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 river stingray Potamotrygon orbignyi (Myliobatiformes: Potamotrygonidae).

ABSTRACT: The river stingray Potamotrygon orbignyi is a carnivorous bottom feeder that is widespread in the Amazonian region. We here assemble the 17,449?bp complete mitochondrial genome of the species, showing a typical gene arrangement as for related Potamotrygonidae. The analysis of the COI gene confirmed the identification of the specimen as P. orbignyi. A phylogenetic analysis of all Potamotrygonidae complete mitochondrial genomes highlights the close relationship between P. orbignyi and P. motoro.

SUBMITTER: Ory D

PROVIDER: S-EPMC7706632 | biostudies-literature | 2019 Sep

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Publications

Complete mitochondrial genome of the river stingray Potamotrygon orbignyi (Myliobatiformes: Potamotrygonidae).

Ory David D Cuenot Yves Y Vigouroux Régis R Covain Raphaël R Brosse Sébastien S Murienne Jérôme J

Mitochondrial DNA. Part B, Resources 20190920 2

The river stingray Potamotrygon orbignyi is a carnivorous bottom feeder that is widespread in the Amazonian region. We here assemble the 17,449 bp complete mitochondrial genome of the species, showing a typical gene arrangement as for related Potamotrygonidae. The analysis of the COI gene confirmed the identification of the specimen as P. orbignyi. A phylogenetic analysis of all Potamotrygonidae complete mitochondrial genomes highlights the close relationship between P. orbignyi ...[more]

PMID: 33365895

Similar Datasets

The complete mitochondrial genome of pitted stingray Bathytoshia brevicaudata (Myliobatiformes: Dasyatoidea).

Project description:The complete mitochondrial genome of pitted stingray, Bathytoshia brevicaudata (Myliobatiformes: Dasyatoidea) was investigated by next-generation sequencing. The analyzed mitochondrial genome was 17,640 nucleotides in length and had 59.2% for AT contents. This genome contains 2 ribosomal RNA genes, 13 protein-coding genes, 22 transfer RNA genes. and 1 putative control region. Five protein-coding genes (ATPase6, COII, ND2, ND3, ND4) including incomplete stop codons and four tRNAs have atypical codons. The phylogenetic inference including 13 species of the same family revealed a close relationship with Pteroplatytrygon violacea. This is the first mitochondrial genome report from genus Bathytoshia.

| S-EPMC7782174 | biostudies-literature

Complete mitochondrial genome of the Devil Ray, Mobula thurstoni (Lloyd, 1908) (Myliobatiformes: Myliobatidae).

Project description:The Devil Ray (Mobula thurstoni) is a species with global distribution and is an important species in conservation terms, here we present its complete mitochondrial genome assembled with Illumina sequencing data. The circular genome was 17,610?bp in length, and consists of 13 protein-coding, two ribosomal RNAs (rRNAs), and 22 transfer RNA (tRNA) genes. Base composition is 30.7% A, 29.1% T, 26.5% C, and 13.7% G, and 40.2% GC content. Protein-coding genes present two start codon (ATG and GUG) and seven stop codon (UAA, AUA, UUU, UUA, AAU, CCU, and UAG). The control region possesses the highest A?+?T (66.6%) content among all mitochondrial regions. These data would contribute to the evolutionary studies of this genus, where there has been recent reclassification.

| S-EPMC7800197 | biostudies-literature

Complete mitochondrial genome and the phylogenetic position of the Jenkins whipray Himantura jenkinsii (Myliobatiformes, Dasyatidae).

Project description:We determined the complete mitochondrial genome of the Jenkins whipray Himantura jenkinsii. The total length of the mitogenome was 17, 670 bp, consisted of 37 genes with typical gene order in vertebrate mitogenome. The nucleotide composition was: 30.5% A, 29.1% T, 26.5% C and 13.9% G. It had 70 bp short intergenic spaces and 22 bp overlaps. Two start codons (GTG and ATG) and two stop codons (TAG and TAA/T) were used in the protein-coding genes. The 22 tRNA genes were ranged from 67 bp (tRNA-Ser2) to 75 bp (tRNA-Leu1). The phylogenetic result showed that H. jenkinsii was clustered with the Hortle's whipray H. hortlei.

| S-EPMC7871659 | biostudies-literature

Characterization of the complete mitochondrial genome of Silurus soldatovi in Korean river.

Project description:The complete mitochondrial genome of Silurus soldatovi firstly collected from a native Korean river was determined by the bioinformatics assembly of the next-generation sequencing (NGS) reads. The circular mitogenome was 16,525 bp in length which harbored canonical 13 protein-coding genes, 22 tRNAs, and 2 rRNAs, which was identical to those of family Siluridae. Twenty-eight genes were located on H strand, whereas the remaining nine genes were on L strand. Except for COX1 gene (GTG), other 12 protein-coding genes were predicted typical start codons (ATG). Among the currently known mitogenome sequences, S. soldatovi showed highest identity (99.38%) to the Chinese haplotype of S. soldatovi (NC022723) followed by the Chinese haplotype of Silurus asotus (JX087351). Interestingly, intraspecies variations of S. asotus are higher than those of interspecies and further study should be made to elucidate the evolutional relationship between two Silurus species.

| S-EPMC7707740 | biostudies-literature

Complete mitochondrial genome sequence of Pseudecheneis Sulcata in the Yarlung Zangbo River, Tibet.

