- We trust that availability of its whole genome sequence data and assembly will greatly solve this problem and help to generate many information including phylogenetic status of mithun. - Recently, the first genome assembly of gayal, mithun of Chinese origin, was published. - However, an improved reference genome assembly would still benefit in understanding genetic variation in mithun populations reared under diverse. - We, therefore, performed deep sequencing of the genome of an adult female mithun from India, assembled and annotated its genome and performed extensive bioinformatic analyses to produce a superior de novo genome assembly of mithun.. - Results: We generated ≈ 300 Gigabyte (Gb) raw reads from whole-genome deep sequencing platforms and assembled the sequence data using a hybrid assembly strategy to create a high quality de novo assembly of mithun with 96% recovered as per BUSCO analysis. - The final genome assembly has a total length of 3.0 Gb, contains 5,015 scaffolds with an N50 value of 1 Mb. - Repeat sequences constitute around 43.66% of the assembly.. - Conclusion: Here we presented the first de novo draft genome assembly of Indian mithun having better coverage, less fragmented, better annotated, and constitutes a reasonably complete assembly compared to the previously published gayal genome. - This comprehensive assembly unravelled the genomic architecture of mithun to a great extent and will provide a reference genome assembly to research community to elucidate the evolutionary history of mithun across its distinct geographical locations.. - 2019 Open Access This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0. - Full list of author information is available at the end of the article Mukherjee et al. - How- ever, the origin of mithun is an on-going debate with no well-supported conclusion [3–5]. - The deviation of the karyotype maybe originated from a 2/27 centric fusion or a Robertsonian translocation of cattle chromosomes 2 and 28 [6]. - Besides ambiguity on its origin, information on genomic architecture of mithun is scanty so far.. - Mai et al. - Another research group presented the first genome assembly for gayal (mithun of Chinese origin) [8].. - Here we performed whole genome sequencing of one Indian adult female mithun (2n = 58,XX) using mul- tiple sequencing platforms (Illumina HiSeq, Illumina Moleculo long reads and Pacific Biosciences: PacBio to generate a de novo genome assembly. - This assembly was compared with genome assemblies of other species in the tribe bovini including the pub- lished gayal genome assembly [8]. - We believe that an improved reference genome assembly would benefit understanding genetic divergence in mithun popula- tions reared under diverse geographical locations and would be helpful in understanding the genomic archi- tecture of this species.. - Genome assembly and assessment. - Genome size of mithun was estimated to be 3.09 Gb and 3.00 Gb was recovered in our assembly. - Our genome assembly consists of 5,015 scaffolds. - The size of the lar- gest scaffold was 6,540,552 bp with N50 value as 1.00 Mb. - The assembly of mithun genome presented here is less fragmented (5,015 vs. - 460,059 scaffolds) and is more complete than the previously published gayal genome assembly [8] (Table 1, Fig. - Figure 1 showed that our mithun genome assembly was evenly distributed across the length of scaffolds. - The result showed 98.70% of the mate-pair reads could be aligned to our mithun genome assembly, 82.99% for 3 kb library and 84.42% of 5 kb library are properly paired with the mithun assembly (Table 2). - This result proved a high de- gree of correct ordering and orientation of sequences in our mithun genome assembly. - To check whether the genome included most of the protein coding genes, a. - Table 1 Summary details of the mithun genome assembly compared with gayal genome. - Mithun genome Gayal genome [8]. - Details of the gen- ome proportion in each families are presented in Table 4.. - more the substitutions, greater the age of the copy of the element). - These differences originate from LINEs and SINEs in the genome.. - We identified 28,044 protein-coding genes in the mithun genome. - The orthologous groups of mithun were compared with those in human, mouse, dog and cattle genome (Fig. - The inner track showed the log10 of the scaffold counts (light purple). - Mukherjee et al. - had hits in the eggNOG database. - 2.60 Gb of the 2.66 Gb cattle genome (leaving out Mt., Y chromosomes and unassigned sequences) aligned with the mithun se- quence (98% alignment). - We also aligned previously published gayal assembly [8] to cattle genome, and 2.62 Gb of the 2.66 Gb cattle genome could be covered (98. - If one of the. - Motivation for mithun genome assembly. - Mithun lives under free-range conditions in the tropical rain forests of the North Eastern Hill region of India, at an altitude ranging from 300 to 3,000 m above mean sea level. - Mithun have great socio-economic importance among the mostly tribal population of the region.. - Meat and milk of mithun have high quality in terms of higher fat%. - Even if the genome assembly of one gayal (mithun of Chinese origin) was re- cently published [8], the Indian mithun we sequenced here is from a diverse geographical location and sepa- rated for long time from the gayal animal sequenced previously [8]. - A superior genome assembly of mithun (Indian origin) will provide valuable information for research into mithun biology and genetics.. - Here we presented the first de novo genome assembly of Indian mithun, which is more complete, less fragmented and better annotated (96. - We used a hybrid genome assembly approach combining second and third generation sequencing data (combining short pair-end Illumina reads and Moleculo &. - It was also reported that performance of genome assembly im- proves significantly from hybrid approach using both short and long sequence reads [34]. - Simultaneously, this approach also keeps overall costs of the projects manage- able [35–39]. - Table 4 The repeat sequence composition in the mithun genome Family Percent of genome Copy number of elements. - genome assembly had smaller scaffolds. - Secondly, we only had access to expression data from muscle tissue of mithun. - The origin and evolution of mithun. - Despite years of cytogenetic and phylogenetic studies, no consensus has been reached on the origin of mithun.. - Molecular phylogeny inferred from cytochrome b (Cytb), subunit II of cytochrome c oxidase (CO2), and the promotor of the. - 2 Interspersed Repeat Landscape of (a) cattle and (b) mithun. - 3 The orthologous groups and evolution of mithun genes. - Table 5 The size distribution of synteny blocks of mithun genome aligned to cattle genome. - 4 The genome alignment of mithun genome to cattle genome. - However, the distribution of the age of certain classes of repeat se- quences clearly differed. - The main objective of the present study is to furnish a genetic resource and a de novo reference genome of mithun to facilitate future research. - Our de novo draft assembly is the first genome assembly of Indian mithun, which is constructed using a hybrid approach. - This im- proved the overall performance of the genome assembly.. - We believe this mithun genome assembly will provide genomic resource to evolutionary studies in combination with other bovine species, and will help to understand the genomic archi- tecture of various phenotype and genotype interactions underlying this unique bovine species from distinct geographical habitat.. - The standard animal ethics normswere followed and care of the animal was taken in accordance with guidelines of the Committee for the Purpose of Control and Supervision on Experiments on Animals (CPCSEA), prescribed by the Indian Council of Agricul- tural Research (ICAR), Ministry of Agriculture and Farmers Welfare, Government of India. - These fragments then undergo end-repair and ligation of amplification adapters, before diluted onto 384-well plates so that each well contains DNA representing approximately 1–2% of the genome (200 molecules, in the case of D. - The hairpin dimers formed during this process were removed at the end of the protocol using a magnetic bead purification step with size-selective conditions. - The final step of the protocol was to remove failed ligation products with exonucleases. - RNA was extracted from each of the four muscle tissues following standard guidelines of Illumina Low Sample Protocol (TruSeq® RNA Sample Preparation v2 Guide).. - These cDNA fragments then went through an end repair process, the addition of a single ‘ A’ base, and then ligation of the adapters. - Final statistics of the assembly were assessed by QUAST [57]. - Part of the PE and MP data were mapped to the draft genome by BWA [58]. - Genome size was estimated by div- iding the total number of k-mers by the peak value of the k-mer frequency distribution [62].. - We also performed genome guided assembly by following procedure: the mixed dataset were aligned to genome assembly by Tophat2 [64]. - The genome assembly were masked by RepeatMasker [23]. - The RepeatLandscape for cattle genome assembly (BTA7) was downloaded from the RepeatMasker website of pre- analysis species. - pathway information of [77] pathway information of the mithun gene set.. - BTA 7: Bos taurus genome assembly v.7. - The authors would like to thank the Director of the Institute and Indian Council of Agricultural Research for funding the Institutional Research Project for this study. - Financial support in the form of DBT Overseas Associateship for the first author played a significant role to carry out some of the bioinformatic analyses and their interpretations at Aarhus University, Denmark.. - All the animal experiments and sample collections procedures were carried out by qualified Veterinarians of the Institute. - Chromosomes of Mithun (Gaveaus-frontalis). - Genetic characterisation of the mithun (Bos frontalis) and studies of. - Whole-genome sequencing of the endangered bovine species Gayal (Bos frontalis) provides new insights into its genetic features.. - Draft genome of the gayal. - Whole-genome sequence assembly of the water buffalo (Bubalus bubalis). - BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs. - A whole-genome assembly of the domestic cow, Bos taurus. - Genetic variability of the coding region for the prion protein gene (PRNP) in gayal (Bos frontalis). - Hybrid De Novo Genome Assembly Using MiSeq and SOLiD Short Read Data. - Hybrid de novo genome assembly and centromere characterization of the gray mouse lemur (Microcebus murinus). - Sohn J-i, Nam K, Kim J-M, Lim D, Lee K-T, Do YJ, Cho CY, Kim N, Nam J-W, Chae H-H: Whole genome hybrid assembly and protein-coding gene annotation of the entirely black native Korean chicken breed Yeonsan Ogye.. - Long-read sequence assembly of the gorilla genome. - Walker EP: Mammals of the world, vol. - Molecular phylogeny of the tribe Bovini (Bovidae, Bovinae) and the taxonomic status of the Kouprey, Bos sauveli Urbain 1937.. - Chromosome conservation in the Bovidae.. - Flow cytometry and K-mer analysis estimates of the genome sizes of Bemisia tabaci B and Q (Hemiptera: Aleyrodidae)
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