The complete mitochondrial genome of the Burmese roofed turtle (Batagur trivittata) (Testudines: Geoemydidae)

Feng, Li; Yang, Jiao; Zhang, Yanping; Zhao, Guifang

doi:10.1007/s12686-016-0629-5

Cited by 9 publications

(10 citation statements)

References 13 publications

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“…Currently, 31 mitogenomes of species comprising seven Geoemydidae genera ( Mauremys , Cuora , Heosemys , Sacalia , Notochelys , Cyclemys , and Batagur ) are available in GenBank. Among them, only four mitogenomes (, , , and ) of four species ( Batagur trivittata , Cuora mouhotii , Cuora trifasciata , and Cyclemys dentata ) are published (Feng, Yang, Zhang, & Zhao, ; Huang et al, ; Li, Zhang, Zhao, Shi, & Zhu, ; Zhang, Nie, Cao, & Zhan, ). However, no complete mitogenome of any species of Pangshura is available.…”

Section: Introductionmentioning

confidence: 99%

The first complete mitochondrial genome of the Indian Tent Turtle, Pangshura tentoria (Testudines: Geoemydidae): Characterization and comparative analysis

Kundu

Kumar

Tyagi

et al. 2019

Ecology and Evolution

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The characterization of a complete mitogenome is widely used in genomics studies for systematics and evolutionary research. However, the sequences and structural motifs contained within the mitogenome of Testudines taxa have rarely been examined. The present study decodes the first complete mitochondrial genome of the Indian Tent Turtle, Pangshura tentoria (16,657 bp) by using next‐generation sequencing. This denovo assembly encodes 37 genes: 13 protein‐coding genes (PCGs), 22 transfer RNA (tRNAs), two ribosomal RNA, and one control region (CR). Most of the genes were encoded on majority strand, except for one PCG (NADH dehydrogenase subunit 6) and eight tRNAs. Most of the PCGs were started with an ATG initiation codon, except for Cytochrome oxidase subunit 1 with “GTG” and NADH dehydrogenase subunit 5 with “ATA.” The termination codons, “TAA” and “AGA” were observed in two subunits of NADH dehydrogenase gene. The relative synonymous codon usage analysis revealed the maximum abundance of alanine, isoleucine, leucine, and threonine. The nonsynonymous/synonymous ratios were <1 in all PCGs, which indicates strong negative selection among all Geoemydid species. The study also found the typical cloverleaf secondary structure in most of the tRNA genes, except for serine with the lack of the conventional DHU arm. The comparative study of Geoemydid mitogenomes revealed the occurrence of tandem repeats was frequent in the 3′ end of CR. Further, two copies of a unique tandem repeat “TTCTCTTT” were identified in P. tentoria. The Bayesian and maximum‐likelihood phylogenetic trees using concatenation of 13 PCGs revealed the close relationships of P. tentoria with Batagur trivittata in the studied dataset. All the Geoemydid species showed distinct clustering with high bootstrap support congruent with previous evolutionary hypotheses. We suggest that the generations of more mitogenomes of Geoemydid species are required, to improve our understanding of their in‐depth phylogenetic and evolutionary relationships.

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Section: Introductionmentioning

confidence: 99%

The first complete mitochondrial genome of the Indian Tent Turtle, Pangshura tentoria (Testudines: Geoemydidae): Characterization and comparative analysis

Kundu

Kumar

Tyagi

et al. 2019

Ecology and Evolution

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“…Similar results have also been reported in several turtles, such as Pangshura spps. (Kundu et al, 2019;2020), Cyclemys dentata (Huang et al, 2015), Pyxidea mouhotii (Zhang et al, 2008b), Cuora trifasciata (Li et al, 2015), and B. trivittata (Feng et al, 2017).…”

Section: Mitogenome Structure and Organizationmentioning

confidence: 99%

“…Complete mitogenomes have been widely employed in Testudines systematic research, conservation, and biodiversity assessment (Galtier et al 2009;Kundu et al, 2019;2020). Feng et al (2017) sequenced the mitochondrial genome of B. trivittata from genus Batagur. In the present study, we sequenced, annotated, and analyzed the mitochondrial genome of B. kachuga and B. dhongoka and perform a comparative analysis with other Geoemydid species.…”

