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Whole genome sequence and de novo assembly revealed genomic architecture of Indian Mithun (Bos frontalis)

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Title Whole genome sequence and de novo assembly revealed genomic architecture of Indian Mithun (Bos frontalis)
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Creator Sabyasachi Mukherjee1*† , Zexi Cai2†, Anupama Mukherjee1,3, Imsusosang Longkumer1, Moonmoon Mech1, Kezhavituo Vupru1, Kobu Khate1, Chandan Rajkhowa1, Abhijit Mitra1, Bernt Guldbrandtsen2, Mogens Sandø Lund2 and Goutam Sahana2
 
Subject Mithun
Bos frontalis
Genome
de novo assembly
 
Description Not Available
Background: Mithun (Bos frontalis), also called gayal, is an endangered bovine species, under the tribe bovini with 2n = 58 XX chromosome complements and reared under the tropical rain forests region of India, China, Myanmar, Bhutan and Bangladesh. However, the origin of this species is still disputed and information on its genomic architecture is scanty so far. 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 geographical locations and for building a superior consensus assembly. 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. The genomic alignments between mithun to cattle showed that their genomes, as expected, are highly conserved. Gene annotation identified 28,044 protein-coding genes presented in mithun genome. The gene orthologous groups of mithun showed a high degree of similarity in comparison with other species, while fewer mithun specific coding sequences were found compared to those in cattle.
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.
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Date 2019-09-06T04:42:04Z
2019-09-06T04:42:04Z
2019-08-03
 
Type Research Paper
 
Identifier Not Available
Not Available
http://krishi.icar.gov.in/jspui/handle/123456789/22964
 
Language English
 
Relation Not Available;
 
Publisher BMC Genomics