Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

The first complete mitochondrial DNA of Tenuidactylus dadunensis (Squamata: Gekkonidae) and its phylogeny.

ABSTRACT: The complete mitochondrial DNA (mtDNA) of Tenuidactylus dadunensis (Squamata: Gekkonidae) was described by using next-generation sequencing. The total length of mtDNA was 16,893 bp, which contained 13 PCGs (COX1-3, ND1-6, ND4L, ATP6, ATP8, and CYTB), 22 transfer RNA(tRNA) genes, 2 ribosomal RNA (rRNA) genes, and a control region (D-loop). The Bayesian inference tree showed that T. dadunensis was included in Gekkonidae and was a sister taxon to Cyrtopodion scabrum. The complete mtDNA of T. dadunensis will be an important genetic resource to the studies of conservation and research of geckonids.

SUBMITTER: Liang QR

PROVIDER: S-EPMC10993739 | biostudies-literature | 2024

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Publications

The first complete mitochondrial DNA of Tenuidactylus dadunensis (Squamata: Gekkonidae) and its phylogeny.

Liang Qian-Ru QR Shi Lei L

Mitochondrial DNA. Part B, Resources 20240402 4

The complete mitochondrial DNA (mtDNA) of Tenuidactylus dadunensis (Squamata: Gekkonidae) was described by using next-generation sequencing. The total length of mtDNA was 16,893 bp, which contained 13 PCGs (COX1-3, ND1-6, ND4L, ATP6, ATP8, and CYTB), 22 transfer RNA(tRNA) genes, 2 ribosomal RNA (rRNA) genes, and a control region (D-loop). The Bayesian inference tree showed that T. dadunensis was included in Gekkonidae and was a sister taxon ...[more]

PMID: 38586508

Similar Datasets

Complete mitochondrial genomes of two gecko species, Gekko hokouensis and Gekko japonicus (Squamata, Gekkonidae).

Project description:The Gekkonidae is the second-most-numerous Family in Sauria and widely distributed around the world. In this paper, the complete mitochondrial genomes of two gecko species, Gekko hokouensis and Gekko japonicas, were sequenced. The lengths of the two mitochondrial genomes (G. hokouensis and G. japonicus) are 17 956 bp and 17 769 bp, respectively. These mitochondrial genomes both contain 13 protein-coding genes, two ribosomal RNA genes, 22 transfer RNA genes and a non-coding region (control region). The overall base compositions of the H-strand of G. hokouensis and G. japonicus are 32.1% A, 26.7% T, 27.0% C, 14.2% G and 31.6% A, 25.2% T, 28.6% C, 14.7% G, respectively. Phylogenetic analysis showed that G. hokouensis is a sister clade with G. swinhonis. G. japonicus has a close phylogenetic relationship to the clade of G. hokouensis and G. swinhonis.

| S-EPMC7800641 | biostudies-literature

Small and overlooked: Phylogeny of the genus Trigonodactylus (Squamata: Gekkonidae), with the first record of Trigonodactylus arabicus from Jordan.

Project description:Geckos of the genus Trigonodactylus are widely distributed in the sand deserts of the Arabian Peninsula. Three species of this genus are currently recognized, with a fourth one, Stenodactylus pulcher, which placement within Trigonodactylus has been tentatively suggested, but not yet confirmed. We present a phylogenetic analysis of the genus Trigonodactylus with new specimens collected in central Saudi Arabia and southern Jordan. New genetic data has been generated from three mitochondrial markers to investigate the phylogenetic relationships of all species of the genus and to assess the putative generic assignment of S. pulcher. Our results confirm that S. pulcher indeed belongs within Trigonodactylus, branching as a sister lineage to all other species of the genus. The new samples cluster within Trigonodactylus arabicus, thus confirming the genetic homogeneity of the species across its large and seemingly inhospitable range. The new specimen collected in southern Jordan represents the first record for the country and a considerable range extension to the northwest from all previously reported localities. Our findings and discovery of a new species for Jordan highlight the need of more field surveys to be carried out in the underexplored parts of Jordan and northern Saudi Arabia, as these places still hold a potential for new discoveries and are crucial for understating the biogeography of the Arabian herpetofauna.

| S-EPMC8176046 | biostudies-literature

The complete mitochondrial genome of Pseudoxenodon stejnegeri (Squamata: Colubridae: Pseudoxenodontinae) and its phylogeny.

