Browse
Submit Data
Databases
API
Help

Dataset Information

29 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

The complete mitochondrial genome of Lesser Sand-Plover Charadrius mongolus atrifrons and its phylogenetic position.

ABSTRACT: The Lesser Sand-Plover (Charadrius mongolus atrifrons) is a small shorebird in Charadriiformes. Here we assembled the complete mitochondrial genome of C. m. atrifrons (Aves: Charadriiformes) which is 16,919 bp in length and consisting of 13 protein-coding (PCGs), 2 ribosomal RNA, 22 transfer RNA and 1 control region. The overall A + T content of was 55.5%. The Maximum Likelihood (ML) tree based on the 12 concatenated mitochondrial protein-coding genes (except ND6 gene) placed C. m. atrifrons in a clade with C. alexandrines but separate from C. vociferus.

SUBMITTER: Zhang S

PROVIDER: S-EPMC8439239 | biostudies-literature |

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Similar Datasets

The mitochondrial genome of the long-billed plover, Charadrius placidus (Charadriiformes: Charadriidae).

Project description:The present study provides the first full mitochondrial genome sequence of a long-billed plover from South Korea. This mitogenome is 16,895 bp in length and consists of 13 protein-coding genes, 2 ribosomal-RNA genes, 22 transfer-RNA genes, and a non-coding control region. Overall, base composition was: A, 31.4%; C, 31.1%; G, 13.8%; and T, 23.8%. A frameshift mutation in the ND3 gene was identified and a tandem repeat (AACA) was observed in the D-loop region. The phylogenetic analysis based on concatenated coding genes indicated Charadriidae's monophyly. These results contribute to further understanding of long-billed plover phylogenetic relationships and species identification.

| S-EPMC7800784 | biostudies-literature

Complete mitochondrial genome and phylogenetic position of Chaenodraco wilsoni.

Project description:Chaenodraco wilsoni, a species of Channichthyidae, inhabits in southern ocean. The total length of complete mitochondrial genome of C. wilsoni is 17,432?bp, which encoded 37 genes. Similar to most Antarctic fishes, the ND6/tRNA (glu) translocation and an additional non-coding region linked with ND6 have also occurred in C. wilsoni. The ML tree supports that C. wilsoni has closer relationship with Chionodraco species. Our research will provide more molecular biology information about C. wilsoni and deepen the understanding of Antarctic fishes.

| S-EPMC7800782 | biostudies-literature

Complete mitochondrial genomes of two sand diver species (Perciformes, Trichonotidae): novel gene orders and phylogenetic position within Gobiiformes.

Project description:The complete mitochondrial genome sequences of two species of the family Trichonotidae, Trichonotus elegans (Shimada and Yoshino 1984) and Trichonotus filamentosus (Steindachner 1867), were determined using a polymerase chain reaction-based method. The genomes ranged from 16,517 to 17,235 bp in length and included 37 genes (13 protein-coding genes, 22 transfer RNA genes, and 2 ribosomal RNA genes) and two non-coding regions (control region and origin of the light strand replication) as in other vertebrates. However, they shared a unique gene order among vertebrates with multiple gene switching and insertions. Phylogenetic analysis showed that Trichonotidae and Apogonidae are sister groups, which together with Kurtidae are placed as a closely related clade of Gobioidei. These results would be useful for analyzing the evolutionary relationships of Gobiiformes and the evolutionary study of fish mitogenomes.

| S-EPMC8676643 | biostudies-literature

Complete mitochondrial genome and phylogenetic position of Pangasius sanitwongsei (Siluriformes: Pangasiidae).

Project description:In this study, the complete mitochondrial genome of Pangasius sanitwongsei was firstly reported and analyzed. It had a double-stand DNA molecule with 16536 bp in length, consisting of 13 protein-coding genes, 2 ribosomal RNA genes, 22 transfer RNA genes and one control region. The structural organization and gene order was similar to other bony fishes. The complete mitochondrial genome of P. sanitwongsei provided in this work would be helpful for further research on phylogenetics and conservation genetics of the Siluriformes and other orders.

| S-EPMC7748851 | biostudies-literature

The complete mitochondrial genome sequence and phylogenetic position of Gobio coriparoides.

Project description:In this paper, we determined the complete mitochondrial DNA (mtDNA) sequence of Gobio coriparoides and analyzed its phylogenetic position. The complete mitogenome is 16,604 bp in length. It consists of 13 protein-coding genes, 2 rRNA genes, 22 tRNA genes, and 1 control region. Among the 37 genes, 28 were encoded on the heavy strand, while 9 were encoded on the light strand. The overall base composition was 28.97% for A, 18.06% for G, 26.54% for T, and 26.43% for C, with a higher A + T content (55.51%). There are some overlaps existing in G. coriparoides mitochondrial genome. The neighbor-joining (NJ) phylogenetic tree based on whole mitogenome sequences supported that G. coriparoides is the closest to G. cynocephalus. This result will provide a basic reference for understanding the genetic structure, molecular evolution, and phylogeny of G. coriparoides and related species.

| S-EPMC7748591 | biostudies-literature

The complete mitochondrial genome of Aquila nipalensis and its phylogenetic position.

