Assembling mitogenome of Himalayan Black Bear (U. t. laniger) from low depth reads and its application in drawing phylogenetic inferences

Abstract The complete mitogenome of Himalayan black bear (Ursus thibetanus laniger) from Indian Himalayan region was assembled following the modified approach of mitochondrial baiting and mapping using the next-generation sequencing reads. The complete mitogenome was of 16,556 bp long, consisted of...

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Autores principales:	Amrita Bit, Mukesh Thakur, Sujeet Kumar Singh, Bheem Dutt Joshi, Vinay Kumar Singh, Lalit Kumar Sharma, Basudev Tripathy, Kailash Chandra
Formato:	article
Lenguaje:	EN
Publicado:	Nature Portfolio 2021
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/9e1e232b980f4ee99da94a151cd0314b
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spelling	oai:doaj.org-article:9e1e232b980f4ee99da94a151cd0314b2021-12-02T15:23:03ZAssembling mitogenome of Himalayan Black Bear (U. t. laniger) from low depth reads and its application in drawing phylogenetic inferences10.1038/s41598-020-76872-y2045-2322https://doaj.org/article/9e1e232b980f4ee99da94a151cd0314b2021-01-01T00:00:00Zhttps://doi.org/10.1038/s41598-020-76872-yhttps://doaj.org/toc/2045-2322Abstract The complete mitogenome of Himalayan black bear (Ursus thibetanus laniger) from Indian Himalayan region was assembled following the modified approach of mitochondrial baiting and mapping using the next-generation sequencing reads. The complete mitogenome was of 16,556 bp long, consisted of 37 genes that contained 13 protein-coding genes, 22 tRNAs, 2 rRNAs and 1 control region. The complete base composition was 31.33% A, 15.24% G, 25.45%C, and 27.98%T and gene arrangement was similar to the other sub-species of Asiatic black bear. The relative synonymous codon usage analysis revealed the maximum abundance of Isoleucine, Tyrosine, Leucine and Threonine. The assembled mitogenome of U. t. laniger exhibited 99% similarity with the mitogenomes of Himalayan black bear available from Nepal and Tibetan Plateau-Himalaya region. The findings of the present study has proven low depth sequencing data, adequate and highly efficient in rapid recovering the mitochondrial genome by overcoming the conventional strategies of obtaining long-range PCR and subsequently drawing phylogenetic inferences.Amrita BitMukesh ThakurSujeet Kumar SinghBheem Dutt JoshiVinay Kumar SinghLalit Kumar SharmaBasudev TripathyKailash ChandraNature PortfolioarticleMedicineRScienceQENScientific Reports, Vol 11, Iss 1, Pp 1-11 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Amrita Bit Mukesh Thakur Sujeet Kumar Singh Bheem Dutt Joshi Vinay Kumar Singh Lalit Kumar Sharma Basudev Tripathy Kailash Chandra Assembling mitogenome of Himalayan Black Bear (U. t. laniger) from low depth reads and its application in drawing phylogenetic inferences
description	Abstract The complete mitogenome of Himalayan black bear (Ursus thibetanus laniger) from Indian Himalayan region was assembled following the modified approach of mitochondrial baiting and mapping using the next-generation sequencing reads. The complete mitogenome was of 16,556 bp long, consisted of 37 genes that contained 13 protein-coding genes, 22 tRNAs, 2 rRNAs and 1 control region. The complete base composition was 31.33% A, 15.24% G, 25.45%C, and 27.98%T and gene arrangement was similar to the other sub-species of Asiatic black bear. The relative synonymous codon usage analysis revealed the maximum abundance of Isoleucine, Tyrosine, Leucine and Threonine. The assembled mitogenome of U. t. laniger exhibited 99% similarity with the mitogenomes of Himalayan black bear available from Nepal and Tibetan Plateau-Himalaya region. The findings of the present study has proven low depth sequencing data, adequate and highly efficient in rapid recovering the mitochondrial genome by overcoming the conventional strategies of obtaining long-range PCR and subsequently drawing phylogenetic inferences.
format	article
author	Amrita Bit Mukesh Thakur Sujeet Kumar Singh Bheem Dutt Joshi Vinay Kumar Singh Lalit Kumar Sharma Basudev Tripathy Kailash Chandra
author_facet	Amrita Bit Mukesh Thakur Sujeet Kumar Singh Bheem Dutt Joshi Vinay Kumar Singh Lalit Kumar Sharma Basudev Tripathy Kailash Chandra
author_sort	Amrita Bit
title	Assembling mitogenome of Himalayan Black Bear (U. t. laniger) from low depth reads and its application in drawing phylogenetic inferences
title_short	Assembling mitogenome of Himalayan Black Bear (U. t. laniger) from low depth reads and its application in drawing phylogenetic inferences
title_full	Assembling mitogenome of Himalayan Black Bear (U. t. laniger) from low depth reads and its application in drawing phylogenetic inferences
title_fullStr	Assembling mitogenome of Himalayan Black Bear (U. t. laniger) from low depth reads and its application in drawing phylogenetic inferences
title_full_unstemmed	Assembling mitogenome of Himalayan Black Bear (U. t. laniger) from low depth reads and its application in drawing phylogenetic inferences
title_sort	assembling mitogenome of himalayan black bear (u. t. laniger) from low depth reads and its application in drawing phylogenetic inferences
publisher	Nature Portfolio
publishDate	2021
url	https://doaj.org/article/9e1e232b980f4ee99da94a151cd0314b
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Assembling mitogenome of Himalayan Black Bear (U. t. laniger) from low depth reads and its application in drawing phylogenetic inferences

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