Project description:The mitochondrial genome sequence of Pseudoxenodon stejnegeri (Squamata: Colubridae: Pseudoxenodontinae) from Taishun County, Zhejiang Province, China, which is 18,475 bp in length and contains 25 tRNAs (including extra two tRNA-Tyr genes and extra one tRNA-Met gene), two rRNAs, 13 protein-coding genes and two identical control regions. The overall AT content of the mitogenome is 59.6% (A = 32.6%, T = 27%, C = 27%, G = 13.4%). In BI and ML phylogenetic analyses, the monophyly of the family Colubridae was well supported and P. stejnegeri was a basal clade of Colubridae.

| S-EPMC7671704 | biostudies-literature

Phylogeny of east Asian mitochondrial DNA lineages inferred from complete sequences.

Project description:The now-emerging mitochondrial DNA (mtDNA) population genomics provides information for reconstructing a well-resolved mtDNA phylogeny and for discerning the phylogenetic status of the subcontinentally specific haplogroups. Although several major East Asian mtDNA haplogroups have been identified in studies elsewhere, some of the most basal haplogroups, as well as numerous minor subhaplogroups, were not yet determined or fully characterized. To fill the lacunae, we selected 48 mtDNAs from >2,000 samples across China for complete sequencing that cover virtually all (sub)haplogroups discernible to date in East Asia. This East Asian mtDNA phylogeny can henceforth serve as a solid basis for phylogeographic analyses of mtDNAs, as well as for studies of mitochondrial diseases in East and Southeast Asia.

| S-EPMC1180693 | biostudies-literature

First Insights on the Karyotype Diversification of the Endemic Malagasy Leaf-Toed Geckos (Squamata: Gekkonidae: Uroplatus).

Project description:We provide here the first karyotype description of eight Uroplatus species and a characterization of their chromosomal diversity. We performed a molecular taxonomic assessment of several Uroplatus samples using the mitochondrial 12S marker and a comparative cytogenetic analysis with standard karyotyping, silver staining (Ag-NOR) and sequential C-banding + Giemsa, +Chromomycin A3 (CMA3), +4',6-diamidino-2-phenylindole (DAPI). We found chromosomal variability in terms of chromosome number (2n = 34-38), heterochromatin composition and number and localization of loci or Nucleolar Organizer Regions (NORs) (alternatively on the 2nd, 6th, 10th or 16th pair). Chromosome morphology is almost constant, with karyotypes composed of acrocentric chromosomes, gradually decreasing in length. C-banding evidenced a general low content of heterochromatin, mostly localized on pericentromeric and telomeric regions. Centromeric bands varied among the species studied, resulting in CMA3 positive and DAPI negative or positive to both fluorochromes. We also provide evidence of a first putative heteromorphic sex chromosome system in the genus. In fact, in U. alluaudi the 10th pair was highly heteromorphic, with a metacentric, largely heterochromatic W chromosome, which was much bigger than the Z. We propose an evolutionary scenario of chromosome reduction from 2n = 38 to 2n = 34, by means of translocations of microchromosomes on larger chromosomes (often involving the NOR-bearing microchromosomes). Adding our data to those available from the literature, we show that similar processes characterized the evolutionary radiation of a larger gecko clade. Finally, we hypothesize that sex chromosome diversification occurred independently in different genera.

| S-EPMC9404452 | biostudies-literature

The complete mitochondrial DNA sequence and the phylogenetic position of Rhabdophis tigrinus (Reptilia: Squamata).

