Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Complete mitochondrial genome of the Ijima's Sea Snake (Emydocephalus ijimae) (Squamata, Elapidae).

ABSTRACT: In this study, we provide the first report of the complete mitochondrial genome of Emydocephalus ijimae. The mitogenome length is 18,259?bp and includes 13 protein-coding genes, two rRNA genes, 22 tRNA genes, and three non-coding regions. The sequence presented could be very useful for further phylogenetic and evolutionary study.

SUBMITTER: Yi CH

PROVIDER: S-EPMC7706457 | biostudies-literature | 2019 Jul

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Publications

Complete mitochondrial genome of the Ijima's Sea Snake (Emydocephalus ijimae) (Squamata, Elapidae).

Yi Chang-Ho CH Park Jaejin J Sasai Takahide T Kim Hye Seon HS Kim Jong-Gwan JG Kim Min-Seop MS Cho In-Young IY Kim Il-Hun IH

Mitochondrial DNA. Part B, Resources 20190722 2

In this study, we provide the first report of the complete mitochondrial genome of Emydocephalus ijimae. The mitogenome length is 18,259 bp and includes 13 protein-coding genes, two rRNA genes, 22 tRNA genes, and three non-coding regions. The sequence presented could be very useful for further phylogenetic and evolutionary study. ...[more]

PMID: 33365670

Similar Datasets

The complete mitochondrial genome of a yellow-bellied sea snake (Hydrophis platurus) (Squamata, Elapidae).

Project description:In this study, we provide the first report of the complete mitochondrial genomic sequencing of a yellow-bellied sea snake (Hydrophis platurus) that has the broadest distribution range of all Squamata species. The mitogenome length was 18,101 bp and consisted of 13 protein-coding genes, 2 rRNA genes, 22 tRNA genes, and 3 non-coding regions. The sequence presented could be very useful for further phylogenetic and evolutionary studies.

| S-EPMC7755313 | biostudies-literature

Next-generation sequencing yields the complete mitogenome of the Shaw's sea-snake (Squamata: Elapidae).

Project description:We report the complete mitogenome of Hydrophis curtus, which is 17,702?bp in size and includes 13 protein-coding (PCGs), two rRNA genes, 22 tRNA genes, and two control regions. PCGs, with 13 genes, are 11,261?bp in length. All PCGs use as the start codon ATN except ND1 (CTA) and COX1 (GTG); ATP8, ATP6, ND4L, ND5, and Cytb use the typical stop codon TAA; but COX2 and ND4 with a single T-. Phylogeny recon-structed using the Bayesian inference (BI) method with 13 PCGs indicates that H. curtus at the root of Laticaudinae.

| S-EPMC7707276 | biostudies-literature

Next-generation sequencing yields the complete mitogenome of the blue-banded sea-snake (Squamata: Elapidae).

Project description:We report the complete mitogenome of Hydrophis cyanocinctus, which is 17,750 bp in size and includes 13 protein-coding (PCGs), 2 rRNA genes, 22 tRNA genes, and 2 control regions. PCGs, with 13 genes, is 11,427 bp in length. All PCGs use ATN as the typical start codon except COX1 with GTG; the TAG was found as the stop codon in ND1 and ND2, the AGA was found as the stop codon in COI and ND6, the TAA was found as the stop codon in ATP8, ATP6, ND4L, ND5 and Cytb; while other 3 PCGs stop with a single T. Phylogeny reconstructed using the Bayesian inference (BI) method with 13 PCGs indicates the presence of H. cyanocinctus at the root of Laticaudinae.

| S-EPMC7687521 | biostudies-literature

Evolution of the Noncoding Features of Sea Snake Mitochondrial Genomes within Elapidae.

Project description:Mitochondrial genomes of four elapid snakes (three marine species [Emydocephalus ijimae, Hydrophis ornatus, and Hydrophis melanocephalus], and one terrestrial species [Sinomicrurus japonicus]) were completely sequenced by a combination of Sanger sequencing, next-generation sequencing and Nanopore sequencing. Nanopore sequencing was especially effective in accurately reading through long tandem repeats in these genomes. This led us to show that major noncoding regions in the mitochondrial genomes of those three sea snakes contain considerably long tandem duplications, unlike the mitochondrial genomes previously reported for same and other sea snake species. We also found a transposition of the light-strand replication origin within a tRNA gene cluster for the three sea snakes. This change can be explained by the Tandem Duplication-Random Loss model, which was further supported by remnant intervening sequences between tRNA genes. Mitochondrial genomes of true snakes (Alethinophidia) have been shown to contain duplicate major noncoding regions, each of which includes the control region necessary for regulating the heavy-strand replication and transcription from both strands. However, the control region completely disappeared from one of the two major noncoding regions for two Hydrophis sea snakes, posing evolutionary questions on the roles of duplicate control regions in snake mitochondrial genomes. The timing and molecular mechanisms for these changes are discussed based on the elapid phylogeny.

| S-EPMC9407768 | biostudies-literature

Population dynamics of the sea snake Emydocephalus annulatus (Elapidae, Hydrophiinae).

