Browse
Submit Data
Databases
API
Help

Dataset Information

15 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Complete mitochondrial genome of freshwater flea Simocephalus sibiricus Sars, 1899 (Crustacea: Cladocera: Anomopoda).

ABSTRACT: In this study, we presented the first complete mitochondrial genome of the genus Simocephalus determined by next-generation sequencing. The mitogenome of S. sibiricus is 15,818 bp in length, including 13 protein-coding genes (PCGs), two ribosomal RNAs, 22 tRNAs, and one putative control region, and has the same gene order with Daphnia. ATG and ATT were used as start codons in 11 PCGs, TTG was used in COX1 and GTG in ATP8. Six PCGs used an incomplete stop codon. Phylogenetic analysis based on 13 PCGs showed that, on genus level, Simocephalus was closely related to Daphnia.

SUBMITTER: Gu YL

PROVIDER: S-EPMC8491729 | biostudies-literature |

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Similar Datasets

Complete mitochondrial DNA of the marine water flea Diaphanosoma celebensis (Cladocera, Sididae).

Project description:The complete mitochondrial genome was sequenced from the marine water flea Diaphanosoma celebensis. The sequenced mitochondrial genome size was 17,060 bp, possessing identical gene order of 13 protein-coding genes (PGCs) to those of the congeneric freshwater species Diaphanosoma dubium in the genus Diaphanosoma. The mitochondrial genome of D. celebensis had 13 PGCs, two rRNAs, and 22 tRNAs. Of 13 PGCs, three genes (CO3, ND3, and ND4) had incomplete stop codons. Furthermore, the stop codons of the remaining ten PGCs were TAA (for CO1, ATP8, ATP6, ND5, ND6, and ND1) and TAG (for NL4L, Cytb, and ND2). The second and third base composition of codon on 9 PCGs on the L strand in D. celebensis mitogenome showed an anti-G bias (11.0% and 15.0%), respectively.

| S-EPMC7510615 | biostudies-literature

Complete mitochondrial genome of the freshwater prawn Palaemon capensis (Crustacea: Palaemonidae).

Project description:The complete mitogenome of Palaemon capensis is presented here. The mitogenome is 15,925?bp in length and comprises 13 protein coding genes, 2 ribosomal subunit genes, 22 transfer RNAs, and a non-coding AT-rich region. The PCGs were used to perform a phylogenetic analysis together with other Caridea representatives with mitogenome data from GenBank, placing P. capensis sister to a clade comprising P. serenus, P. gravieri, and P. carinicauda in the family Palaemonidae.

| S-EPMC7800094 | biostudies-literature

The mitochondrial genome of Diaphanosoma excisum Sars, 1885 (Crustacea: Branchiopoda: Cladocera) from Hainan Island, China.

Project description:Diaphanosoma excisum is the only Cladoceran in tropical freshwaters and parapatrically occurs with Diaphanosoma dubium in the transition between the tropics and subtropics. Here, we present the complete mitochondrial genome (MG) determined by next-generation sequencing and offer a phylogenetic analysis of D. excisum. The MG of D. excisum is 17,615 bp in size, including 13 protein-coding genes (PCGs), 2 ribosomal RNA, 23 tRNA, and 2 putative control regions. The MG has a biased A + T of 65.34% for base composition. Compared to D. dubium, the MG of D. excisum has one more tRNA-Met, one unknown extra putative control region and is different in the arrangement of its tRNAs. The MG sequence and tRNA order provide valuable molecular data for understanding the phylogeny and speciation of Diaphanosoma.

| S-EPMC8009117 | biostudies-literature

Complete mitochondrial genome of Gampsocleis fletcheri (Burr, 1899).

Project description:Species of Gampsocleis have a long history as singing pets in China. The complete mitochondrial genome of Gampsocleis fletcheri (Burr, 1899) is 15,719 bp in size. It consists of 13 protein-coding genes (PCGs), 22 tRNA genes, two rRNA genes, and an A + T-rich region. The base composition of G. fletcheri mitochondrial genome is A (34.7%), T (30.4%), G (12.0%), and C (22.9%), with an A + T bias (65.1%). Phylogenetic analyses based on the 13 PCGs showed that G. fletcheri was sister to G. gratiosa. The present genomic-level and male genitalia evidences support to restore the taxonomic status of G. fletcheri.

| S-EPMC7954433 | biostudies-literature

The complete mitochondrial genome of the Chinese Daphnia pulex (Cladocera, Daphniidae).

Project description:Daphnia pulex has played an important role in fresh-water ecosystems. In this study, the complete mitochondrial genome of Daphnia pulex from Chaohu, China was sequenced for the first time. It was accomplished using long-PCR methods and a primer-walking sequencing strategy with genus-specific primers. The mitogenome was found to be 15,306 bp in length. It contained 13 protein-coding genes, two rRNA genes, 22 tRNA genes and a typical control region. This research revealed an overall A+T content of 64.50%. All of the 22 typical animal tRNA genes had a classical clover-leaf structure except for trnS1, in which its DHU arm simply formed a loop. The lengths of small and large rRNA were 744 bp and 1,313 bp, respectively. The A+T-rich region was 723 bp in length, which is longer than that from the North American species (689 bp). In terms of structure and composition, many similarities were found between the Chinese and North American Daphnia pulex.

| S-EPMC5027777 | biostudies-literature

The complete mitochondrial genome of the South American freshwater crayfish, Parastacus nicoleti (Crustacea, Decapoda, Parastacidae).

