA genes, and 22 tRNA genes. Molecular phylogenetic analyses using the 13 PCGs including the two species were performed. This study should be basic data to investigate the evolution of Gonideinae and genetic diversity of Hyriposis species in local populations.

| S-EPMC7510820 | biostudies-literature

Roles of Keber's valve and foot chamber for foot manipulation in the mussel Nodularia douglasiae.

Project description:In order to analyse the roles of Keber's valve for foot manipulation in the mussel Nodularia douglasiae, the anatomy and haemolymph flow in the cardiovascular system were detected by magnetic resonance imaging. The superficial layer of the foot was covered by a dense muscle layer, which extended to the dorsal side and connected with the shell. This closed space, the foot chamber, had an inlet (anterior aorta) and an outlet (Keber's valve). At rest, in the beginning of the systolic phase, flows in the anterior aorta and the pedal artery increased, followed by the pedal and visceral sinuses. Then these flows ceased at the end of the systolic phase, followed by inflow to the ventricle in the diastolic phase; therefore, the compliance of the foot chamber is low enough to transfer pressure pulses to the visceral sinus. Extension of the foot started with relaxation of the foot muscle, so the compliance of the foot chamber increased. Then, Keber's valve closed so that the haemolymph filled the foot haemocoel. Retraction of the foot is initiated by the opening of Keber's valve. Judging from these results Keber's valve and the foot chamber are essential for circulation at rest, foot extension and retraction.This article has an associated First Person interview with the first author of the paper.

| S-EPMC6361212 | biostudies-literature

Complete maternal mitochondrial genome of the freshwater mussel Cuneopsis celtiformis (Bivalvia: Unionidae).

Project description:The genus Cuneopsis Simpson, 1900 comprises seven valid species, and Cuneopsis celtiformis (Heude, 1874) is the type species of this genus. Previous phylogenetic studies using complete mitochondrial genomes showed that Cuneopsis was not monophyletic, but the result was hampered by incomplete species sampling and lack of the type species of this genus. In this study, we collected C. celtiformis from the type locality and determined its complete maternal mitochondrial genome. This mitogenome is 15,922 bp in length and contains 14 protein-coding genes (including one F-orf), two rRNA genes, 22 tRNA genes, and 1 putative control region. Our mitochondrial phylogenomic analysis confirms that currently recognized genus Cuneopsis is polyphyletic, and C. celtiformis is the closest to C. heudei with high maximum likelihood bootstrap support value. Comprehensive sampling of all Cuneopsis species is needed for phylogenetic analysis to erect new genera in future studies.

| S-EPMC8344230 | biostudies-literature

Molecular phylogenetic, population genetic and demographic studies of Nodularia douglasiae and Nodularia breviconcha based on CO1 and 16S rRNA.

Project description:Freshwater mussels belonging to the genus Nodularia (Family Unionidae) are known to be widely distributed in East Asia. Although phylogenetic and population genetic studies have been performed for these species, there still remain unresolved questions in their taxonomic status and biogeographic distribution pathways. Here, the nucleotide sequences of CO1 and 16S rRNA were newly determined from 86 N. douglasiae and 83 N. breviconcha individuals collected on the Korean Peninsula. Based on these data, we revealed the following results: (1) N. douglasiae can be divided into the three genetic clades of A (only found in Korean Peninsula), B (widely distributed in East Asia), and C (only found in the west of China and Russia), (2) the clade A is not an independent species but a concrete member of N. douglasiae given the lack of genetic differences between the clades A and B, and (3) N. breviconcha is not a subspecies of N. douglasiae but an independent species apart from N. douglasiae. In addition, we suggested the plausible scenarios of biogeographic distribution events and demographic history of Nodularia species.

| S-EPMC7538972 | biostudies-literature

The Complete Maternally and Paternally Inherited Mitochondrial Genomes of a Freshwater Mussel Potamilus alatus (Bivalvia: Unionidae).

Project description:Doubly uniparental inheritance (DUI) of mitochondrial DNA, found only in some bivalve families and characterized by the existence of gender-associated mtDNA lineages that are inherited through males (M-type) or females (F-type), is one of the very few exceptions to the general rule of strict maternal mtDNA inheritance in animals. M-type sequences are often undetected and hence still underrepresented in the GenBank, which hinders the progress of the understanding of the DUI phenomenon. We have sequenced and analyzed the complete M and F mitogenomes of a freshwater mussel, Potamilus alatus. The M-type was 493 bp longer (M = 16 560, F = 16 067 bp). Gene contents, order and the distribution of genes between L and H strands were typical for unionid mussels. Candidates for the two ORFan genes (forf and morf) were found in respective mitogenomes. Both mitogenomes had a very similar A+T bias: F = 61% and M = 62.2%. The M mitogenome-specific cox2 extension (144 bp) is much shorter than in other sequenced unionid mitogenomes (531-576 bp), which might be characteristic for the Potamilus genus. The overall topology of the phylogenetic tree is in very good agreement with the currently accepted phylogenetic relationships within the Unionidae: both studied sequences were placed within the Ambleminae subfamily clusters in the corresponding M and F clades.

| S-EPMC5222514 | biostudies-literature

The complete maternally and paternally inherited mitochondrial genomes of the endangered freshwater mussel Solenaia carinatus (Bivalvia: Unionidae) and implications for Unionidae taxonomy.

Project description:Doubly uniparental inheritance (DUI) is an exception to the typical maternal inheritance of mitochondrial (mt) DNA in Metazoa, and found only in some bivalves. In species with DUI, there are two highly divergent gender-associated mt genomes: maternal (F) and paternal (M), which transmit independently and show different tissue localization. Solenaia carinatus is an endangered freshwater mussel species exclusive to Poyang Lake basin, China. Anthropogenic events in the watershed greatly threaten the survival of this species. Nevertheless, the taxonomy of S. carinatus based on shell morphology is confusing, and the subfamilial placement of the genus Solenaia remains unclear. In order to clarify the taxonomic status and discuss the phylogenetic implications of family Unionidae, the entire F and M mt genomes of S. carinatus were sequenced and compared with the mt genomes of diverse freshwater mussel species. The complete F and M mt genomes of S. carinatus are 16716 bp and 17102 bp in size, respectively. The F and M mt genomes of S. carinatus diverge by about 40% in nucleotide sequence and 48% in amino acid sequence. Compared to F counterparts, the M genome shows a more compact structure. Different gene arrangements are found in these two gender-associated mt genomes. Among these, the F genome cox2-rrnS gene order is considered to be a genome-level synapomorphy for female lineage of the subfamily Gonideinae. From maternal and paternal mtDNA perspectives, the phylogenetic analyses of Unionoida indicate that S. carinatus belongs to Gonideinae. The F and M clades in freshwater mussels are reciprocal monophyly. The phylogenetic trees advocate the classification of sampled Unionidae species into four subfamilies: Gonideinae, Ambleminae, Anodontinae, and Unioninae, which is supported by the morphological characteristics of glochidia.

| S-EPMC3866145 | biostudies-literature