Project description:Pseudecheneis sulcata belongs to Sisoridae, Pseudecheneis, which is mainly distributed in India and Tibet of China, and is located in the Motuo and Chayu in the lower reaches of the Yarlung Zangbo River in Tibet. In the present study, we obtained the complete mitochondrial genome sequence of Pseudecheneis sulcata, which was 16,535 bp in length. This genome consisted of 13 protein-coding genes, 22 tRNAgenes, 2 rRNA genes and a non-coding control region. The protein-coding genes have three start codons (GTG, ATG, and CTA) and four stop codons, including three complete stop codons and one incomplete stop codon. To verify the accuracy and utility of newly determined mitogenome sequences by constructing a species phylogenetic relationship tree of species, we expect to use the full mitochondrial gene sequence to interpret related evolutionary events.

| S-EPMC7687525 | biostudies-literature

Complete mitochondrial genome of the river cooter (Pseudemys concinna, Testudines: Emydidae) in Korea.

Project description:The complete mitochondrial genome of Pseudemys concinna in Korea was sequenced and characterized. The mitochondrial genome is constituted of 37 genes (13 protein-coding genes, 22 transfer RNA (tRNA) genes, and two ribosomal RNA (rRNA) genes) and a noncoding region. Phylogenetic analysis based on the complete mitochondrial genome showed that P. concinna has closer relationship with Chrysemys picta than Trachemys scripta elegans. This is the first case for complete mitochondrial genome from P. concinna in Korea, which will provide information for biogeographical studies and management plan for invasive species.

| S-EPMC9487955 | biostudies-literature

Complete mitochondrial genome sequence of Pareuchiloglanis kamengensis in the Yarlung Zangbo River, Tibet.

Project description:Pareuchiloglanis kamengensis belongs to the family of Sisoridae, Pareuchiloglanis. It is distributed in the Yarlung Zangbo River, the Irrawaddy River, the Nujiang River, and the Lancang River in southwestern China. In this study, we first published the complete mitochondrial genome sequence of Pareuchiloglanis kamengensis, which was 16,589 bp in length. This genome consists of 13 protein-coding genes (PCGs), 22 tRNA genes, two rRNA genes, and a non-coding A + T-rich region. The PCGs start with a traditional ATG except for COX1 and NAD3, which start with GTG and ATA instead, respectively, and end with stop codon TAA, TAG, TA, or a single T base. All tRNA have the typical clover-leaf structure. The phylogenetic tree of the whole mitogenome sequence is constructed by using neighbor-joining (NJ) method and the phylogenetic relationship among the family Sisoridae is further analyzed. We except to provide the theoretical basis for the further study of the phylogenetic relationship, taxonomic status, and conservation and management of genetic resources of Sisoridae catfishes.

| S-EPMC7748630 | biostudies-literature

Complete mitochondrial genome sequence of Glyptothorax annandalei in the Yarlung Zangbo River, Tibet.

Project description:Glyptothorax annandalei belongs to the family of Sisoridae, Glyptothorax. It is distributed in the Yarlung Zangbo River of southwestern China. In this study, we first published the complete mitochondrial genome sequence of Glyptothorax annandalei, which was 16,541 bp in length. This genome consists of two rRNA genes, 22 tRNA genes, 13 protein-coding genes (PCGs), and a putative control region. The overall base composition was for A(31.25%,) for T(25.67%), for C(27.66%), for G(15.42%). The PCGs start with a traditional ATG except for COX1 start with GTG, respectively, and end with stop codon TAA, TAG, or a single T base. All tRNA have the typical clover-leaf structure. The phylogenetic tree of the whole mitogenome sequence is constructed by maximum likelihood (ML) method and the phylogenetic relationship among the family Sisoridae is further analyzed. We expect to provide the theoretical basis for the further study of the phylogenetic relationship, taxonomic status, conservation and management of genetic resources of Sisoridae catfishes.

| S-EPMC8843123 | biostudies-literature

Characterization of the complete mitochondrial genome of Odontobutis platycephala collected from Nakdong River, South Korea.

Project description:The complete mitochondrial genome of Odontobutis platycephala collected from a native Korean river was determined by the bioinformatics assembly of the next-generation sequencing (NGS) reads. The circular mitogenome was 17,590 bp length which harbored canonical 13 protein-coding genes, 22 tRNAs, and 2 rRNAs, which was identical to those of family Odontobutidae. Twenty-eight genes were located on H strand, whereas remaining nine genes were on L strand. Except for COX1 gene (GTG), other 12 protein-coding genes were predicted typical start codons (ATG). Among the currently known mitogenome sequences, O. platycephala showed highest identity (96.98%) to Korean haplotype of O. platycephala (NC010199).

| S-EPMC7707751 | biostudies-literature

The complete mitochondrial genome sequence of Schizothorax dulongensis (Cypriniformes, Cyprinidae) from Irrawaddy River in China.

Project description:Schizothorax dulongensis Huang (1985) is an endemic species in China, which is mainly distributed in the Irrawaddy River and its tributaries. In this study, the complete mitochondrial genome was sequenced. Its length is 16,579 bp, containing 22 tRNAs, two rRNAs, and 13 PCGs. The phylogenetic results showed that S. dulongensis and these species from Brahmaputra River clustered a clade, and supported the Brahmaputra River and the Irrawaddy River have been reorganized of drainage.

| S-EPMC8381953 | biostudies-literature