Browse
Submit Data
Databases
API
Help

Dataset Information

27 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Complete mitochondrial genome of the marine polychaete Hediste japonica (Phyllodocida, Nereididae).

ABSTRACT: To date, only five species are registered in the genus Hediste, and complete mitochondrial genome is reported in one species, Hediste diadroma. In this study, a complete 15,783 bp genome for the marine polychaete H. japonica mitochondrion was assembled through Illumina HiSeq platform. The complete mitochondrial genome of H. japonica contained 13 protein-coding genes (PCGs), 22 transfer RNA (tRNA) genes, two ribosomal RNA (rRNA) genes, and one control region. Overall genomic structure and gene orientation of H. japonica mitogenome are identical to those of H. diadroma. Phylogenetic analysis using the maximum likelihood method validated the sister relationship between Hediste sp. and other polychaetes. This information will be useful to understand geographical distribution, phylogenetic relationship, and evolutionary history of marine polychates.

SUBMITTER: Park HS

PROVIDER: S-EPMC7748599 | biostudies-literature |

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Similar Datasets

The complete mitochondrial genome of the marine polychaete: Hediste diadroma (Phyllodocida, Nereididae).

Project description:The mitogenome sequence of a polychaete Hediste diadroma (Phyllodocida, Nereididae) was determined first in the genus Hediste. The circular genome is 15,765bp in size including 13 protein-coding genes (PCGs), 2 rRNA and 22 tRNA of which the order and structure is same as those of other Nereididae species. All PCGs use ATG as the start codon while for the stop codon, COI, ND5 and ND1 use an incomplete codon of T. The genome consists of 32.4% A, 18.2% C, 14.2% G, 35.2% T, showing a high content of A + T similar to the other Phyllodocid polychaetes.

| S-EPMC7800692 | biostudies-literature

Complete mitochondrial genome of the marine polychaete, Nereis zonata (Phyllodocida, Nereididae) isolated from the Beaufort Sea.

Project description:Here, we present the first whole mitogenome sequence of the marine polychaete, Nereis zonata, isolated from the Beaufort Sea. The mitochondrial genome of N. zonata is 15,757 bp in length and consists of 13 protein-coding genes (PCGs), 22 transfer RNA (tRNA) genes, 2 ribosomal RNA (rRNA) genes, and a non-coding region that is typical of polychaetes. GC content of the N. zonata mitogenome is 37.2%. A maximum-likelihood gene tree based on the N. zonata mitogenome combined with previously published annelid mitogenome data revealed that N. zonata is clustered with Cheilonereis cyclurus, which form a sister group to Nereis sp.

| S-EPMC7832487 | biostudies-literature

The complete mitochondrial genome of epitokous Nereis species (Phyllodocida, Nereididae) from Dok-do, Korea.

Project description:The mitogenome sequence of the epitokous Nereis species (Phyllodocida, Nereididae) was determined first in the genus Nereis. The complete mitogenome is 15,667?bp in length, containing 13 protein-coding genes, two ribosomal RNAs, 22 transfer RNAs and a control region, and their gene order and structure is identical to those of other nereidid species. The mitogenome consists of 33.5% A, 20.0% C, 13.3% G, 33.1% T, showing a high content of A?+?T similar to the other phyllodocid polychaetes. These results will be useful for inferring the phylogenetic relationships among the members of Nereididae within the phyllodocids.

| S-EPMC7800097 | biostudies-literature

The complete mitochondrial genome of a marine polychaete, Prionospio cf. japonica (Annelida: Spionidae).

Project description:Prionospio Malmgren 1867 is one of the abundant genera of the family Spionidae Grube, 1850. Despite its rich diversity, information on their complete mitochondrial genome has remained unknown. In this study, we determined the complete mitochondrial genome of a spionid polychaete, Prionospio cf. japonica Okuda 1935. The specimen was collected from the fine sand in the intertidal zone of South Korea. The mitogenome consists of 15,267 base pairs, harboring 13 protein-coding genes (PCGs), 22 transfer RNAs, and two ribosomal RNAs. The maximum-likelihood phylogenetic tree based on the 11 PCGs showed that Prionospio cf. japonica grouped with other spionid polychaetes and formed a monophyletic group. Also, the mtDNA of P. cf. japonica was more closely related to that of non-polydorin spionid, Marenzelleria neglecta, than polydorin spionids. The molecular data will be valuable for studying evolutionary relationships among annelids.

| S-EPMC10515661 | biostudies-literature

Complete mitochondrial genome of the Loligo japonica.

Project description:In this study, we determined the complete mitochondrial genome of Loligo japonica. The genome was 17,232?bp in length and contained 13 protein-coding genes, 22 transfer RNA genes, 2 ribosomal RNA genes and 3 main non-coding regions. The overall base composition of L. japonica is A 39.60%, C 18.22%, T33.38% and G 8.80%, with a highly A?+?T bias of 72.98%. All of the three control regions (CR) contain termination-associated sequences and conserved sequence blocks. Here, we describe a phylogenetic analysis of 11 species Cephalopoda based on the complete mitochondrial genome, and the result showed that the Loligo Beka and Loligo uyii are most closely related to L. japonica. This mitogenome sequence data would play an important role in the investigation of phylogenetic relationship, taxonomic resolution and phylogeography of the Cephalopoda.

| S-EPMC7800932 | biostudies-literature

The complete mitochondrial genome of the terebellid polychaete Thelepus plagiostoma (Terebellida; Terebellidae).

