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  1. Article ; Online: Dataset from genome sequencing, assembly and mining of microsatellite markers in barred-button quail (

    Dey, Prateek / Ray, Swapna Devi / Pramod, Padmanabhan / Singh, Ram Pratap

    Data in brief

    2023  Volume 48, Page(s) 109288

    Abstract: ... Turnix ... ...

    Abstract Turnix suscitator
    Language English
    Publishing date 2023-06-01
    Publishing country Netherlands
    Document type Journal Article
    ZDB-ID 2786545-9
    ISSN 2352-3409 ; 2352-3409
    ISSN (online) 2352-3409
    ISSN 2352-3409
    DOI 10.1016/j.dib.2023.109288
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article ; Online: Dataset from genome sequencing, assembly and mining of microsatellite markers in barred-button quail (Turnix suscitator)

    Dey, Prateek / Ray, Swapna Devi / Pramod, Padmanabhan / Singh, R. P.

    Data in Brief. 2023 June, v. 48, p. 109288

    2023  , Page(s) 109288

    Abstract: Turnix suscitator (barred-button quail) is a member of the primitive genus Turnix in the highly diverse order of shore birds Charadriiformes. Absence of genome scale data of T. suscitator has limited our understanding about its systematics, taxonomic and ...

    Abstract Turnix suscitator (barred-button quail) is a member of the primitive genus Turnix in the highly diverse order of shore birds Charadriiformes. Absence of genome scale data of T. suscitator has limited our understanding about its systematics, taxonomic and evolutionary history as well has hindered the characterization of genome wide microsatellite markers of the same. Hence we generated whole genome short read sequences of T. suscitator, created a high quality assembly and mined genome-wide microsatellite markers from the same. A total of 34142524 reads were sequenced with an estimated genome size of 817 mb. SPAdes assembly consisted of 320761 total contigs and an estimated N50 value of 907 base pairs. Krait identified a total of 77028 microsatellite motifs covering 0.64% of the total sequences in the SPAdes assembly. Further the whole genome sequence and genome wide microsatellites dataset of T. suscitator will facilitate future genomic/evolutionary studies of Turnix species.
    Keywords Charadriiformes ; data collection ; genome ; genomics ; microsatellite repeats ; quails ; Whole-genome ; SSR ; Turnix
    Language English
    Dates of publication 2023-0601
    Size p. 109288
    Publishing place Elsevier Inc.
    Document type Article ; Online
    Note Pre-press version ; Use and reproduction
    ZDB-ID 2786545-9
    ISSN 2352-3409
    ISSN 2352-3409
    DOI 10.1016/j.dib.2023.109288
    Database NAL-Catalogue (AGRICOLA)

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  3. Article ; Online: Genome survey sequencing and mining of genome-wide microsatellite markers in yellow-billed babbler (Turdoides affinis)

    Mondal, Trisha / Dey, Prateek / Kumari, Divya / Ray, Swapna Devi / Quadros, Goldin / Sastry Kochiganti, Venkata Hanumat / Singh, R. P.

    Heliyon. 2023 Jan., v. 9, no. 1 p.e12735-

    2023  

    Abstract: Turdoides affinis is a species of group dwelling old world passerine of family Leiothrichidae. Unavailability of genome-wide sequence and species-specific molecular markers have hindered comprehensive understanding of cooperative breeding behaviour in T. ...

