Browse
Submit Data
Databases
API
Help

Dataset Information

22 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

The complete mitochondrial genomes of two talitrid amphipods, Platorchestia japonica and P. parapacifica (Crustacea, Amphipoda).

ABSTRACT: In this paper, we determined the complete mitochondrial genome (mitogenome) sequences of two talitrid amphipods, Platorchestia japonica and P. parapacifica. The complete mitogenomes of P. japonica and P. parapacifica were 14,780 and 14,787?bp in length, respectively, with the typical 13 protein coding genes (PCGs), 22 transfer RNAs (tRNAs), two ribosomal RNAs (rRNAs) and a control region (CR). In the gene order analysis, two PCGs (nad3 and nad6) were rearranged in comparison to the typical pan-crustacean ground pattern. A maximum-likelihood tree, constructed based on 31 eumalacostracan mitogenomes, confirmed that P. japonica and P. parapacifica (Talitridae) were closely related to Parhyale hawaiensis (Hyalidae), and supports the monophyly of the superfamily Talitroidea.

SUBMITTER: Yang HM

PROVIDER: S-EPMC7799624 | biostudies-literature | 2017 Nov

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Publications

The complete mitochondrial genomes of two talitrid amphipods, Platorchestia japonica and P. parapacifica (Crustacea, Amphipoda).

Yang Hee-Min HM Song Ji-Hun JH Kim Min-Seop MS Min Gi-Sik GS

Mitochondrial DNA. Part B, Resources 20171106 2

In this paper, we determined the complete mitochondrial genome (mitogenome) sequences of two talitrid amphipods, Platorchestia japonica and P. parapacifica. The complete mitogenomes of P. japonica and P. parapacifica were 14,780 and 14,787 bp in length, respectively, with the typical 13 protein coding genes (PCGs), 22 transfer RNAs (tRNAs), two ribosomal RNAs (rRNAs) and a control region (CR). In the gene order analysis, two PCGs (nad3 and nad6) were rea ...[more]

PMID: 33473971

Similar Datasets

The mitochondrial genomes of five spring and groundwater amphipods of the family Crangonyctidae (Crustacea: Amphipoda) from eastern North America.

Project description:We sequenced the mitochondrial genomes of one spring-dwelling (Crangonyx forbesi) and four groundwater amphipods (Bactrurus brachycaudus, Stygobromus allegheniensis, S. pizzinii, and S. t. potomacus) from eastern North America using a shotgun sequencing approach on an Illumina HiSeq 4000 (Illumina, San Diego, CA). All five mitochondrial genomes encoded 13 protein-coding genes, 22 transfer RNAs (tRNAs), and two ribosomal RNAs (rRNAs) representative of subphylum Crustacea. Although the four groundwater species exhibited gene orders nearly identical to the ancestral pancrustacean gene order, the spring-dwelling species, C. forbesi, possessed a transposition of the trnH-nad4-nad4l loci downstream after nad6-cytb-trnS2. Moreover, a long nad5 locus, longer rrnL, and rrnS loci, and unconventional start codons distinguished C. forbesi from the four groundwater amphipods. Overall, our five amphipod mitogenomes add to the increasing publicly available mitogenome resources for amphipods that are not only valuable for studying the evolutionary relationships of this diverse group of crustaceans but for exploring the evolution of mitochondrial genomes in general.

| S-EPMC8143621 | biostudies-literature

Complete mitochondrial genome of Pseudocrangonyx joolaei (Crustacea: Amphipoda: Pseudocrangonyctidae).

Project description:The complete mitochondrial genome of a subterranean pseudocrangonyctid amphipod, Pseudocrangonyx joolaei, was determined in this paper. The complete mitogenome of P. joolaei was 14,814 bp in length with the typical 13 protein-coding genes, 22 transfer RNAs, two ribosomal RNAs, and a control region (CR). The gene order of P. joolaei was unique in that the CR was an inversion, and the gene order of Pseudocrangonyx was not concordant when compared to that of P. daejeonensis, a subterranean amphipod found in Korea. A maximum-likelihood tree, constructed based on 26 eumalacostracan mitogenomes, confirmed that P. joolaei supported monophyly in the family Pseudocrangonyctidae and is most closely related to the superfamily Crangonyctoidea.

| S-EPMC7782889 | biostudies-literature

The complete mitochondrial genome of Pseudocrangonyx daejeonensis (Crustacea: Amphipoda: Pseudocrangonyctidae).

