Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

The complete mitochondrial genome of freshwater gammarid Gammarus nipponensis (Crustacea: Amphipoda: Gammaridae).

ABSTRACT: This study presents the complete mitochondrial genome sequence of Gammarus nipponensis, a freshwater crustacean found in the western regions of Honshu, Shikoku and Kyushu in Japan. The entire genome is 16,429 bp in length, encoding a standard set of 13 protein-coding genes, two ribosomal RNA genes and 22 transfer RNA genes, as well as the putative control regions. The mitochondrial genome of G. nipponensis is characterized by a high concentration of A and T nucleotides (67.1%). Notably, the mitogenome contains long TATTTTA repeats in the control region 2 at 686 bp long. This newly available genome information will be useful for studying the evolutionary relationships within the genus Gammarus and for understanding diversification among G. nipponensis populations.

SUBMITTER: de la Cruz-Huervana JJ

PROVIDER: S-EPMC10993753 | biostudies-literature | 2024

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Publications

The complete mitochondrial genome of freshwater gammarid Gammarus nipponensis (Crustacea: Amphipoda: Gammaridae).

de la Cruz-Huervana Joana Joy JJ Miyamoto Norio N Kano Yuichi Y Onikura Norio N Kurita Yoshihisa Y

Mitochondrial DNA. Part B, Resources 20240403 4

This study presents the complete mitochondrial genome sequence of Gammarus nipponensis, a freshwater crustacean found in the western regions of Honshu, Shikoku and Kyushu in Japan. The entire genome is 16,429 bp in length, encoding a standard set of 13 protein-coding genes, two ribosomal RNA genes and 22 transfer RNA genes, as well as the putative control regions. The mitochondrial genome of G. nipponensis is characterized by a high concentration of A and T nucleotides (67.1%). Not ...[more]

PMID: 38586505

Similar Datasets

Seven new freshwater species of Gammarus from southern China (Crustacea, Amphipoda, Gammaridae).

Project description:Seven new species of the genus Gammarus are described and illustrated from southern China. The new species Gammarus vallecula Hou & Li, sp. n., G. qinling Hou & Li, sp. n., G. zhigangi Hou & Li, sp. n. and G. jidutanxian Hou & Li, sp. n. are characterized by inner ramus of uropod III half the length of outer ramus. Gammarus longdong Hou & Li, sp. n. is characterized by inner ramus of uropod III 0.9 times as long as outer ramus. Gammarus mosuo Hou & Li, sp. n. is characterized by pereopods V-VII with long setae on anterior margins and both rami of uropod III armed with simple setae. Gammarus caecigenus Hou & Li, sp. n. can be distinguished from other species by eyes absent. DNA barcodes of the new species are documented as proof of molecular differences between species. A key to the new species and a map of their distributions are provided.

| S-EPMC5904484 | biostudies-literature

The complete mitogenome of freshwater gammarid Grandidierella taihuensis (Crustacea: Amphipoda).

Project description:The freshwater gammarid Grandidierella taihuensis is an important composition of benthic community. In this study, the complete mitogenome sequences of G. taihuensis are determined using next-generation and PacBio long-read sequencing. The mitogenome of G. taihuensis is 15,099 bp in size, and consisted of 13 protein-coding genes, two ribosomal RNA genes, 22 tRNA genes, and a putative control region. Gene arrangement is as same as that of G. rubroantennata. The base composition of the entire mitogenome showed a conspicuous A + T bias of 69.4%. The mitogenome data produced in this study provides a useful resource for future evolutionary and ecological studies.

| S-EPMC8043560 | biostudies-literature

Four new Gammarus species from Tibetan Plateau with a key to Tibetan freshwater gammarids (Crustacea, Amphipoda, Gammaridae).

Project description:Four new species of the genus Gammarus are described and illustrated from Tibetan Plateau. Gammarus altussp. n. and G. limosussp. n. are characterized by pereopods III-IV with a few short setae and uropod III with marginal spines accompanied by short setae. Gammarus kangdingensissp. n. and G. gonggaensissp. n. are characterized by pereopods III-IV with long straight setae on posterior margins and inner ramus of uropod III 0.4 times as long as outer ramus. Detailed morphological comparisons with related species are discussed. A key to 15 Gammarus species from the Tibetan Plateau and a map of their distributions are provided.

| S-EPMC5904427 | biostudies-literature

A new species of Gammarus (Crustacea, Amphipoda, Gammaridae) from South Korea.

