The first draft genome of Picrorhiza kurrooa, an endangered medicinal herb from Himalayas

Abstract Picrorhiza kurrooa is an endangered medicinal herb which is distributed across the Himalayan region at an altitude between 3000–5000 m above mean sea level. The medicinal properties of P. kurrooa are attributed to monoterpenoid picrosides present in leaf, rhizome and root of the plant. Howe...

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Autores principales:	Tanvi Sharma, Nitesh Kumar Sharma, Prakash Kumar, Ganesh Panzade, Tanuja Rana, Mohit Kumar Swarnkar, Anil Kumar Singh, Dharam Singh, Ravi Shankar, Sanjay Kumar
Formato:	article
Lenguaje:	EN
Publicado:	Nature Portfolio 2021
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/1cdccf38da4f410d80fb22f038f8f854
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spelling	oai:doaj.org-article:1cdccf38da4f410d80fb22f038f8f8542021-12-02T16:17:21ZThe first draft genome of Picrorhiza kurrooa, an endangered medicinal herb from Himalayas10.1038/s41598-021-93495-z2045-2322https://doaj.org/article/1cdccf38da4f410d80fb22f038f8f8542021-07-01T00:00:00Zhttps://doi.org/10.1038/s41598-021-93495-zhttps://doaj.org/toc/2045-2322Abstract Picrorhiza kurrooa is an endangered medicinal herb which is distributed across the Himalayan region at an altitude between 3000–5000 m above mean sea level. The medicinal properties of P. kurrooa are attributed to monoterpenoid picrosides present in leaf, rhizome and root of the plant. However, no genomic information is currently available for P. kurrooa, which limits our understanding about its molecular systems and associated responses. The present study brings the first assembled draft genome of P. kurrooa by using 227 Gb of raw data generated by Illumina and PacBio RS II sequencing platforms. The assembled genome has a size of n = ~ 1.7 Gb with 12,924 scaffolds. Four pronged assembly quality validations studies, including experimentally reported ESTs mapping and directed sequencing of the assembled contigs, confirmed high reliability of the assembly. About 76% of the genome is covered by complex repeats alone. Annotation revealed 24,798 protein coding and 9789 non-coding genes. Using the assembled genome, a total of 710 miRNAs were discovered, many of which were found responsible for molecular response against temperature changes. The miRNAs and targets were validated experimentally. The availability of draft genome sequence will aid in genetic improvement and conservation of P. kurrooa. Also, this study provided an efficient approach for assembling complex genomes while dealing with repeats when regular assemblers failed to progress due to repeats.Tanvi SharmaNitesh Kumar SharmaPrakash KumarGanesh PanzadeTanuja RanaMohit Kumar SwarnkarAnil Kumar SinghDharam SinghRavi ShankarSanjay KumarNature PortfolioarticleMedicineRScienceQENScientific Reports, Vol 11, Iss 1, Pp 1-21 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Tanvi Sharma Nitesh Kumar Sharma Prakash Kumar Ganesh Panzade Tanuja Rana Mohit Kumar Swarnkar Anil Kumar Singh Dharam Singh Ravi Shankar Sanjay Kumar The first draft genome of Picrorhiza kurrooa, an endangered medicinal herb from Himalayas
description	Abstract Picrorhiza kurrooa is an endangered medicinal herb which is distributed across the Himalayan region at an altitude between 3000–5000 m above mean sea level. The medicinal properties of P. kurrooa are attributed to monoterpenoid picrosides present in leaf, rhizome and root of the plant. However, no genomic information is currently available for P. kurrooa, which limits our understanding about its molecular systems and associated responses. The present study brings the first assembled draft genome of P. kurrooa by using 227 Gb of raw data generated by Illumina and PacBio RS II sequencing platforms. The assembled genome has a size of n = ~ 1.7 Gb with 12,924 scaffolds. Four pronged assembly quality validations studies, including experimentally reported ESTs mapping and directed sequencing of the assembled contigs, confirmed high reliability of the assembly. About 76% of the genome is covered by complex repeats alone. Annotation revealed 24,798 protein coding and 9789 non-coding genes. Using the assembled genome, a total of 710 miRNAs were discovered, many of which were found responsible for molecular response against temperature changes. The miRNAs and targets were validated experimentally. The availability of draft genome sequence will aid in genetic improvement and conservation of P. kurrooa. Also, this study provided an efficient approach for assembling complex genomes while dealing with repeats when regular assemblers failed to progress due to repeats.
format	article
author	Tanvi Sharma Nitesh Kumar Sharma Prakash Kumar Ganesh Panzade Tanuja Rana Mohit Kumar Swarnkar Anil Kumar Singh Dharam Singh Ravi Shankar Sanjay Kumar
author_facet	Tanvi Sharma Nitesh Kumar Sharma Prakash Kumar Ganesh Panzade Tanuja Rana Mohit Kumar Swarnkar Anil Kumar Singh Dharam Singh Ravi Shankar Sanjay Kumar
author_sort	Tanvi Sharma
title	The first draft genome of Picrorhiza kurrooa, an endangered medicinal herb from Himalayas
title_short	The first draft genome of Picrorhiza kurrooa, an endangered medicinal herb from Himalayas
title_full	The first draft genome of Picrorhiza kurrooa, an endangered medicinal herb from Himalayas
title_fullStr	The first draft genome of Picrorhiza kurrooa, an endangered medicinal herb from Himalayas
title_full_unstemmed	The first draft genome of Picrorhiza kurrooa, an endangered medicinal herb from Himalayas
title_sort	first draft genome of picrorhiza kurrooa, an endangered medicinal herb from himalayas
publisher	Nature Portfolio
publishDate	2021
url	https://doaj.org/article/1cdccf38da4f410d80fb22f038f8f854
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The first draft genome of Picrorhiza kurrooa, an endangered medicinal herb from Himalayas

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