Project description:The complete mitogenome sequence of a subterranean pseudocrangonyctid amphipod, Pseudocrangonyx daejeonensis, was determined. The complete mitogenome of P. daejeonensis was 15,069?bp in length with the typical 13 protein-coding genes (PCGs), 22 transfer RNAs (tRNAs), 2 ribosomal RNAs (rRNAs), and a control region (CR). This is the first complete mitogenome sequence in the family Pseudocrangonyctidae. Interestingly, gene arrangements of most amphipod species were almost identical to the typical pan-crustacean ground pattern, whereas two PCGs, both of rRNAs and CR were translocated in P. daejeonensis. A maximum-likelihood tree, constructed based on 30 eumalacostracan mitogenomes, confirmed that P. daejeonensis is closely related to the crangonyctid Stygobromus indentatus and S. tenuis potomacus and supported the monophyly of the superfamily Crangonyctoidea.

| S-EPMC7799821 | biostudies-literature

The complete mitochondrial genome of Haustorioides koreanus Jo, 1988 (Crustacea: Amphipoda: Dogielinotidae).

Project description:The mitochondrial genome of a dogielinotid amphipod, Haustorioides koreanus, was completely sequenced for the first time. The total mitogenome length of H. koreanus was 14,839 bp with 13 protein-coding genes, two ribosomal RNA genes, and 22 transfer RNA genes. The phylogenetic tree confirmed that H. koreanus belongs to the families Hyalellidae in the same clade and to the suborder Senticaudata within Amphipoda. This is the first record of the complete mitochondrial genome sequence of the family Dogielinotidae.

| S-EPMC7748501 | biostudies-literature

The complete mitochondrial genome of the estuarine amphipod Grandidierella osakaensis (Crustacea: Amphipoda).

Project description:The complete mitochondrial genome sequence of an estuarine amphipod Grandidierella osakaensis was determined. The mitochondrial genome was 14,658 bp in length with 37 mitochondrial genes (13 protein-coding genes [PCGs], 2 ribosomal RNAs [rRNAs], and 22 transfer RNAs [tRNAs]). The order of PCGs of G. osakaensis was identical to those of other two Grandidierella species. A maximum likelihood-based phylogenetic analysis showed that G. osakaensis formed a monophyletic clade with the other two Grandidierella species within the infraorder Corophiida. The mitochondrial genome sequence obtained in this study provides useful information for further phylogenetic and ecological studies.

| S-EPMC7717501 | biostudies-literature

Five new subterranean amphipods of the genus Pseudocrangonyx from Korea (Crustacea, Amphipoda, Pseudocrangonyctidae).

Project description:Although the majority of the species belonging to the genus Pseudocrangonyx Akatsuka & Komai, 1922 are found among the subterranean fauna of eastern Asia, the taxonomic knowledge is very poor and only four species have been recorded in Korea. In this study, the morphology of the stygobitic pseudocrangonyctid amphipods from Korean subterranean waters was examined and five new species were identified: Pseudocrangonyx concavus sp. nov. has a characteristic emarginated posteroventral margin of epimeral plate 3; Pseudocrangonyx gracilipes sp. nov. differs from other pseudocrangonyctids by the slender and elongated pereopods and more produced posterodistal corner of epimeral plate 3. Pseudocrangonyx crassus sp. nov. shows the expanded peduncular articles and a reduced flagellum of antenna 2. Pseudocrangonyx minutus sp. nov. is distinguished by more reduced pleopod articles compare to other pseudocrangonyctids. Pseudocrangonyx villosus sp. nov. has the more setose bases of pereopods 3 and 4. Detailed descriptions and illustrations are presented for these five new species.

| S-EPMC7522114 | biostudies-literature

The complete mitochondrial genome of the deep-sea amphipod Eurythenes magellanicus (Crustacea: Amphipoda: Lysianassidae).