    Abstract Turdoides affinis is a species of group dwelling old world passerine of family Leiothrichidae. Unavailability of genome-wide sequence and species-specific molecular markers have hindered comprehensive understanding of cooperative breeding behaviour in T. affinis. Therefore, we generated genome-wide microsatellite markers through whole genome short read sequencing of T. affinis. A total of 68.8 gigabytes of paired-end raw data were sequenced containing 195,067,054 reads. Total sequenced reads spanned a coverage of 17X with genome size of 1.18 Gb. A large number of microsatellite markers (265,297) were mined in the T. affinis genome using Krait, and 50 most informative markers were identified and validated further. In-silico PCR results validated 47 markers. Of these 47 markers, five were randomly selected and validated in-vitro in twelve individuals of T. affinis. Genotyping data on these five loci estimated observed heterozygosity (H₀) and expected heterozygosity (Hₑ) ratios between 0.333 – 0.833 and 0.851–0.906, respectively. Effective allele size ranged from 6.698 to 10.667, inbreeding coefficient of the population ranged from 0.080 to 0.631 and null allele frequency was calculated at 0.055 to 0.303. Polymorphic information content of all the five loci varied between 0.850 and 0.906. Probabilities of exclusion and identity across 5 loci was estimated to be 0.95 and 0.0036, respectively. All the loci showed significant adherence to Hardy-Weinberg equilibrium. The microsatellite markers reported in this study will facilitate future population genetics studies on T. affinis and other congeneric species.
    Keywords Leiothrichidae ; computer simulation ; gene frequency ; genotyping ; heterozygosity ; microsatellite repeats ; null alleles ; surveys ; WGS ; Microsatellites ; Co-operative breeding ; Turdoides affinis
    Language English
    Dates of publication 2023-01
    Publishing place Elsevier Ltd
    Document type Article ; Online
    Note Use and reproduction
    ZDB-ID 2835763-2
    ISSN 2405-8440
    ISSN 2405-8440
    DOI 10.1016/j.heliyon.2022.e12735
    Database NAL-Catalogue (AGRICOLA)

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  4. Article ; Online: Retraction Note: Turdoides affinis mitogenome reveals the translational efficiency and importance of NADH dehydrogenase complex-I in the Leiothrichidae family.

    Sarkar, Indrani / Dey, Prateek / Sharma, Sanjeev Kumar / Ray, Swapna Devi / Kochiganti, Venkata Hanumat Sastry / Singh, Renu / Pramod, Padmanabhan / Singh, Ram Pratap

    Scientific reports

    2023  Volume 13, Issue 1, Page(s) 18144

    Language English
    Publishing date 2023-10-24
    Publishing country England
    Document type Retraction of Publication
    ZDB-ID 2615211-3
    ISSN 2045-2322 ; 2045-2322
    ISSN (online) 2045-2322
    ISSN 2045-2322
    DOI 10.1038/s41598-023-45261-6
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  5. Article ; Online: Turdoides affinis mitogenome reveals the translational efficiency and importance of NADH dehydrogenase complex-I in the Leiothrichidae family.

    Sarkar, Indrani / Dey, Prateek / Sharma, Sanjeev Kumar / Ray, Swapna Devi / Kochiganti, Venkata Hanumat Sastry / Singh, Renu / Pramod, Padmanabhan / Singh, Ram Pratap

    publication RETRACTED

    Scientific reports

    2020  Volume 10, Issue 1, Page(s) 16202

    Abstract: Mitochondrial genome provides useful information about species concerning its evolution and phylogenetics. We have taken the advantage of high throughput next-generation sequencing technique to sequence the complete mitogenome of Yellow-billed babbler ( ... ...

