Biology subjects

Baghel, D. S.

Publications and source records attributed to Baghel, D. S..

4 recordsLinked to original sources

bioRxiv2024

Whole genome assembly of the Little Millet (Panicum sumatrense) genome: A climate resilient crop species

Little millet (Panicum sumatrense) belongs to one of the largest genera, Panicum comprising of 500 species that are distributed especially in tropical and sub-tropical Asia as well as Africa. This is a climate resilient crop that has the ability to adapt to adverse growing conditions, especially drought. Added to this is the better nutritional profile of little millet, which has higher iron and fibre contents as compared with rice. These characteristics make it an important crop species that would be pivotal for ensuring food security. Generating genomic resources for the species is significant and will have implications in crop improvement. Therefore, in the present study we report the de novo whole genome sequence of P. sumatrense. Long read sequencing and Hi-C based scaffolding resulted in a total of 279 scaffolds with N50 of 7.8Mb. The genome was annotated to predict protein coding genes and orthologous groups were analysed after comparison with various plant genomes. This high-quality genome assembly can be a valuable resource as future reference for genomic studies in this crop and related crop species.

genomics↗

bioRxiv2019

First near complete haplotype phased genome assembly of River buffalo (Bubalus bubalis)

This study reports the first haplotype phased reference quality genome assembly of Murrah an Indian breed of river buffalo. A mother-father-progeny trio was used for sequencing so that the individual haplotypes could be assembled in the progeny. Parental DNA samples were sequenced on the Illumina platform to generate a total of 274 Gb paired-end data. The progeny DNA sample was sequenced using PacBio long reads and 10x Genomics linked reads at 166x coverage along with 802Gb of optical mapping data. Trio binning based FALCON assembly of each haplotype was scaffolded with 10x Genomics reads and super-scaffolded with BioNano Maps to build reference quality assembly of sire and dam haplotypes of 2.63Gb and 2.64Gb with just 59 and 64 scaffolds and N50 of 81.98Mb and 83.23Mb, respectively. BUSCO single copy core gene set coverage was > 91.25%, and gVolante-CEGMA completeness was >96.14% for both haplotypes. Finally, RaGOO was used to order and build the chromosomal level assembly with 25 scaffolds and N50 of 117.48 Mb (sire haplotype) and 118.51 Mb (dam haplotype). The improved haplotype phased genome assembly of river buffalo may provide valuable resources to discover molecular mechanisms related to milk production and reproduction traits.

genomics↗

bioRxiv2018

The Cuon Enigma: Genome survey and comparative genomics of the endangered Dhole (Cuon alpinus)

The Asiatic wild dog is an endangered monophyletic canid restricted to Asia; facing threats from habitat fragmentation and other anthropogenic factors. Dholes have unique adaptations as compared to other wolf-like canids for large litter size (larger number of mammae) and hypercarnivory making it evolutionarily notable. Over evolutionary time, dhole and the subsequent divergent wild canids have lost coat patterns found in African wild dog. Here we report the first high coverage genome survey of Asiatic wild dog and mapped it with African wild dog, dingo and domestic dog to assess the structural variants. We generated a total of 124.8 Gb data from 416140921 raw read pairs and retained 398659457 reads with 52X coverage and mapped 99.16% of the clean reads to the three reference genomes. We identified ~13553269 SNVs, ~2858184 InDels, ~41000 SVs, ~1854109 SSRs and about 1000 CNVs. We compared the annotated genome of dingo and domestic dog with dhole genome sequence to understand the role of genes responsible in pelage pattern, dentition and mammary glands. Positively selected genes for these phenotypes were looked for SNP variants and top ranked genes for coat pattern, dentition and mammary glands were found to play a role in signalling and developmental pathways. Mitochondrial genome assembly predicted 35 genes, 11 CDS and 24 tRNA. This genome information will help in understanding the divergence of two monophlyletic canids, Cuon and Lycaon, and the evolutionary adaptations of dholes with respect to other canids.

genomics↗

bioRxiv2018

High coverage genome sequencing and identification of genomic variants in Bengal tiger (Panthera tigris tigris)

Bengal tiger (Panthera tigris tigris), one of six extant tiger subspecies, occurs solely in the Indian subcontinent. Although endangered and threatened by various extinction risks, this is the most populous tiger subspecies with the highest genetic diversity and strongest chance of survival in the wild. Availability of high quality genomic information on this animal will help us understand its ability to adapt to different habitats and environmental changes, in addition to comparative studies with other subspecies. Here we report high coverage sequencing of the Bengal tiger genome and its mapping to the Amur tiger genome in order to discover single nucleotide to large structural variants. A total of 345 Gb, roughly equivalent to 144X coverage of the genome, was generated from 1,149,381,669 raw read pairs. Further, 990,060,729 clean read pairs, again equivalent to 115X coverage, were retained from the raw read data and considered for comparative analysis with the Amur tiger genome. This alignment showed that 97.35% of the bases mapped at 5X depth, 97.26% at 10X and 90.44% at 50X depth. We identified a total of 3,601,882 single nucleotide variants, 948 structural variants, 56,649 copy number variants and 1,760,347 simple sequence repeats. We report the first high coverage genome sequence of Bengal tiger with an overview of its genomic variants when compared to the Amur tiger genome. Of the several variants identified, we further have to assess and validate variants potentially associated with the ability of the animal to adapt to environmental changes, disease susceptibility and other important biological phenomena.

genomics↗