Organization and variation of mitochondrial DNA control region in pleurodiran turtles

Wang, Ling; Zhou, Xuming; Nie, Liuwang

doi:10.1590/s1984-46702011000400011

Cited by 13 publications

(12 citation statements)

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“…The relative position of the four CSBs was the same as that reported in some vertebrates (Fig. 8) [70–73]. Continuous poly-T chains spanning more than eight nucleotides, presumably functioning as a hindrance to the sequencing reaction, were observed in the upper region of CSB-I in almost all fishes examined.…”

Section: Resultssupporting

confidence: 77%

Structure and variation of the mitochondrial genome of fishes

et al. 2016

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BackgroundThe mitochondrial (mt) genome has been used as an effective tool for phylogenetic and population genetic analyses in vertebrates. However, the structure and variability of the vertebrate mt genome are not well understood. A potential strategy for improving our understanding is to conduct a comprehensive comparative study of large mt genome data. The aim of this study was to characterize the structure and variability of the fish mt genome through comparative analysis of large datasets.ResultsAn analysis of the secondary structure of proteins for 250 fish species (248 ray-finned and 2 cartilaginous fishes) illustrated that cytochrome c oxidase subunits (COI, COII, and COIII) and a cytochrome bc1 complex subunit (Cyt b) had substantial amino acid conservation. Among the four proteins, COI was the most conserved, as more than half of all amino acid sites were invariable among the 250 species. Our models identified 43 and 58 stems within 12S rRNA and 16S rRNA, respectively, with larger numbers than proposed previously for vertebrates. The models also identified 149 and 319 invariable sites in 12S rRNA and 16S rRNA, respectively, in all fishes. In particular, the present result verified that a region corresponding to the peptidyl transferase center in prokaryotic 23S rRNA, which is homologous to mt 16S rRNA, is also conserved in fish mt 16S rRNA. Concerning the gene order, we found 35 variations (in 32 families) that deviated from the common gene order in vertebrates. These gene rearrangements were mostly observed in the area spanning the ND5 gene to the control region as well as two tRNA gene cluster regions (IQM and WANCY regions). Although many of such gene rearrangements were unique to a specific taxon, some were shared polyphyletically between distantly related species.ConclusionsThrough a large-scale comparative analysis of 250 fish species mt genomes, we elucidated various structural aspects of the fish mt genome and the encoded genes. The present results will be important for understanding functions of the mt genome and developing programs for nucleotide sequence analysis. This study demonstrated the significance of extensive comparisons for understanding the structure of the mt genome.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-016-3054-y) contains supplementary material, which is available to authorized users.

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Section: Resultssupporting

confidence: 77%

Structure and variation of the mitochondrial genome of fishes

et al. 2016

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“…The CD domain with flexible numbers of tandem repeats (VNTRs) considered as the origin of the H‐strand transcription (Brown, Gadaleta, Pepe, Saccone, & Sbisà, ). These patterns of conserved sequences alter within different vertebrate groups, including turtles (Ruokonen & Kvist, ; Wang, Zhou, & Nie, ). The CR is also known for the initiation of replication in vertebrates, including Geoemydid species, and is located between trnP and trnF with a varying size (Bing, Fei, Yi, & Qing‐Wei, ; Zheng et al, ).…”

Section: Resultsmentioning

confidence: 99%

“…These patterns of conserved sequences alter within different vertebrate groups, including turtles (Ruokonen & Kvist, 2002;Wang, Zhou, & Nie, 2011). The CR is also known for the initiation of replication in vertebrates, including Geoemydid species, and is located between trnP and trnF with a varying size (Bing, Fei, Yi, & Qing-Wei, 2006;Zheng et al, 2013).…”

Section: Control Regions (Crs)mentioning

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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“…As compared to the TAS and CSB domain with varying numbers of tandem repeats, the CD domain consisted of highly conserved sequences. Hence, the pattern of CR was varied among different vertebrates, including Testudines [60,61]. The total length of P. sylhetensis CR was 1,067 bp, compared to a range of 600 bp (Lepidochelys olivacea) to 3,885 bp (S. pardalis) in other species in the present dataset.…”

Section: Control Regionsmentioning

confidence: 57%

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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Organization and variation of mitochondrial DNA control region in pleurodiran turtles

Cited by 13 publications

References 50 publications

Structure and variation of the mitochondrial genome of fishes

Structure and variation of the mitochondrial genome of fishes

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

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

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