    Abstract Mitochondrial genome provides useful information about species concerning its evolution and phylogenetics. We have taken the advantage of high throughput next-generation sequencing technique to sequence the complete mitogenome of Yellow-billed babbler (Turdoides affinis), a species endemic to Peninsular India and Sri Lanka. Both, reference-based and de-novo assemblies of mitogenome were performed and observed that de-novo assembled mitogenome was most appropriate. The complete mitogenome of yellow-billed babbler (assembled de-novo) was 17,672 bp in length with 53.2% AT composition. Thirteen protein-coding genes along with two rRNAs and 22 tRNAs were detected. The arrangement pattern of these genes was found conserved among Leiothrichidae family mitogenomes. Duplicated control regions were found in the newly sequenced mitogenome. Downstream bioinformatics analysis revealed the effect of translational efficiency and purifying selection pressure over thirteen protein-coding genes in yellow-billed babbler mitogenome. Ka/Ks analysis indicated the highest synonymous substitution rate in the nad6 gene. Evolutionary analysis revealed the conserved nature of all the protein-coding genes across Leiothrichidae family mitogenomes. Our limited phylogeny results placed T. affinis in a separate group, a sister group of Garrulax. Overall, our results provide a useful information for future studies on the evolutionary and adaptive mechanisms of birds belong to the Leiothrichidae family.
    MeSH term(s) Animals ; DNA, Mitochondrial/analysis ; DNA, Mitochondrial/genetics ; Evolution, Molecular ; Genome, Mitochondrial ; NADH Dehydrogenase/genetics ; NADH Dehydrogenase/metabolism ; Passeriformes/classification ; Passeriformes/genetics ; Passeriformes/metabolism ; Phylogeny ; Protein Biosynthesis ; RNA, Transfer/genetics ; RNA, Transfer/metabolism ; Sequence Analysis, DNA
    Chemical Substances DNA, Mitochondrial ; RNA, Transfer (9014-25-9) ; NADH Dehydrogenase (EC 1.6.99.3)
    Language English
    Publishing date 2020-10-01
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't ; Retracted Publication
    ZDB-ID 2615211-3
    ISSN 2045-2322 ; 2045-2322
    ISSN (online) 2045-2322
    ISSN 2045-2322
    DOI 10.1038/s41598-020-72674-4
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  6. Article ; Online: Complete mitogenome of endemic plum-headed parakeet Psittacula cyanocephala - characterization and phylogenetic analysis.

    Dey, Prateek / Sharma, Sanjeev Kumar / Sarkar, Indrani / Ray, Swapna Devi / Pramod, Padmanabhan / Kochiganti, Venkata Hanumat Sastry / Quadros, Goldin / Rathore, Saurabh Singh / Singh, Vikram / Singh, Ram Pratap

    PloS one

    2021  Volume 16, Issue 4, Page(s) e0241098

    Abstract: Psittacula cyanocephala is an endemic parakeet from the Indian sub-continent that is widespread in the illegal bird trade. Previous studies on Psittacula parakeets have highlighted taxonomic ambiguities, warranting studies to resolve the issues. Since ... ...

    Abstract Psittacula cyanocephala is an endemic parakeet from the Indian sub-continent that is widespread in the illegal bird trade. Previous studies on Psittacula parakeets have highlighted taxonomic ambiguities, warranting studies to resolve the issues. Since the mitochondrial genome provides useful information concerning the species evolution and phylogenetics, we sequenced the complete mitogenome of P. cyanocephala using NGS, validated 38.86% of the mitogenome using Sanger Sequencing and compared it with other available whole mitogenomes of Psittacula. The complete mitogenome of the species was 16814 bp in length with 54.08% AT composition. P. cyanocephala mitogenome comprises of 13 protein-coding genes, 2 rRNAs and 22 tRNAs. P. cyanocephala mitogenome organization was consistent with other Psittacula mitogenomes. Comparative codon usage analysis indicated the role of natural selection on Psittacula mitogenomes. Strong purifying selection pressure was observed maximum on nad1 and nad4l genes. The mitochondrial control region of all Psittacula species displayed the ancestral avian CR gene order. Phylogenetic analyses revealed the Psittacula genus as paraphyletic nature, containing at least 4 groups of species within the same genus, suggesting its taxonomic reconsideration. Our results provide useful information for developing forensic tests to control the illegal trade of the species and scientific basis for phylogenetic revision of the genus Psittacula.
    MeSH term(s) Animals ; Codon Usage/genetics ; Gene Order/genetics ; Genome, Mitochondrial/genetics ; Mitochondria/genetics ; Mitogens/genetics ; Phylogeny ; Psittacula/genetics ; RNA, Ribosomal/genetics ; RNA, Transfer/genetics ; Selection, Genetic/genetics
    Chemical Substances Mitogens ; RNA, Ribosomal ; RNA, Transfer (9014-25-9)
    Language English
    Publishing date 2021-04-09
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2267670-3
    ISSN 1932-6203 ; 1932-6203
    ISSN (online) 1932-6203
    ISSN 1932-6203
    DOI 10.1371/journal.pone.0241098
    Database MEDical Literature Analysis and Retrieval System OnLINE

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