Project description:A new species of freshwater gammarid, Gammarussomaemulensis sp. nov., was collected from Somaemuldo Island, South Korea. This new species is morphologically characterised by the absence of calceoli in antenna 2, absence of anteroproximal setae on bases in pereopods 6 and 7, outer ramus in uropod 3 with plumose setae on both margins, and a small terminal article of the outer ramus, which is shorter than adjacent spines. A description of the new species and morphological differences from related species are provided in the text. The new species was also compared to related species using partial sequences of the mitochondrial cytochrome c oxidase subunit I (COI) gene. Genetic distances of COI sequences between the new species and related species, consisting of 21.5-26.3% difference, support Gammarussomaemulensis sp. nov. as a valid species. Additionally, a key to identifying Gammarus species in South Korea is provided.

| S-EPMC9848722 | biostudies-literature

A new Gammarus species from Xinjiang Uygur Autonomous Region (China) with a key to Xinjiang freshwater gammarids (Crustacea, Amphipoda, Gammaridae).

Project description:A new species of the genus Gammarus Fabricius, 1775 is described and illustrated from Xinjiang Uygur Autonomous Region, China. Gammaruszhouqiongi sp. nov. is characterized by pereopods III-IV with long straight setae on posterior margins; inner ramus of uropod III more than twice as long as peduncle, reaching 0.7 times the length of outer ramus; inner ramus with plumose setae, and outer ramus with both plumose setae and long simple setae. Detailed morphological comparisons with related species are discussed. The K2P distances for each marker (CO1, 16S, 28S, and EF1α) of the new species differ from those of other Gammarus species in Xinjiang. Both phylogenetic trees based on separate (CO1, 16S, 28S, and EF1α) and combined (CO1+16S+28S+EF1α) markers show that the new species is an independent branch. A key to identify Gammarus species in Xinjiang is provided.

| S-EPMC8975802 | biostudies-literature

Redescription of Gammarus pseudosyriacus (Karaman & Pinkster, 1977) and description of a new subspecies from southern Iran (Crustacea, Amphipoda, Gammaridae).

Project description:The present study focused on redescription of Gammarus pseudosyriacus (Karaman & Pinkster, 1977) based on new materials from Zagros Mountains and describes a new subspecies of freshwater amphipod, Gammarus pseudosyriacus issatisi subsp. n., from the southern Zagros Mountains. The work is based on morphological and morphometric comparisons. This new subspecies has features similar to Gammarus pseudosyriacus. The distinct features that distinguish Gammarus pseudosyriacus issatisi subsp. n. from Gammarus pseudosyriacus are the smaller eyes, shorter body length, and shorter flagellum of antenna 1 and 2.

| S-EPMC4926672 | biostudies-literature

Characterization of the complete mitogenome of Gammarus lacustris (G.O. Sars, 1863) (Amphipoda: Gammaridae) and its phylogenetic position within Amphipoda.

Project description:Gammarus lacustris is native to the Qinghai-Tibet Plateau (QTP), widely distributed in alpine lakes. The complete mitochondrial DNA sequence of G. lacustris was 15,349 base pairs in length and comprised 13 protein-coding genes, 22 transfer RNA genes, 2 ribosomal RNA genes, and 1 control region. The BI tree showed that G. lacustris was most closely related to Gammarus duebeni, and indicated that Gammarus, Gmelinoides, Brachyuropus, Pallaseopsis, and Eulimnogammarus evolved from a common ancestor. The mitogenome of G. lacustris provides new molecular data for further taxonomic and phylogenetic studies of Amphipoda.

| S-EPMC8330746 | 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

Continental-scale patterns of hyper-cryptic diversity within the freshwater model taxon Gammarus fossarum (Crustacea, Amphipoda).

Project description:Traditional morphological diagnoses of taxonomic status remain widely used while an increasing number of studies show that one morphospecies might hide cryptic diversity, i.e. lineages with unexpectedly high molecular divergence. This hidden diversity can reach even tens of lineages, i.e. hyper cryptic diversity. Even well-studied model-organisms may exhibit overlooked cryptic diversity. Such is the case of the freshwater crustacean amphipod model taxon Gammarus fossarum. It is extensively used in both applied and basic types of research, including biodiversity assessments, ecotoxicology and evolutionary ecology. Based on COI barcodes of 4926 individuals from 498 sampling sites in 19 European countries, the present paper shows (1) hyper cryptic diversity, ranging from 84 to 152 Molecular Operational Taxonomic Units, (2) ancient diversification starting already 26 Mya in the Oligocene, and (3) high level of lineage syntopy. Even if hyper cryptic diversity was already documented in G. fossarum, the present study increases its extent fourfold, providing a first continental-scale insight into its geographical distribution and establishes several diversification hotspots, notably south-eastern and central Europe. The challenges of recording hyper cryptic diversity in the future are also discussed.

| S-EPMC7538970 | 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