Browse
Submit Data
Databases
API
Help

Dataset Information

18 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Characterization of the complete mitochondrial genome of Okenia hiroi (Baba, 1938) (Nudibranchia, Goniodorididae).

ABSTRACT: Okenia is a speciose genus of the family Goniodorididae with more than 50 valid species. The phylogenetic relationships within the genus are little known. The mitogenome is a good marker to understand the phylogenetic relationships of relative species. This study was performed to sequence the mitogenome of O. hiroi. The mitogenome of O. hiroi was 14,583 bp in size and was composed of 37 genes, including 13 protein-coding genes, two ribosomal RNA genes, and 22 tRNA genes. The nucleotide composition was 30.5% A, 13.6% C, 16.5% G, and 39.4% T. The phylogenetic analysis showed that O. hiroi is sister to Notodoris gardineri (Aegiridae). This study recorded the first mitochondrial genome sequence of the family Goniodorididae.

SUBMITTER: Dinh Do T

PROVIDER: S-EPMC7995900 | biostudies-literature |

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Similar Datasets

Complete mitochondrial genome analysis of Sakuraeolis japonica (Baba, 1937) (Mollusca, Gastropoda, Nudibranchia).

Project description:In this study, a complete mitochondrial genome of a nudibranch species, Sakuraeolis japonica was sequenced and analyzed. The mitochondrial genome size is 15,059 bp with 28.1% A, 14.9% C, 19.3% G, and 37.7% T nucleotide distributions. This is the eighth record for complete mitochondrial genome of the Nudibranchia and first record for the genus. Furthermore, phylogenetic relationship of S. Japonica in the Nudibranchia was investigated by using protein-coding genes of complete mitochondrial genome. The present study suggests that S. japonica belongs to the family Facelinidae and it is placed in monophyletic Nudibranchia. The closest species to S. japonica are Chromodoris magnifica and Chromodoris quadricolor that belong to the family Chromodorididae.

| S-EPMC7870149 | biostudies-literature

The complete mitochondrial genome of Neocaridina heteropoda koreana Kubo, 1938 (Decapoda: Atyidae).

Project description:Neocaridina heteropoda koreana Kubo, 1938 is a freshwater shrimp native to the Korean peninsula. We have determined the mitogenome of N. heteropoda koreana, which's length is 15,558 bp long including 13 protein-coding genes, 2 ribosomal RNA genes, 22 transfer RNAs, and a single large non-coding region of 674 bp. Its GC ratio is 33.0%. Gene order of N. heteropoda koreana is identical to those of other known Atyidae species. Phylogenetic trees show that N. heteropoda koreana is sister to N. davidi and placed within genus Caridina. Our mitogenome will be a useful resource for understanding molecular phylogeny of genus Neocradina.

| S-EPMC7687589 | biostudies-literature

The complete mitochondrial genome of the Oriental sea slug: Chromodoris orientalis (Nudibranchia, Chromodorididae).

Project description:The mitogenome sequence of sea slug, Chromodoris orientalis (Nudibranchia, Chromodorididae), has been decoded for the first time by coverage genome sequencing method. The overall base composition of C. orientalis mitogenome is 30.5% for A, 14.7% for C, 18.0% for G and 36.9% for T, and has low GC content 32.6%. The assembled mitogenome, consisting of 14,266 bp, has unique 13 protein-coding genes, 22 transfer RNAs, and two ribosomal RNAs genes. The C. orientalis mitogenome has the common mitogenome gene order and feature of Nudipleura (a clade of sea slugs and sea snails). The complete mitogenome of C. orientalis provides essential and important DNA molecular data for further phylogenetic and evolutionary analysis for sea slugs and sea snails.

| S-EPMC7800301 | biostudies-literature

Complete sequences of mitochondrial genome of Hypselodoris festiva (A. Adams, 1861) (Mollusca, Gastropoda, Nudibranchia).

Project description:In this study, complete nucleotide sequences of the mitochondrial genome of a nudibranch species, Hypselodoris festiva (A. Adams, 1861) were determined and characterized. The mitogenome size is 14 880 bp. This is the longest among the known nudibranch mitochondrial genomes. Furthermore, phylogenetic relationship of H. festiva in the Nudibranchia reconstructed due to amino acid sequences of mitochondrial protein coding genes. This is the sixth record for complete mitochondrial genome of the Nudibranchia.

| S-EPMC7871837 | biostudies-literature

The complete mitochondrial genome of a non-biting midge Polypedilum unifascium (Tokunaga, 1938) (Diptera: Chironomidae).

Project description:The complete mitochondrial genome of Polypedilum unifascium (Diptera: Chironomidae) was determined by Illumina sequencing technology. The whole mitogenome is 16,452 bp in length with an A + T bias of 79.3%, and contains 13 protein-coding genes (PCGs), 22 transfer RNAs (tRNAs), and two ribosomal RNAs (rRNAs). All PCGs start with ATN codon and use TAA as the stop codon. Gene arrangement of the 13 PCGs is identical to that of other known Chironomidae mitochondrial genomes. The resultant Bayesian inference and maximum-likelihood trees based on the sequence data of 13 PCGs support its close relationship with P. vanderplanki.

| S-EPMC8259822 | biostudies-literature

Characterization of the complete chloroplast genome of Barbella flagellifera (Cardot) Nog. 1938 (Bryidae, Meteoriaceae).

