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 superscaffolded 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.
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35The Asiatic wild dog is an endangered monophyletic canid restricted to Asia; facing threats 36 from habitat fragmentation and other anthropogenic factors. Dholes have unique adaptations 37 as compared to other wolf-like canids for large litter size (larger number of mammae) and 38 hypercarnivory making it evolutionarily notable. Over evolutionary time, dhole and the 39 subsequent divergent wild canids have lost coat patterns found in African wild dog. Here we 40 report the first high coverage genome survey of Asiatic wild dog and mapped it with African 41 wild dog, dingo and domestic dog to assess the structural variants. We generated a total of 42 124.8 Gb data from 416140921 raw read pairs and retained 398659457 reads with 52X 43 coverage and mapped 99.16% of the clean reads to the three reference genomes. We 44 identified ~13553269 SNV's, ~2858184 InDels, ~41000 SVs, ~1854109 SSRs and about 45 1000 CNVs. We compared the annotated genome of dingo and domestic dog with dhole 46 genome sequence to understand the role of genes responsible in pelage pattern, dentition and 47 mammary glands. Positively selected genes for these phenotypes were looked for SNP 48 variants and top ranked genes for coat pattern, dentition and mammary glands were found to 49 play a role in signalling and developmental pathways. Mitochondrial genome assembly 50 predicted 35 genes, 11 CDS and 24 tRNA. This genome information will help in 51 understanding the divergence of two monophlyletic canids, Cuon and Lycaon, and the 52 evolutionary adaptations of dholes with respect to other canids. 53 54 55 56 57 58 59The Asiatic wild dog (Cuon alpinus) or dhole is monotypic canid belonging to the genus 60 Cuon. Dholes were widely distributed across the continents of North America, Europe and 61
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.
Pomegranate ( Punica granatum L.) is an important fruit crop, rich in fiber, vitamins, antioxidants, minerals and source of different biologically active compounds. The bacterial blight caused by Xanthomonas axonopodis pv. punicae is a serious threat to the crop leading to 60–80% yield loss under epiphytotic conditions. In this work, we have generated comparative transcriptome profile to mark the gene expression signatures during resistance and susceptible interactions. We analyzed leaf and fruits samples of moderately resistant genotype (IC 524207) and susceptible variety (Bhagawa) of pomegranate at three progressive infection stages upon inoculation with the pathogen. RNA-Seq with the Illumina HiSeq 2500 platform revealed 1,88,337 non-redundant (nr) transcript sequences from raw sequencing data, for a total of 34,626 unigenes with size >2 kb. Moreover, 85.3% unigenes were annotated in at least one of the seven databases examined. Comparative analysis of gene-expression signatures in resistant and susceptible varieties showed that the genes known to be involved in defense mechanism in plants were up-regulated in resistant variety. Gene Ontology (GO) analysis successfully annotated 90,485 pomegranate unigenes, of which 68,464 were assigned to biological, 78,107 unigenes molecular function and 44,414 to cellular components. Significantly enriched GO terms in DEGs were related to oxidations reduction biological process, protein binding and oxidoreductase activity. This transcriptome data on pomegranate could help in understanding resistance and susceptibility nature of cultivars and further detailed fine mapping and functional validation of identified candidate gene would provide scope for resistance breeding programme in pomegranate.
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