Section: Introductionmentioning

confidence: 99%

Comparative Mitogenomics of Two Critically Endangered Turtles, Batagur Kachuga and Batagur Dhongoka (Testudines: Geoemydidae): Implications in Phylogenetics of Freshwater Turtles

Kumar

Yadav

Usmani

et al. 2021

Preprint

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The Red-crowned roofed turtle (Batagur kachuga) and Three-striped roofed turtle (B. dhongoka) are ‘critically endangered’ turtles in the Geoemydidae family. Herein, we generated the novel mitochondrial genome sequence of B. kachuga (16,155) and B. dhongoka (15,620) and compared it with other turtles species. Batagur mitogenome has 22 transfer RNAs (tRNAs), 13 protein-coding genes (PCGs), two ribosomal RNAs (rRNAs), and one control region (CR). The genome composition was biased toward A + T, with positive AT-skew and negative GC-skew. In the examined species, all 13 PCGs were started by ATG codons, except COI gene, which was initiated by GTG. The majority of mito-genes were encoded on the heavy strand, except eight tRNAs and the ND6 region. We observed a typical cloverleaf structure for all tRNA, excluding tRNASer (AGN), where the base pairs of the dihydrouridine (DHU) arm were abridged. Bayesian Inference (BI) based phylogenetic analysis was constructed among 39 species from six Testudines families, exhibited a close genetic relationship between Batagur and Pangshura with a high supporting value (PP ~ 0.99). It provides additional mitogenomic resources for further study of the Testudines evolutionary patterns.

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“…Testudines mitochondrial genomes are circular and double stranded with a size of 16-19 kb and contain typically 37 genes [16][17][18][19][20]. Remarkably, some of the reptile species, including turtles, have variable numbers of genes in their mitogenome due to the loss of protein-coding genes (PCGs), duplication of control regions (CRs), and occurrence of multiple contiguous numbers of one or more transfer RNA genes (tRNAs) [21].…”

Section: Introductionmentioning

confidence: 99%

The complete mitochondrial genome of the endangered Assam Roofed Turtle, Pangshura sylhetensis (Testudines: Geoemydidae): Genomic features and phylogeny

et al. 2020

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The Assam Roofed Turtle, Pangshura sylhetensis is an endangered and least studied species endemic to India and Bangladesh. The present study decodes the first complete mitochondrial genome of P. sylhetensis (16,568 bp) by using next-generation sequencing. The assembly encodes 13 protein-coding genes (PCGs), 22 transfer RNAs (tRNAs), two ribosomal RNAs (rRNAs), and one control region (CR). Most of the genes were encoded on the majority strand, except NADH dehydrogenase subunit 6 (nad6) and eight tRNAs. All PCGs start with an ATG initiation codon, except for Cytochrome oxidase subunit 1 (cox1) and NADH dehydrogenase subunit 5 (nad5), which both start with GTG codon. The study also found the typical cloverleaf secondary structures in most of the predicted tRNA structures, except for serine (trnS1) which lacks of conventional DHU arm and loop. Both Bayesian and maximum-likelihood phylogenetic inference using 13 concatenated PCGs demonstrated strong support for the monophyly of all 52 Testudines species within their respective families and revealed Batagur trivittata as the nearest neighbor of P. sylhetensis. The mitogenomic phylogeny with other amniotes is congruent with previous research, supporting the sister relationship of Testudines and Archosaurians (birds and crocodilians). Additionally, the mitochondrial Gene Order (GO) analysis indicated plesiomorphy with the typical vertebrate GO in most of the Testudines species.

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The complete mitochondrial genome of the Burmese roofed turtle (Batagur trivittata) (Testudines: Geoemydidae)

Cited by 9 publications

References 13 publications

The first complete mitochondrial genome of the Indian Tent Turtle, Pangshura tentoria (Testudines: Geoemydidae): Characterization and comparative analysis

The first complete mitochondrial genome of the Indian Tent Turtle, Pangshura tentoria (Testudines: Geoemydidae): Characterization and comparative analysis

Comparative Mitogenomics of Two Critically Endangered Turtles, Batagur Kachuga and Batagur Dhongoka (Testudines: Geoemydidae): Implications in Phylogenetics of Freshwater Turtles

The complete mitochondrial genome of the endangered Assam Roofed Turtle, Pangshura sylhetensis (Testudines: Geoemydidae): Genomic features and phylogeny

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