Project description:Mitochondrial genome sequences are valuable resources for systematics and conservation biology studies. In this paper, we present the complete mitogenome of Aquila nipalensis which was 18,450 bp in length. The gene content and arrangement were typical for avian mtDNA. The overall A + T content of was 54.1%, and the AT skew was calculated as 0.12 for the complete mitogenome of A. nipalensis. The maximum-likelihood (ML) tree based on the concatenated 12 protein-coding genes (PCGs) revealed the basal phylogenetic position of A. nipalensis in Aquila.

| S-EPMC7687378 | biostudies-literature

The complete mitochondrial genome of grey plover Pluvialis squatarola (Charadriiformes, charadriidae).

Project description:The complete mitochondrial genome of grey plover Pluvialis squatarola was obtained by next-generation sequencing. The circular genome was 16,860 bp in length, consisting of 13 protein-coding genes, 22 transfer RNA genes, 2 ribosomal RNA genes, and a control region. The overall nucleotide composition was A: 30.9%, T: 23.4%, C: 31.6%, G: 14.1%. Nine genes were encoded on the light strand, and the remaining 28 genes were encoded on the heavy strand. Most of the PCGs began with the ATG as the start codon, and four kinds of termination codons were used in this mitogenome. This study improves our understanding of the mitogenomic characteristics and its phylogenetic relationships within Charadriiformes.

| S-EPMC7782006 | biostudies-literature

The Complete Mitochondrial Genome of Stichopus naso (Aspidochirotida: Stichopodidae: Stichopus) and Its Phylogenetic Position.

Project description:The mitochondrial genome is widely used to study the molecular evolution of and perform phylogenetic analyses on animals. In this study, the complete mitochondrial genome (mitogenome) of Stichopus naso was sequenced. The mitogenome was 16,239 bp in length and contained 13 protein-coding genes (PCGs), 22 transfer RNA genes (tRNAs), and 2 ribosomal RNA genes (rRNAs). The genome composition showed positive AT-skew (0.023) and negative GC-skew (-0.158). The order of the mitochondrial genes was consistent with those from the Stichopus and Isostichopus species, whereas it was different from those of other species of Aspidochirotida. The phylogenetic analysis, based on the nucleotide sequences of 13 PCGs through the methods of Bayesian inference (BI) and maximum likelihood (ML), indicated that S. naso has close relationships with S. horrens and S. monotuberculatus, and belongs to a member of Stichopodidae. Our study provides a reference mitogenome for further molecular evolution studies and phylogenetic research on sea cucumbers.

| S-EPMC9141342 | biostudies-literature

Complete mitochondrial genome and the phylogenetic position of Halcyon smyrnensis (Aves: Coraciiformes).

Project description:The complete mitochondrial genome of Halcyon smyrnensis was determined in this study. The mitogenomic length of Halcyon smyrnensis was 17 318 bp, including 13 protein-coding genes, 22 transfer RNA genes, two ribosomal RNA genes and one control region. Phylogenetic analyses show that H. leucocephala, H. pileata and H. smyrnensis congregated together, and our sample was sister to H. pileata.

| S-EPMC7800661 | biostudies-literature

Phylogenetic position and subspecies divergence of the endangered New Zealand Dotterel (Charadrius obscurus).

Project description:The New Zealand Dotterel (Charadrius obscurus), an endangered shorebird of the family Charadriidae, is endemic to New Zealand where two subspecies are recognized. These subspecies are not only separated geographically, with C. o. aquilonius being distributed in the New Zealand North Island and C. o. obscurus mostly restricted to Stewart Island, but also differ substantially in morphology and behavior. Despite these divergent traits, previous work has failed to detect genetic differentiation between the subspecies, and the question of when and where the two populations separated is still open. Here, we use mitochondrial and nuclear markers to address molecular divergence between the subspecies, and apply maximum likelihood and Bayesian methods to place C. obscurus within the non-monophyletic genus Charadrius. Despite very little overall differentiation, distinct haplotypes for the subspecies were detected, thus supporting molecular separation of the northern and southern populations. Phylogenetic analysis recovers a monophyletic clade combining the New Zealand Dotterel with two other New Zealand endemic shorebirds, the Wrybill and the Double-Banded Plover, thus suggesting a single dispersal event as the origin of this group. Divergence dates within Charadriidae were estimated with BEAST 2, and our results indicate a Middle Miocene origin of New Zealand endemic Charadriidae, a Late Miocene emergence of the lineage leading to the New Zealand Dotterel, and a Middle to Late Pleistocene divergence of the two New Zealand Dotterel subspecies.

| S-EPMC3808304 | 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