Project description:For sea snakes as for many types of animals, long-term studies on population biology are rare and hence, we do not understand the degree to which annual variation in population sizes is driven by density-dependent regulation versus by stochastic abiotic factors. We monitored three populations of turtle-headed sea snakes (Emydocephalus annulatus) in New Caledonia over an 18-year period. Annual recruitment (% change in numbers) showed negative density-dependence: that is, recruitment increased when population densities were low, and decreased when densities were high. Windy weather during winter increased survival of neonates, perhaps by shielding them from predation; but those same weather conditions reduced body condition and the reproductive output of adult snakes. The role for density-dependence in annual dynamics of these populations is consistent with the slow, K-selected life-history attributes of the species; and the influence of weather conditions on reproductive output suggests that females adjust their allocation to reproduction based on food availability during vitellogenesis.

| S-EPMC8526600 | biostudies-literature

The complete mitochondrial genome of Goniurosaurus varius (Squamata: Eublepharidae)

Project description: Not available

| S-EPMC10796122 | biostudies-literature

Complete mitochondrial genome of Scincella modesta (Squamata: Scincidae).

Project description:The first complete mitochondrial genome sequence was determined for an oviparous lizard, Scincella modesta (Scincella, Scincidae). The total length of the complete mitochondrial genome was 17,511 bp, encodes 13 protein-coding genes, 22 tRNAs, 2 rRNA genes, and 2 non-coding regions. The overall base composition of S. modesta is A: 31.9%, T: 27.2%, G: 14.5%, and C: 26.5%. Most of the S. modesta mitochondrial genes are encoded on the H-strand except for the ND6 gene and eight tRNA genes, which are encoded on the L-strand. Mrbayes and ML tree based on 13 protein-coding genes indicated that S. vandenburghi is the sister group of the S. modesta within the genus Scincella. The complete mitogenome sequence of S. modesta provided fundamental data for resolving phylogenetic and genetic problems related to genus Scincella.

| S-EPMC7748724 | biostudies-literature

The complete mitochondrial genome of Lycodon liuchengchaoi (squamata: colubridae).

Project description:Lycodon liuchengchaoi is a new species discovered in recent years which is widely distribute in Anhui, Hubei and Sichuan Province. In this study, we determined the complete mitochondrial genome of L. liuchengchaoi. The result shows that the complete mitogenome of L. liuchengchaoi is 17,171bp. It is similar with the typical mtDNA of Serpentes, which contains 13 protein-coding genes, 2 rRNA genes, 22 tRNA genes, 2 control regions, and a stem-loop region. The phylogenetic tree, contains 17 Serpentiforms species, is divided into two clades which correspond to six genera in Colubridae. The L. liuchengchaoi which appeared into Clade A, clustered within Lycodon.

| S-EPMC7875199 | biostudies-literature

The complete mitochondrial genome of Protobothrops kaulbacki (Squamata: Viperidae).

Project description:Protobothrops kaulbacki is a new record in China, and in this study, the complete mitochondrial genome sequence of P. kaulbacki had been determined. The length of mitogenome is 17,237 bp, including 13 protein-coding genes, 22 tRNA genes, 2 rRNA genes (12S and 16S rRNA), 1 origin of L-strand replication (OL), and 2 control regions (CRs). The maximum-likelihood (ML) tree based on the whole mitogenome shown that P. kaulbacki belongs to the genus Protobothrops.

| S-EPMC7800973 | biostudies-literature

The complete mitochondrial genome of Takydromus amurensis (Squamata: Lacertidae).

Project description:The complete mitogenome sequence of Takydromus amurensis (Squamata: Lacertidae) is determined using long PCR for the first time in this study. It is a circular molecule of 17 333 bp in length (GenBank accession number: KU641018). Similar to the most other lizards, the complete mtDNA sequence of T. amurensis contained two rRNA genes (12S rRNA and 16S rRNA), 22 tRNA genes, 13 protein-coding genes (PCGs) and a control region (D-loop). The nucleotide composition was 31.23% A, 26.06% C, 13.91% G and 28.8% T. Mitochondrial genomes analyses based on NJ method yield phylogenetic trees, including 14 reported lizards belonging to three families (Lacertidae, Gekkonidae and Agamidae). These molecular data presented here provide a useful tool for systematic analyses of genus Takydromus.

| S-EPMC7800021 | biostudies-literature