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Variability in DNA COI sequences reveals new haplotypes in freshwater turtles from northern region of India.

ABSTRACT: The chelonian represents a diverse order of turtles. Little is known about this group from India at molecular level. Cytochrome c oxidase I (COI) sequences of 125 individuals from nine species of freshwater turtles were generated and analyzed. A total of 118 nucleotide positions in COI gene as character-based DNA barcodes for each species were identified. Neighbour-joining (NJ) analyses tree well differentiated freshwater hard shell and softshell turtle. Overall species divergence (K2P) was 13.3%. Analysis of COI sequences from present study, combined with sequences downloaded from NCBI GenBank, revealed new COI haplotypes from Northern region of India.

SUBMITTER: Bhaskar R

PROVIDER: S-EPMC7800049 | biostudies-literature | 2018 Mar

REPOSITORIES: biostudies-literature

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Variability in DNA COI sequences reveals new haplotypes in freshwater turtles from northern region of India.

Bhaskar Ranjana R Mohindra Vindhya V

Mitochondrial DNA. Part B, Resources 20180307 1

The chelonian represents a diverse order of turtles. Little is known about this group from India at molecular level. Cytochrome c oxidase I (COI) sequences of 125 individuals from nine species of freshwater turtles were generated and analyzed. A total of 118 nucleotide positions in <i>COI</i> gene as character-based DNA barcodes for each species were identified. Neighbour-joining (NJ) analyses tree well differentiated freshwater hard shell and softshell turtle. Overall species divergence (K2P) w ...[more]

PMID: 33474158

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Project description:BackgroundCholera infection continues to be a threat to global public health. The current cholera pandemic associated with Vibrio cholerae El Tor has now been ongoing for over half a century.Methodology/principal findingsThirty-eight V. cholerae El Tor isolates associated with a cholera outbreak in 2009 from the Chandigarh region of India were characterised by a combination of microbiology, molecular typing and whole-genome sequencing. The genomic analysis indicated that two clones of V. cholera circulated in the region and caused disease during this time. These clones fell into two distinct sub-clades that map independently onto wave 3 of the phylogenetic tree of seventh pandemic V. cholerae El Tor. Sequence analyses of the cholera toxin gene, the Vibrio seventh Pandemic Island II (VSPII) and SXT element correlated with this phylogenetic position of the two clades on the El Tor tree. The clade 2 isolates, characterized by a drug-resistant profile and the expression of a distinct cholera toxin, are closely related to the recent V. cholerae isolated elsewhere, including Haiti, but fell on a distinct branch of the tree, showing they were independent outbreaks. Multi-Locus Sequence Typing (MLST) distinguishes two sequence types among the 38 isolates, that did not correspond to the clades defined by whole-genome sequencing. Multi-Locus Variable-length tandem-nucleotide repeat Analysis (MLVA) identified 16 distinct clusters.Conclusions/significanceThe use of whole-genome sequencing enabled the identification of two clones of V. cholerae that circulated during the 2009 Chandigarh outbreak. These clones harboured a similar structure of ICEVchHai1 but differed mainly in the structure of CTX phage and VSPII. The limited capacity of MLST and MLVA to discriminate between the clones that circulated in the 2009 Chandigarh outbreak highlights the value of whole-genome sequencing as a route to the identification of further genetic markers to subtype V. cholerae isolates.

Project description:Background:Turtle shells tend to exhibit frequent and substantial variability, both in bone and scute layout. Aside from secondary changes, caused by diseases, parasites, and trauma, this variability appears to be inherent and result from stochastic or externally induced flaws of developmental programs. It is, thus, expected to be present in fossil turtle species at least as prominently, as in modern populations. Descriptions of variability and ontogeny are, however, rare for fossil turtles, mainly due to rarity, incompleteness, damage, and post-mortem deformation of their remains. This paper is an attempt at description and interpretation of external shell variability in representatives of the oldest true turtles, Proterochersis robusta and Proterochersis porebensis (Proterochersidae, the sister group to all other known testudinatans) from the Late Triassic (Norian) of Germany and Poland. Methods:All the available shell remains of Proterochersis robusta (13 specimens) and Proterochersis porebensis (275 specimens) were studied morphologically in order to identify any ontogenetic changes, intraspecific variability, sexual dimorphism, and shell abnormalities. To test the inferred sexual dimorphism, shape analyses were performed for two regions (gular and anal) of the plastron. Results:Proterochersis spp. exhibits large shell variability, and at least some of the observed changes seem to be correlated with ontogeny (growth of gulars, extragulars, caudals, and marginals, disappearance of middorsal keel on the carapace). Several specimens show abnormal layout of scute sulci, several others unusual morphologies of vertebral scute areas, one has an additional pair of plastral scutes, and one extraordinarily pronounced, likely pathological, growth rings on the carapace. Both species are represented in a wide spectrum of sizes, from hatchlings to old, mature individuals. The largest fragmentary specimens of Proterochersis porebensis allow estimation of its maximal carapace length at approximately 80 cm, while Proterochersis robusta appears to have reached lower maximal sizes. Discussion:This is the second contribution describing variability among numerous specimens of Triassic turtles, and the first to show evidence of unambiguous shell abnormalities. Presented data supplement the sparse knowledge of shell scute development in the earliest turtles and suggest that at least some aspects of the developmental programs governing scute development were already similar in the Late Triassic to these of modern forms.

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Variability in DNA COI sequences reveals new haplotypes in freshwater turtles from northern region of India.

Publications

Variability in DNA COI sequences reveals new haplotypes in freshwater turtles from northern region of India.

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