Mining of miRNAs using Next Generation Sequencing (NGS) data generated for Okra (Abelmoschus esculentus)

MicroRNAs (miRNAs) are small, highly conserved non-coding RNA molecules involved in the regulation of gene expression in eukaryotes. Gene expression involves post-transcriptional gene regulation by miRNAs. miRNAs are formed from precursor RNA molecules that fold into a stem loop secondary structure....

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Autores principales: Rekha Gupta, M Gayathri, V Radhika, M Pichaimuthu, K V Ravishankar
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Publicado: Society for Promotion of Horticulture - Indian Institute of Horticultural Research 2018
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Acceso en línea:https://doaj.org/article/effcaa5fcc7840b693ec46c2ced9bbc3
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spelling oai:doaj.org-article:effcaa5fcc7840b693ec46c2ced9bbc32021-12-02T04:02:03ZMining of miRNAs using Next Generation Sequencing (NGS) data generated for Okra (Abelmoschus esculentus)0973-354X2582-4899https://doaj.org/article/effcaa5fcc7840b693ec46c2ced9bbc32018-12-01T00:00:00Zhttps://jhs.iihr.res.in/index.php/jhs/article/view/474https://doaj.org/toc/0973-354Xhttps://doaj.org/toc/2582-4899MicroRNAs (miRNAs) are small, highly conserved non-coding RNA molecules involved in the regulation of gene expression in eukaryotes. Gene expression involves post-transcriptional gene regulation by miRNAs. miRNAs are formed from precursor RNA molecules that fold into a stem loop secondary structure. The mature miRNA is one end of the precursor miRNA, defined by the cut from ‘Drosha’ on either the 5’ or 3’ arm. In this study, we have used a bioinformatics approach to identify miRNAs in 3,361 contigs obtained from partial genome sequence data of Abelmoschus esculentus (okra) sequenced by NGS technology. Using C-mii and psRNA Target tools, we identified two miRNAs and their target RNAs for which a regulatory miRNA binding has been verified. Their targets consisted of transcription factors involved in growth and development, gene regulation and metabolism. Phylogenetic analysis of the newly identified miRNA family has been done to compare their level of conservation with respect to the other members of the plant kingdom.Rekha GuptaM GayathriV RadhikaM PichaimuthuK V RavishankarSociety for Promotion of Horticulture - Indian Institute of Horticultural Researcharticlemicrornanext generation sequencingabelmoschus esculentusmirna targetsPlant cultureSB1-1110ENJournal of Horticultural Sciences, Vol 13, Iss 2, Pp 137-145 (2018)
institution DOAJ
collection DOAJ
language EN
topic microrna
next generation sequencing
abelmoschus esculentus
mirna targets
Plant culture
SB1-1110
spellingShingle microrna
next generation sequencing
abelmoschus esculentus
mirna targets
Plant culture
SB1-1110
Rekha Gupta
M Gayathri
V Radhika
M Pichaimuthu
K V Ravishankar
Mining of miRNAs using Next Generation Sequencing (NGS) data generated for Okra (Abelmoschus esculentus)
description MicroRNAs (miRNAs) are small, highly conserved non-coding RNA molecules involved in the regulation of gene expression in eukaryotes. Gene expression involves post-transcriptional gene regulation by miRNAs. miRNAs are formed from precursor RNA molecules that fold into a stem loop secondary structure. The mature miRNA is one end of the precursor miRNA, defined by the cut from ‘Drosha’ on either the 5’ or 3’ arm. In this study, we have used a bioinformatics approach to identify miRNAs in 3,361 contigs obtained from partial genome sequence data of Abelmoschus esculentus (okra) sequenced by NGS technology. Using C-mii and psRNA Target tools, we identified two miRNAs and their target RNAs for which a regulatory miRNA binding has been verified. Their targets consisted of transcription factors involved in growth and development, gene regulation and metabolism. Phylogenetic analysis of the newly identified miRNA family has been done to compare their level of conservation with respect to the other members of the plant kingdom.
format article
author Rekha Gupta
M Gayathri
V Radhika
M Pichaimuthu
K V Ravishankar
author_facet Rekha Gupta
M Gayathri
V Radhika
M Pichaimuthu
K V Ravishankar
author_sort Rekha Gupta
title Mining of miRNAs using Next Generation Sequencing (NGS) data generated for Okra (Abelmoschus esculentus)
title_short Mining of miRNAs using Next Generation Sequencing (NGS) data generated for Okra (Abelmoschus esculentus)
title_full Mining of miRNAs using Next Generation Sequencing (NGS) data generated for Okra (Abelmoschus esculentus)
title_fullStr Mining of miRNAs using Next Generation Sequencing (NGS) data generated for Okra (Abelmoschus esculentus)
title_full_unstemmed Mining of miRNAs using Next Generation Sequencing (NGS) data generated for Okra (Abelmoschus esculentus)
title_sort mining of mirnas using next generation sequencing (ngs) data generated for okra (abelmoschus esculentus)
publisher Society for Promotion of Horticulture - Indian Institute of Horticultural Research
publishDate 2018
url https://doaj.org/article/effcaa5fcc7840b693ec46c2ced9bbc3
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