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

ABSTRACT: 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.

SUBMITTER: Kim YR

PROVIDER: S-EPMC7808371 | biostudies-literature |

REPOSITORIES: biostudies-literature

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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 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

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

Project description: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.

| S-EPMC7707249 | 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.

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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

The complete mitochondrial genome of the hermaphroditic freshwater mussel Anodonta cygnea (Bivalvia: Unionidae): in silico analyses of sex-specific ORFs across order Unionoida.

Project description:BackgroundDoubly uniparental inheritance (DUI) of mitochondrial DNA in bivalves is a fascinating exception to strictly maternal inheritance as practiced by all other animals. Recent work on DUI suggests that there may be unique regions of the mitochondrial genomes that play a role in sex determination and/or sexual development in freshwater mussels (order Unionoida). In this study, one complete mitochondrial genome of the hermaphroditic swan mussel, Anodonta cygnea, is sequenced and compared to the complete mitochondrial genome of the gonochoric duck mussel, Anodonta anatina. An in silico assessment of novel proteins found within freshwater bivalve species (known as F-, H-, and M-open reading frames or ORFs) is conducted, with special attention to putative transmembrane domains (TMs), signal peptides (SPs), signal cleavage sites (SCS), subcellular localization, and potential control regions. Characteristics of TMs are also examined across freshwater mussel lineages.ResultsIn silico analyses suggests the presence of SPs and SCSs and provides some insight into possible function(s) of these novel ORFs. The assessed confidence in these structures and functions was highly variable, possibly due to the novelty of these proteins. The number and topology of putative TMs appear to be maintained among both F- and H-ORFs, however, this is not the case for M-ORFs. There does not appear to be a typical control region in H-type mitochondrial DNA, especially given the loss of tandem repeats in unassigned regions when compared to F-type mtDNA.ConclusionIn silico analyses provides a useful tool to discover patterns in DUI and to navigate further in situ analyses related to DUI in freshwater mussels. In situ analysis will be necessary to further explore the intracellular localizations and possible role of these open reading frames in the process of sex determination in freshwater mussel.

| S-EPMC5870820 | biostudies-literature

The male-type mitochondrial genome of the freshwater mussel Potamilus streckersoni Smith, Johnson, Inoue, Doyle, & Randklev, 2019 (Bivalvia: Unionidae).

Project description:The global decline of freshwater mussels emphasizes the need to establish genetic resources to better understand their biology, including a unique mitochondrial biology known as doubly uniparental inheritance. In this study, we present the complete male-type (M-type) mitochondrial genome of the freshwater mussel, Potamilus streckersoni Smith, Johnson, Inoue, Doyle, & Randklev, 2019. The M-type mtDNA is approximately 16 kilobases and contains 22 tRNAs, two rRNAs, and 14 protein-coding genes, including a male-specific open reading frame. Read coverage revealed that M-type mtDNA was more abundant than female-type mtDNA in male gonadal tissue, with respect to a non-spawning male individual. Novel mitogenomes were resolved within previously described sex-specific monophyletic clades across the subfamily Ambleminae. The availability of high-quality nuclear and mitochondrial genomic data for P. streckersoni makes it a model for future research into the potential role of mtDNA in sex determination or sexual development in freshwater mussels.

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Indonaiarectangularis (Tapparone-Canefri, 1889), comb. nov., a forgotten freshwater mussel species from Myanmar (Bivalvia, Unionidae).

Project description:Uniorectangularis Tapparone-Canefri, 1889 is a little-known nominal species of freshwater mussels described from a tributary of the Ayeyarwady River in Myanmar. This taxon was considered a synonym of Gibbosulalaosensis (Lea, 1863), a margaritiferid species. However, the range of Gibbosulalaosensis does not encompass the Ayeyarwady River watershed. Here we re-examine the holotype of Uniorectangularis and provide a conchological re-description of this species. Based on conchological features such as the shell shape, elevated umbo, and the structure of lateral and pseudocardinal teeth, we transfer this taxon to the genus Indonaia Prashad, 1918 and propose I.rectangularis (Tapparone-Canefri, 1889), comb. nov. It appears to be a rare freshwater mussel species with a restricted range, because it has not been found since the original description. Two additional species in this genus are known from Myanmar, i.e. Indonaiaandersoniana (Nevill, 1877) and I.subclathrata (Martens, 1899).

| S-EPMC6562052 | 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

Analysis of mitochondrial genomes resolves the phylogenetic position of Chinese freshwater mussels (Bivalvia, Unionidae).

Project description:The Yangtze River basin is one of the most species-rich regions for freshwater mussels on Earth, but is gravely threatened by anthropogenic activities. However, conservation planning and management of mussel species has been hindered by a number of taxonomic uncertainties. In order to clarify the taxonomic status and phylogenetic position of these species, mitochondrial genomes of four species (Acuticostachinensis, Schistodesmuslampreyanus, Cuneopsisheudei and Cuneopsiscapitatus) were generated and analyzed along with data from 43 other mitogenomes. The complete F-type mitogenomes of A.chinensis, S.lampreyanus, C.heudei, and C.capitatus are 15652 bp, 15855 bp, 15892 bp, and 15844 bp, respectively, and all four F-type mitogenomes have the same pattern of gene arrangement. ML and BI trees based on the mitogenome dataset are completely congruent, and indicate that the included Unionidae belong to three subfamilies with high bootstrap and posterior probabilities, i.e., Unioninae (Aculamprotula, Cuneopsis, Nodularia, and Schistodesmus), Anodontinae (Cristaria, Arconaia, Acuticosta, Lanceolaria, Anemina, and Sinoanodonta), and Gonideinae (Ptychorhynchus, Solenaia, Lamprotula, and Sinohyriopsis). Results also indicate that A.chinensis has affinities with Arconaialanceolata and Lanceolariagrayii and is a member of the subfamily Anodontinae.

| S-EPMC6328525 | biostudies-literature

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