Project description:Whether Barbella flagellifera (Cardot) Nog. belongs to Neodicladiella has not yet been determined, and a study of the complete chloroplast (cp) genome of B. flagellifera would aid in determining its evolutionary position. In this study, we aimed to sequence the complete cp genome of B. flagellifera, an epiphytic species found in tropical and subtropical forests. The complete cp genome is 125,025 base pairs (bp) long and appears as a typical quadrilateral structure with a large single-copy (86,854 bp), a small single-copy (18,473 bp), and a pair of inverted repeats (19,698 bp). The overall GC content of the sequence is 41.0% and the genome encodes 127 genes, including 82 protein-coding genes, 37 tRNAs, and eight rRNAs. Phylogenetic analysis reveals that B. flagellifera clustered into a clade with other Hypnales groups with high bootstrap support. The complete cp genome presented here will provide helpful information for species identification of Barbella genus and Neodicladiella genus in Meteoriaceae.

| S-EPMC10898263 | biostudies-literature

The complete mitochondrial genome of the photosymbiotic sea slug Berghia stephanieae (Valdes, 2005) (Gastropoda, Nudibranchia).

Project description:Berghia stephanieae (Nudibranchia, Cladobranchia) is a photosymbiotic sea slug that feeds exclusively on sea anemones from the genus Exaiptasia. It then specifically incorporates dinoflagellates belonging to the Symbiodiniaceae obtained from their prey. Here, we present the complete mitochondrial genome sequence of B. stephanieae combining Oxford Nanopore long read and Illumina short-read sequencing data. The mitochondrial genome has a total length of 14,786 bp, it contains the 13 protein-encoding genes, 23 tRNAs, and two rRNAs and is similar to other nudibranchs except for the presence of a duplicated tRNA-Ser 1.

| S-EPMC8279152 | biostudies-literature

Characterization of the complete mitochondrial genome of Conus tribblei Walls, 1977.

Project description:The genus Conus sensu lato consists of 500-700 species. However, the mitochondrial genomes of only few species have been fully sequenced and reported so far. In this study, the complete mitochondrial genome of Conus tribblei, a member of the poorly known subgenus Splinoconus is sequenced with the mean coverage of 604×. The mitochondrial genome is 15?570?bp long and consists of genes encoding for 13 respiratory chain proteins, 22 tRNA and 2 rRNA. The gene organization is highly conserved among the Conus species. The longest intergenic region between tRNA-Phe and cytochrome c oxidase subunit III (cox3), which in C. tribblei is 169?bp long and contains a 112?bp long segment of inverted repeat, represents the putative control region. The control regions of Conus species exhibited variability in the length and position of the inverted repeats. Therefore, this region may have the potential to be used as a genetic marker for species discrimination.

| S-EPMC5556944 | biostudies-literature

Characterization and Phylogenetic Implications of the Complete Mitochondrial Genome of Syrphidae.

Project description:In this study, the complete mitochondrial genomes (mitogenomes) of two hoverfly species of Korinchia angustiabdomena (Huo, Ren, and Zheng) and Volucella nigricans Coquillett (Diptera: Syrphidae) were determined and analyzed. The circular mitogenomes were 16,473 bp in K. angustiabdomena (GenBank No. MK870078) and 15,724 bp in V. nigricans (GenBank No. MK870079). Two newly sequenced mitogenomes both contained 37 genes, and the gene order was similar with other syrphine species. All the protein-coding genes (PCGs) were started with the standard ATN codons; and most of PCGs were terminated with a TAA stop codon, while ND1 in K. angustiabdomena ended with a TAG codon, and ND5 terminated with truncated T stop codons in both species. The phylogenetic relationship between K. angustiabdomena and V. nigricans with related lineages was reconstructed using Bayesian inference and Maximum-likelihood analyses. The monophyly of each family considered within Muscomorpha was confirmed by the clades in the phylogenetic tree, and superfamily of the Oestroidea (Calliphoridae, Sarcophagidae, and Oestridae) was unexpectedly found to be a paraphyletic group based on our selected data. This mitogenome information for K. angustiabdomena and V. nigricans could facilitate future studies of evolutionarily related insects.

| S-EPMC6723807 | biostudies-literature

Characterization of the complete mitochondrial genome of Notospermus geniculatus.

Project description:In this study, the complete mitochondrial genome of Notospermus geniculatus, was recovered through Illumina sequencing data. This complete mitochondrial genome of N. geniculatus is 15,180?bp in length and has a base composition of A (14.4%), T (41.3%), C (14.6%), G (29.6%), demonstrating a bias of higher AT content (55.7%) than GC content (44.2%). The mitochondrial genome contains a typically conserved structure among Lineidae mitogenomes, encoding 13 protein-coding genes (PCGs), 23 transfer RNA genes (tRNA), 2 ribosomal RNA genes (12S rRNA and 16S rRNA), and a control region (D-loop region). All PCGs were located on the H-strand. ND4L gene and ND4 gene were overlapped by 6?bp. The whole mt genome of N. geniculatus and other Protostomia mitogenomes (17 species, in total) were used for phylogenetic analysis. The result indicated N. geniculatus has the closest relationship with Lineus viridis (FJ839919.1) and clustered within Heteronemertea Clade, which representing a distinct order.

| S-EPMC7800901 | 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