Project description:The complete mitochondrial genome of Rhabdophis tigrinus (Reptilia: Squamata) is presented for the first time in this study. It is a circular molecule of 17 415 bp in length (GenBank accession no. KU641019), consisting of 13 protein-coding genes, 22 transfer RNA genes, two ribosomal RNA genes (12S and 16S rRNA) and two control regions (D-loop), with the typical gene order and direction of transcription in Serpentes. The overall base composition is 33.65% A, 26.70% C, 13.16% G and 26.49% T. Mitochondrial genomes analyses based on NJ method yield phylogenetic trees, including 14 reported snakes belonging to four families (Colubridae, Elapidae, Viperidae and Typhlopidae). These molecular data presented here provide a useful tool for systematic analyses of genus Rhabdophis and family Colubridae.

| S-EPMC7800361 | biostudies-literature

The biogeography of bent-toed geckos, Cyrtodactylus (Squamata: Gekkonidae).

Project description:The gekkonid genus Cyrtodactylus is the third largest vertebrate genus on the planet with well over 300 species that range across at least eight biogeographic regions from South Asia to Melanesia. The ecological and morphological plasticity within the genus, has contributed to its ability to disperse across ephemeral seaways, river systems, basins, land bridges, and mountain ranges-followed by in situ diversification within specific geographic areas. Ancestral ranges were reconstructed on a mitochondrial phylogeny with 346 described and undescribed species from which it was inferred that Cyrtodactylus evolved in a proto-Himalaya region during the early Eocene. From there, it dispersed to what is currently Indoburma and Indochina during the mid-Eocene-the latter becoming the first major center of origin for the remainder of the genus that seeded dispersals to the Indian subcontinent, Papua, and Sundaland. Sundaland became a second major center of radiation during the Oligocene and gave rise to a large number of species that radiated further within Sundaland and dispersed to Wallacea, the Philippines, and back to Indochina. One Papuan lineage dispersed west to recolonize and radiate in Sundaland. Currently, Indochina and Sundaland still harbor the vast majority of species of Cyrtodactylus.

| S-EPMC8953499 | 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

Phylogeny analysis of complete mitochondrial DNA sequences for pelagic fishes from tuna fishery.

Project description:Pelagic fishes captured in the international tuna fisheries have attracted increasing attention in recent years because of declines in their populations. In this study, 58 complete mitochondrial genomes of pelagic species from the classes Teleostean and Chondrichthyans were analyzed. The length of the 58 mtDNA sequences ranged from 15,598 to 18,880 bp, and all of which contained 13 protein-coding genes, 22 tRNA genes, 2 rRNA genes, and 1 control region. Our results suggested that mitochondrial genomes could be a powerful marker for resolving the phylogeny of pelagic fishes. Phylogenetic relationships based on the complete mitochondrial among 58 species indicated that Teleostean and Chondrichthyans are well separated. However, the control region length of Mobula japonicais was much larger than the other species in this study. Additionally, the Prionace glauca was divided into the clade in the genus Carcharhinus which provided a prospective taxonomic status of P.glauca.

| S-EPMC7799542 | biostudies-literature

Complete mitochondrial DNA genome sequences from the first New Zealanders.

Project description:The dispersal of modern humans across the globe began ~65,000 y ago when people first left Africa and culminated with the settlement of East Polynesia, which occurred in the last 1,000 y. With the arrival of Polynesian canoes only 750 y ago, Aotearoa/New Zealand became the last major landmass to be permanently settled by humans. We present here complete mitochondrial genome sequences of the likely founding population of Aotearoa/New Zealand recovered from the archaeological site of Wairau Bar. These data represent complete mitochondrial genome sequences from ancient Polynesian voyagers and provide insights into the genetic diversity of human populations in the Pacific at the time of the settlement of East Polynesia.

| S-EPMC3494939 | biostudies-literature