Project description:We determined the complete mitochondrial genome (mitogenome) sequence of a Chilean freshwater crayfish, Parastacus nicoleti (Philippi, 1882). This is the first complete mitogenome sequence of a non-Australian crayfish belonging to the family Parastacidae. The complete mitogenome of P. nicoleti is 20,894 bp in length and contains 13 protein-coding genes (PCGs), 22 transfer RNAs (tRNAs), two ribosomal RNAs (rRNAs) and a putative control region (CR). In the phylogenetic analysis, freshwater crayfishes were clearly divided into two monophyly groups, Northern and Southern Hemisphere groups. The P. nicoleti exhibited a sister-group relationship with all other Australian parastacid crayfishes.

| S-EPMC7748494 | biostudies-literature

Unexpected mitochondrial lineage diversity within the genus Alonella Sars, 1862 (Crustacea: Cladocera) across the Northern Hemisphere.

Project description:Representatives of the genus Alonella Sars (Crustacea: Cladocera: Chydorinae) belong to the smallest known water fleas. Although species of Alonella are widely distributed and often abundant in acidic and mountain water bodies, their diversity is poorly studied. Morphological and genetic approaches have been complicated by the minute size of these microcrustaceans. As a result, taxonomists have avoided revising these species. Here, we present genetic data on Alonella species diversity across the Northern Hemisphere with particular attention to the A. excisa species complex. We analyzed 82 16S rRNA sequences (all newly obtained), and 78 COI sequences (39 were newly obtained). The results revealed at least twelve divergent phylogenetic lineages, possible cryptic species, of Alonella, with different distribution patterns. As expected, the potential species diversity of this genus is significantly higher than traditionally accepted. The A. excisa complex is represented by nine divergent clades in the Northern Hemisphere, some of them have relatively broad distribution ranges and others are more locally distributed. Our results provide a genetic background for subsequent morphological analyses, formal descriptions of Alonella species and detailed phylogeographical studies.

| S-EPMC7860113 | biostudies-literature

The complete mitochondrial genome of the freshwater fairy shrimp Branchinella kugenumaensis Ishikawa 1894 (Crustacea: Anostraca: Thamnocephalidae).

Project description:In this study, we determined and analyzed the complete mitochondrial genome of the freshwater fairy shrimp Branchinella kugenumaensis Ishikawa 1894 (Crustacea: Anostraca: Thamnocephalidae). The mitogenome is 15,127 bp in length, consisted of 37 genes that participate in protein production and energy metabolism of mitochondria. The gene order of the B. kugenumaensis mtDNA exhibits major rearrangements compared with the pancrustacean ancestral pattern or other known anostracan mitogenomes, representing a novel mitochondrial genomic organization within the Crustacea. A maximum-likelihood phylogenetic analysis based on concatenated nucleotide sequences of protein-coding genes places B. kugenumaensis next to Streptocephalus sirindhornae, inside the Anostraca clade. Our study will provide new evidence to the less sampled anostracan evolution and take a further step to the completion of the Branchiopoda tree of life.

| S-EPMC7748868 | biostudies-literature

Complete mitochondrial genome of Bosmina fatalis (Cladocera: Bosminidae) and its phylogenetic analysis.

Project description:Bosmina is a globally distributed zooplankton that adapts to a eutrophic environment. In this study, we cultivated monoclonal Bosmina fatalis and determined its complete mitochondrial gene sequence using the Illumina HiSeq 4000 platform. It was 15,209 bp in length, including 13 protein-coding genes, 22 tRNA genes, and 2 rRNA genes, with the A + T content (69.2%) significantly higher than the G + C content (30.9%). All 22 typical tRNA genes had a classical cloverleaf structure, except for tRNAIle. The complete mitochondrial genome of nine other cladoceran species was used to reconstruct a phylogenetic tree, showing that B. fatalis has a closer relationship with Daphnia than other cladocerans.

| S-EPMC8344229 | biostudies-literature

The complete mitochondrial genome of the cat flea, Ctenocephalides felis.

Project description:The cat flea, Ctenocephalides fells, is widely recognized as a global veterinary pest and a vector of pathogenic bacteria. We recently reported on the C. felis nuclear genome, which is characterized by over 38% protein coding gene duplication, extensive tRNA gene family expansion, and remarkable gene copy number variation (CNV) between individual fleas. Herein, we describe the assembly of the C. felis mitochondrial genome, a novel resource for comparative genomics of fleas and other insects. The order and content of mitochondrial genes is highly consistent with four previously sequenced flea mitochondrial genomes, limiting CNV to siphonapteran nuclear genomes.

| S-EPMC7781990 | 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