Project description:The complete mitochondrial genome of the deep sea amphipod Eurythenes magellanicus was determined in this paper. This molecular was 14,988 bp in length, and contained the typical 13 protein coding genes (PCGs), 22 transfer RNAs (tRNAs), two ribosomal RNAs (rRNAs) and one control region (CR). The gene order of E. magellanicus was identical to that from E. maldoror, a deep sea amphipod inhabiting in a deeper habitat than E. magellanicus. A maximum-likelihood tree based on the 13 PCGs from 25 amphipods indicated that E. magellanicus and E. maldoror were closely related and the origin of deep sea amphipods was not monophyletic.

| S-EPMC7748488 | biostudies-literature

Comparative mitogenomic analyses of three North American stygobiont amphipods of the genus Stygobromus (Crustacea: Amphipoda).

Project description:The mitochondrial genomes of three North American stygobiont amphipods Stygobromus tenuis potomacus, S. foliatus and S. indentatus collected from Caroline County, VA, were sequenced using a shotgun sequencing approach on an Illumina NextSeq500 (Illumina Inc., San Diego, CA). All three mitogenomes displayed 13 protein-coding genes, 22 tRNAs and two rRNAs typical of metazoans. While S. tenuis and S. indentatus displayed identical gene orders similar to the pancrustacean ground pattern, S. foliatus displayed a transposition of the trnL2-cox2 genes to after atp8-atp6. In addition, a short atp8 gene, longer rrnL gene and large inverted repeat within the Control Region distinguished S. foliatus from S. tenuis potomacus and S. indentatus. Overall, it appears that gene order varies considerably among amphipods, and the addition of these Stygobromus mitogenomes to the existing sequenced amphipod mitogenomes will prove useful for characterizing evolutionary relationships among various amphipod taxa, as well as investigations of the evolutionary dynamics of the mitogenome in general.

| S-EPMC7800481 | biostudies-literature

The complete mitochondrial genome of Jesogammarus (Jesogammarus) hinumensis (Crustacea: Amphipoda: Anisogammaridae).

Project description:We determined the mitogenome sequence of Jesogammarus (Jesogammarus) hinumensis Morino, 1993, which is the first complete mitogenome sequence in the family Anisogammaridae Bousfield, 1977. The complete mitogenome of J. (J.) hinumensis was 15,186 bp in length with the typical 13 protein-coding genes (PCGs), 22 transfer RNAs (tRNAs), two ribosomal RNAs (rRNAs), and a control region (CR). The gene order of J. (J.) hinumensis was in accordance with the typical pan-crustacean ground pattern. A maximum-likelihood tree constructed using 25 eumalacostracan mitogenomes confirmed that J. (J.) hinumensis is most closely related to the family Micruropodidae, and supported the monophyly of the superfamily Gammaroidea.

| S-EPMC7782921 | biostudies-literature

Evolution of mitochondrial genomes in Baikalian amphipods.

Project description:BackgroundAmphipods (Crustacea) of Lake Baikal are a very numerous and diverse group of invertebrates generally believed to have originated by adaptive radiation. The evolutionary history and phylogenetic relationships in Baikalian amphipods still remain poorly understood. Sequencing of mitochondrial genomes is a relatively feasible way for obtaining a set of gene sequences suitable for robust phylogenetic inferences. The architecture of mitochondrial genomes also may provide additional information on the mechanisms of evolution of amphipods in Lake Baikal.ResultsThree complete and four nearly complete mitochondrial genomes of Baikalian amphipods were obtained by high-throughput sequencing using the Illumina platform. A phylogenetic inference based on the nucleotide sequences of all mitochondrial protein coding genes revealed the Baikalian species to be a monophyletic group relative to the nearest non-Baikalian species with a completely sequenced mitochondrial genome - Gammarus duebeni. The phylogeny of Baikalian amphipods also suggests that the shallow-water species Eulimnogammarus has likely evolved from a deep-water ancestor, however many other species have to be added to the analysis to test this hypothesis. The gene order in all mitochondrial genomes of studied Baikalian amphipods differs from the pancrustacean ground pattern. Mitochondrial genomes of four species possess 23 tRNA genes, and in three genomes the extra tRNA gene copies have likely undergone remolding. Widely varying lengths of putative control regions and other intergenic spacers are typical for the mitochondrial genomes of Baikalian amphipods.ConclusionsThe mitochondrial genomes of Baikalian amphipods display varying organization suggesting an intense rearrangement process during their evolution. Comparison of complete mitochondrial genomes is a potent approach for studying the amphipod evolution in Lake Baikal.

| S-EPMC5249044 | biostudies-literature