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De novo transcriptome assembly and analysis of gene expression in different tissues of moth bean (Vigna aconitifolia) (Jacq.) Marechal

BACKGROUND: The underutilized species Vigna aconitifolia (Moth Bean) is an important legume crop cultivated in semi-arid conditions and is valued for its seeds for their high protein content. It is also a popular green manure cover crop that offers many agronomic benefits including nitrogen fixation...

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Autores principales: Suranjika, Sandhya, Pradhan, Seema, Nayak, Soumya Shree, Parida, Ajay
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2022
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9013028/
https://www.ncbi.nlm.nih.gov/pubmed/35428206
http://dx.doi.org/10.1186/s12870-022-03583-z
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author Suranjika, Sandhya
Pradhan, Seema
Nayak, Soumya Shree
Parida, Ajay
author_facet Suranjika, Sandhya
Pradhan, Seema
Nayak, Soumya Shree
Parida, Ajay
author_sort Suranjika, Sandhya
collection PubMed
description BACKGROUND: The underutilized species Vigna aconitifolia (Moth Bean) is an important legume crop cultivated in semi-arid conditions and is valued for its seeds for their high protein content. It is also a popular green manure cover crop that offers many agronomic benefits including nitrogen fixation and soil nutrients. Despite its economic potential, genomic resources for this crop are scarce and there is limited knowledge on the developmental process of this plant at a molecular level. In the present communication, we have studied the molecular mechanisms that regulate plant development in V. aconitifolia, with a special focus on flower and seed development. We believe that this study will greatly enrich the genomic resources for this plant in form of differentially expressed genes, transcription factors, and genic molecular markers. RESULTS: We have performed the de novo transcriptome assembly using six types of tissues from various developmental stages of Vigna aconitifolia (var. RMO-435), namely, leaves, roots, flowers, pods, and seed tissue in the early and late stages of development, using the Illumina NextSeq platform. We assembled the transcriptome to get 150938 unigenes with an average length of 937.78 bp. About 79.9% of these unigenes were annotated in public databases and 12839 of those unigenes showed a significant match in the KEGG database. Most of the unigenes displayed significant differential expression in the late stages of seed development as compared with leaves. We annotated 74082 unigenes as transcription factors and identified 12096 simple sequence repeats (SSRs) in the genic regions of V.aconitifolia. Digital expression analysis revealed specific gene activities in different tissues which were validated using Real-time PCR analysis. CONCLUSIONS: The Vigna aconitifolia transcriptomic resources generated in this study provide foundational resources for gene discovery with respect to various developmental stages. This study provides the first comprehensive analysis revealing the genes involved in molecular as well as metabolic pathways that regulate seed development and may be responsible for the unique nutritive values of moth bean seeds. Hence, this study would serve as a foundation for characterization of candidate genes which would not only provide novel insights into understanding seed development but also provide resources for improved moth bean and related species genetic enhancement. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12870-022-03583-z.
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spelling pubmed-90130282022-04-17 De novo transcriptome assembly and analysis of gene expression in different tissues of moth bean (Vigna aconitifolia) (Jacq.) Marechal Suranjika, Sandhya Pradhan, Seema Nayak, Soumya Shree Parida, Ajay BMC Plant Biol Research BACKGROUND: The underutilized species Vigna aconitifolia (Moth Bean) is an important legume crop cultivated in semi-arid conditions and is valued for its seeds for their high protein content. It is also a popular green manure cover crop that offers many agronomic benefits including nitrogen fixation and soil nutrients. Despite its economic potential, genomic resources for this crop are scarce and there is limited knowledge on the developmental process of this plant at a molecular level. In the present communication, we have studied the molecular mechanisms that regulate plant development in V. aconitifolia, with a special focus on flower and seed development. We believe that this study will greatly enrich the genomic resources for this plant in form of differentially expressed genes, transcription factors, and genic molecular markers. RESULTS: We have performed the de novo transcriptome assembly using six types of tissues from various developmental stages of Vigna aconitifolia (var. RMO-435), namely, leaves, roots, flowers, pods, and seed tissue in the early and late stages of development, using the Illumina NextSeq platform. We assembled the transcriptome to get 150938 unigenes with an average length of 937.78 bp. About 79.9% of these unigenes were annotated in public databases and 12839 of those unigenes showed a significant match in the KEGG database. Most of the unigenes displayed significant differential expression in the late stages of seed development as compared with leaves. We annotated 74082 unigenes as transcription factors and identified 12096 simple sequence repeats (SSRs) in the genic regions of V.aconitifolia. Digital expression analysis revealed specific gene activities in different tissues which were validated using Real-time PCR analysis. CONCLUSIONS: The Vigna aconitifolia transcriptomic resources generated in this study provide foundational resources for gene discovery with respect to various developmental stages. This study provides the first comprehensive analysis revealing the genes involved in molecular as well as metabolic pathways that regulate seed development and may be responsible for the unique nutritive values of moth bean seeds. Hence, this study would serve as a foundation for characterization of candidate genes which would not only provide novel insights into understanding seed development but also provide resources for improved moth bean and related species genetic enhancement. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12870-022-03583-z. BioMed Central 2022-04-15 /pmc/articles/PMC9013028/ /pubmed/35428206 http://dx.doi.org/10.1186/s12870-022-03583-z Text en © The Author(s) 2022 https://creativecommons.org/licenses/by/4.0/Open AccessThis article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/ (https://creativecommons.org/licenses/by/4.0/) . The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/ (https://creativecommons.org/publicdomain/zero/1.0/) ) applies to the data made available in this article, unless otherwise stated in a credit line to the data.
spellingShingle Research
Suranjika, Sandhya
Pradhan, Seema
Nayak, Soumya Shree
Parida, Ajay
De novo transcriptome assembly and analysis of gene expression in different tissues of moth bean (Vigna aconitifolia) (Jacq.) Marechal
title De novo transcriptome assembly and analysis of gene expression in different tissues of moth bean (Vigna aconitifolia) (Jacq.) Marechal
title_full De novo transcriptome assembly and analysis of gene expression in different tissues of moth bean (Vigna aconitifolia) (Jacq.) Marechal
title_fullStr De novo transcriptome assembly and analysis of gene expression in different tissues of moth bean (Vigna aconitifolia) (Jacq.) Marechal
title_full_unstemmed De novo transcriptome assembly and analysis of gene expression in different tissues of moth bean (Vigna aconitifolia) (Jacq.) Marechal
title_short De novo transcriptome assembly and analysis of gene expression in different tissues of moth bean (Vigna aconitifolia) (Jacq.) Marechal
title_sort de novo transcriptome assembly and analysis of gene expression in different tissues of moth bean (vigna aconitifolia) (jacq.) marechal
topic Research
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9013028/
https://www.ncbi.nlm.nih.gov/pubmed/35428206
http://dx.doi.org/10.1186/s12870-022-03583-z
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