Cargando…

Identification and expression profiling of miRNAs in two color variants of carrot (Daucus carota L.) using deep sequencing

microRNAs represent small endogenous RNAs which are known to play a crucial role in various plant metabolic processes. Carrot being an important vegetable crop, represents one of the richest sources of carotenoids and anthocyanins. Most of the studies on microRNAs have been conducted in the aerial p...

Descripción completa

Detalles Bibliográficos
Autores principales: Bhan, Bhavana, Koul, Archana, Sharma, Deepak, Manzoor, Malik Muzafar, Kaul, Sanjana, Gupta, Suphla, Dhar, Manoj K.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Public Library of Science 2019
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6405255/
https://www.ncbi.nlm.nih.gov/pubmed/30845212
http://dx.doi.org/10.1371/journal.pone.0212746
_version_ 1783401042818367488
author Bhan, Bhavana
Koul, Archana
Sharma, Deepak
Manzoor, Malik Muzafar
Kaul, Sanjana
Gupta, Suphla
Dhar, Manoj K.
author_facet Bhan, Bhavana
Koul, Archana
Sharma, Deepak
Manzoor, Malik Muzafar
Kaul, Sanjana
Gupta, Suphla
Dhar, Manoj K.
author_sort Bhan, Bhavana
collection PubMed
description microRNAs represent small endogenous RNAs which are known to play a crucial role in various plant metabolic processes. Carrot being an important vegetable crop, represents one of the richest sources of carotenoids and anthocyanins. Most of the studies on microRNAs have been conducted in the aerial parts of the plants. However, carrot has the rare distinction of storing these compounds in roots. Therefore, carrot represents a good model system to unveil the regulatory roles of miRNAs in the underground edible part of the plant. For the first time, we report the genome wide identification and expression profiling of miRNAs in two contrasting color variants of carrot namely Orange Red and Purple Black using RNA-seq. Illumina sequencing resulted in the generation of 25.5M and 18.9M reads in Orange Red and Purple Black libraries, respectively. In total, 144 and 98 (read count >10), conserved microRNAs and 36 and 66 novel microRNAs were identified in Orange Red and Purple Black, respectively. Functional categorization and differential gene expression revealed the presence of several miRNA genes targeting various secondary metabolic pathways including carotenoid and anthocyanin biosynthetic pathways in the two libraries. 11 known and 2 novel microRNAs were further validated using Stem-Loop PCR and qRT-PCR. Also, target validation was performed for selected miRNA genes using RLM-RACE approach. The present work has laid a foundation towards understanding of various metabolic processes, particularly the color development in carrot. This information can be further employed in targeted gene expression for increasing the carotenoid and anthocyanin content in crop plants.
format Online
Article
Text
id pubmed-6405255
institution National Center for Biotechnology Information
language English
publishDate 2019
publisher Public Library of Science
record_format MEDLINE/PubMed
spelling pubmed-64052552019-03-17 Identification and expression profiling of miRNAs in two color variants of carrot (Daucus carota L.) using deep sequencing Bhan, Bhavana Koul, Archana Sharma, Deepak Manzoor, Malik Muzafar Kaul, Sanjana Gupta, Suphla Dhar, Manoj K. PLoS One Research Article microRNAs represent small endogenous RNAs which are known to play a crucial role in various plant metabolic processes. Carrot being an important vegetable crop, represents one of the richest sources of carotenoids and anthocyanins. Most of the studies on microRNAs have been conducted in the aerial parts of the plants. However, carrot has the rare distinction of storing these compounds in roots. Therefore, carrot represents a good model system to unveil the regulatory roles of miRNAs in the underground edible part of the plant. For the first time, we report the genome wide identification and expression profiling of miRNAs in two contrasting color variants of carrot namely Orange Red and Purple Black using RNA-seq. Illumina sequencing resulted in the generation of 25.5M and 18.9M reads in Orange Red and Purple Black libraries, respectively. In total, 144 and 98 (read count >10), conserved microRNAs and 36 and 66 novel microRNAs were identified in Orange Red and Purple Black, respectively. Functional categorization and differential gene expression revealed the presence of several miRNA genes targeting various secondary metabolic pathways including carotenoid and anthocyanin biosynthetic pathways in the two libraries. 11 known and 2 novel microRNAs were further validated using Stem-Loop PCR and qRT-PCR. Also, target validation was performed for selected miRNA genes using RLM-RACE approach. The present work has laid a foundation towards understanding of various metabolic processes, particularly the color development in carrot. This information can be further employed in targeted gene expression for increasing the carotenoid and anthocyanin content in crop plants. Public Library of Science 2019-03-07 /pmc/articles/PMC6405255/ /pubmed/30845212 http://dx.doi.org/10.1371/journal.pone.0212746 Text en © 2019 Bhan et al http://creativecommons.org/licenses/by/4.0/ This is an open access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/) , which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
spellingShingle Research Article
Bhan, Bhavana
Koul, Archana
Sharma, Deepak
Manzoor, Malik Muzafar
Kaul, Sanjana
Gupta, Suphla
Dhar, Manoj K.
Identification and expression profiling of miRNAs in two color variants of carrot (Daucus carota L.) using deep sequencing
title Identification and expression profiling of miRNAs in two color variants of carrot (Daucus carota L.) using deep sequencing
title_full Identification and expression profiling of miRNAs in two color variants of carrot (Daucus carota L.) using deep sequencing
title_fullStr Identification and expression profiling of miRNAs in two color variants of carrot (Daucus carota L.) using deep sequencing
title_full_unstemmed Identification and expression profiling of miRNAs in two color variants of carrot (Daucus carota L.) using deep sequencing
title_short Identification and expression profiling of miRNAs in two color variants of carrot (Daucus carota L.) using deep sequencing
title_sort identification and expression profiling of mirnas in two color variants of carrot (daucus carota l.) using deep sequencing
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6405255/
https://www.ncbi.nlm.nih.gov/pubmed/30845212
http://dx.doi.org/10.1371/journal.pone.0212746
work_keys_str_mv AT bhanbhavana identificationandexpressionprofilingofmirnasintwocolorvariantsofcarrotdaucuscarotalusingdeepsequencing
AT koularchana identificationandexpressionprofilingofmirnasintwocolorvariantsofcarrotdaucuscarotalusingdeepsequencing
AT sharmadeepak identificationandexpressionprofilingofmirnasintwocolorvariantsofcarrotdaucuscarotalusingdeepsequencing
AT manzoormalikmuzafar identificationandexpressionprofilingofmirnasintwocolorvariantsofcarrotdaucuscarotalusingdeepsequencing
AT kaulsanjana identificationandexpressionprofilingofmirnasintwocolorvariantsofcarrotdaucuscarotalusingdeepsequencing
AT guptasuphla identificationandexpressionprofilingofmirnasintwocolorvariantsofcarrotdaucuscarotalusingdeepsequencing
AT dharmanojk identificationandexpressionprofilingofmirnasintwocolorvariantsofcarrotdaucuscarotalusingdeepsequencing