Project description:Here, we report the complete mitogenome information of the terebellid polychaete, Thelepus plagiostoma (Schmarda, 1861). Genome sequencing by Illumina HiSeq platform permitted assembly of a circular mitochondrial genome of 15,628 bp from T. plagiostoma consisting of 67% AT nucleotides, 13 protein-coding genes (PCGs), 2 ribosomal RNA (rRNA) genes, 22 transfer RNA (tRNA) genes, and a non-coding region in the typical annelid gene composition. Gene order of the T. plagiostoma mitochondrion is identical to those of the Terebelliformia mitogenomes. Phylogenetic reconstruction places T. plagiostoma within the monophyletic subclass Sedentaria, a sister to Pista cristata in the suborder Terebelliformia.

| S-EPMC8510596 | biostudies-literature

The complete mitochondrial genome of the terebellid polychaete Neoamphitrite affinis (Polychaeta; Terebellidae).

Project description:Here, we sequenced and annotated the complete mitochondrial genome for the terebellid polychaete, Neoamphitrite affinis (Malmgren 1866). The complete mitogenome of N. affinis is 15,823 bp, with 33.4% A, 18.2% C, 11.5% G, and 37.0% T. The circular N. affinis mitochondrial genome comprises 13 protein-coding genes (PCGs), 23 transfer RNA (tRNA) genes including 2 methionine tRNA genes, 2 ribosomal RNA (rRNA) genes, and a non-coding region. Phylogenomic analysis based on 26 in-group taxa belonging to the two main clades, Sedentaria and Errantia, is congruent with published phylogenetic relationship for annelids, which N. affinis was grouped with Pista cristata (Terebellida; Terebellidae). This mitogenome resource will be useful for future phylogenetic studies of families belonging to Sedentaria.

| S-EPMC9629097 | biostudies-literature

The complete mitochondrial genome of Alveopora japonica (Scleractinia: Acroporidae).

Project description:Here, for the first time, we sequenced the complete mitogenome of Alveopora japonica Eguchi, 1968 (Scleractinia: Acroporidae). Genome size was 17,886?bp with 13 protein-coding, two rRNA, and two tRNA genes. This gene composition was identical to the typical scleractinian pattern. Our results strongly support the recent transfer of this coral species to the family Acroporidae.

| S-EPMC7800935 | biostudies-literature

Complete mitochondrial genome of Amorophaga japonica Robinson, 1986 (Lepidoptera: Tineidae).

Project description:The complete mitochondrial genome (mitogenome) of Amorophaga japonica Robinson, 1986 (Lepidoptera: Tineidae), comprises 15,027 base pairs (bp) and contains a typical set of genes (13 protein-coding genes [PCGs], 2 rRNA genes, and 22 tRNA genes), and 1 non-coding region. The genome has an arrangement, trnW-trnY-trnC, instead of typical trnW- trnC-trnY at the ND2 and COI junction. This arrangement is unique in lepidopteran mitogenomes. Unlike most lepidopteran insects, which have CGA as the start codon for the COI gene sequence, A. japonica COI had a typical ATT codon. The A + T-rich region was unusually short, with only 199 bp. Phylogenetic analyses with concatenated sequences of the 13 PCGs and two rRNA genes using the Bayesian inference method placed A. japonica in Tineidae as a sister to the cofamilial species, Tineola bisselliella, with high nodal support (Bayesian posterior probability [BPP] = 0.99), presenting the superfamily Tineoidea in a monophyletic group with a BPP of 0.99. Gracillarioidea, represented by three species of Gracillariidae, formed a monophyletic group with the highest BPP, but the Leucoptera malifoliella in Yponomeutoidea was unusually grouped together with the Gracillarioidea with the highest nodal support. As more mitogenome sequences are available, further analysis to infer the relationships among superfamilies of Lepidoptera might be possible.

| S-EPMC7782908 | biostudies-literature

Characterization of the complete mitochondrial genome of the scale worm, Eunoe nodosa (Phyllodocida; Polynoidae) from the Beaufort Sea.

Project description:To increase the mitogenome data available for robust phylogeny, we sequenced the complete mitochondrial DNA of the scale worm Eunoe nodosa (Sars, 1861) in the family Polynoidae of the order Phyllodocida. The complete mitogenome has 15,366 bp and has 28.9% A, 13.2% C, 19.0% G, and 38.8% T. Using MITOS and tRNAscan-SE, we identified the 13 typical protein-coding genes (PCGs), 2 ribosomal RNA (rRNA) genes, 22 transfer RNA (tRNA) genes, and a non-coding region. Phylogenomic analysis based on 27 in-group taxa belonging to five families of the subclass Errantia show congruence with the published phylogenetic relationship within the Polynoidae, in which E. nodosa lies in the clade of shallow water species.

| S-EPMC8425739 | 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