Browse
Submit Data
Databases
API
Help

Dataset Information

29 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

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

ABSTRACT: 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.

SUBMITTER: Li J

PROVIDER: S-EPMC8330746 | biostudies-literature |

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Similar Datasets

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

Project description: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.

| S-EPMC10993753 | biostudies-literature

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

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

Complete mitogenome of Gobiopterus lacustris (Perciformes: Gobiidae).

Project description:In this study, combining the gonad transcripts of the both sexes by RNA-Seq with the DNA sequences by conventional PCRs, we have determined the complete mitogenome of Gobiopterus lacustris collected from the mangrove waters of the Leizhou Peninsula in tropical South China. This mitochondrial genome is 16593?bp in length and consists of 37 genes in the typical vertebrate mitochondrial gene arrangement. This study will contribute on the phylogenetics of genus Gobiopterus and the other genera of Gobiidae.

| S-EPMC7510680 | 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

Complete mitogenome of Asiatic lion resolves phylogenetic status within Panthera.

Project description:BackgroundThe origin, evolution and speciation of the lion, has been subject of interest, debate and study. The present surviving lions of the genus Panthera comprise of eight sub-species inclusive of Asiatic lion Panthera leo persica of India's Gir forest. Except for the Asiatic lion, the other seven subspecies are found in different parts of Africa. There have been different opinions regarding the phylogenetic status of Panthera leo, as well as classifying lions of different geographic regions into subspecies and races. In the present study, mitogenome sequence of P. leo persica deduced, using Ion Torrent PGM to assess phylogeny and evolution which may play an increasingly important role in conservation biology.ResultsThe mtDNA sequence of P. leo persica is 17,057 bp in length with 40.8% GC content. Annotation of mitogenome revealed total 37 genes, including 13 protein coding, 2 rRNA and 22 tRNA. Phylogenetic analysis based on whole mitogenome, suggests Panthera pardus as a neighbouring species to P. leo with species divergence at ~2.96 mya.ConclusionThis work presents first report on complete mitogenome of Panthera leo persica. It sheds light on the phylogenetic and evolutionary status within and across Felidae members. The result compared and evaluated with earlier reports of Felidae shows alteration of phylogenetic status and species evolution. This study may provide information on genetic diversity and population stability.

| S-EPMC3765570 | biostudies-literature

Characterization of the complete mitogenome of Haifa grouper, Hyporthodus haifensis (Perciformes: Serranidae), and its phylogenetic position within Epinephelini.

Project description:The complete mitochondrial genome of the Haifa grouper, Hyporthodus haifensis (Ben-Tuvia, 1953), has been obtained, through Illumina next-generation sequencing, and annotated. This mitogenome was found to be 16,525 bp long and to contain 37 genes, a control region, and the L-strand replication origin. The overall base composition of the complete mitogenome for this species was found to be 28.55% A, 28.07% C, 16.32% G, and 27.06% T. This study also looked into the mitogenome phylogenetic relationships of H. haifensis within the tribe Epinephelini and adds to the genetic resources currently available for the species.

| S-EPMC8018344 | 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

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

The diversity of opsins in Lake Baikal amphipods (Amphipoda: Gammaridae).

Project description:BackgroundVision is a crucial sense for the evolutionary success of many animal groups. Here we explore the diversity of visual pigments (opsins) in the transcriptomes of amphipods (Crustacea: Amphipoda) and conclude that it is restricted to middle (MWS) and long wavelength-sensitive (LWS) opsins in the overwhelming majority of examined species.ResultsWe evidenced (i) parallel loss of MWS opsin expression in multiple species (including two independently evolved lineages from the deep and ancient Lake Baikal) and (ii) LWS opsin amplification (up to five transcripts) in both Baikal lineages. The number of LWS opsins negatively correlated with habitat depth in Baikal amphipods. Some LWS opsins in Baikal amphipods contained MWS-like substitutions, suggesting that they might have undergone spectral tuning.ConclusionsThis repeating two-step evolutionary scenario suggests common triggers, possibly the lack of light during the periods when Baikal was permanently covered with thick ice and its subsequent melting. Overall, this observation demonstrates the possibility of revealing climate history by following the evolutionary changes in protein families.

| S-EPMC8108468 | biostudies-literature

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data