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Spatiotemporal Transcriptomic Atlas of Developing Embryos and Vegetative Tissues in Flax
Flax (Linum usitatissimum L.) is an important multipurpose crop widely grown for oil and fiber. Despite recent advances in genomics, detailed gene activities during the important reproductive phase of its development are not well defined. In this study, we employed high-throughput RNA-sequencing met...
Autores principales: | , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
MDPI
2022
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9370790/ https://www.ncbi.nlm.nih.gov/pubmed/35956508 http://dx.doi.org/10.3390/plants11152031 |
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author | Gao, Peng Qiu, Shuqing Ma, Xingliang Parkin, Isobel A. P. Xiang, Daoquan Datla, Raju |
author_facet | Gao, Peng Qiu, Shuqing Ma, Xingliang Parkin, Isobel A. P. Xiang, Daoquan Datla, Raju |
author_sort | Gao, Peng |
collection | PubMed |
description | Flax (Linum usitatissimum L.) is an important multipurpose crop widely grown for oil and fiber. Despite recent advances in genomics, detailed gene activities during the important reproductive phase of its development are not well defined. In this study, we employed high-throughput RNA-sequencing methods to generate in-depth transcriptome profiles of flax tissues with emphasis on the reproductive phases of five key stages of embryogenesis (globular embryo, heart embryo, torpedo embryo, cotyledon embryo, and mature embryo), mature seed, and vegetative tissues viz. ovary, anther, and root. These datasets were used to establish the co-expression networks covering 36 gene modules based on the expression patterns for each gene through weighted gene co-expression network analysis (WGCNA). Functional interrogation with Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) of dominantly expressed genetic modules in tissues revealed pathways involved in the development of different tissues. Moreover, the essential genes in embryo development and synthesis of storage reserves were identified based on their dynamic expression patterns. Together, this comprehensive dataset for developing embryos, mature seeds and vegetative tissues provides new insights into molecular mechanisms of seed development with potential for flax crop improvement. |
format | Online Article Text |
id | pubmed-9370790 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2022 |
publisher | MDPI |
record_format | MEDLINE/PubMed |
spelling | pubmed-93707902022-08-12 Spatiotemporal Transcriptomic Atlas of Developing Embryos and Vegetative Tissues in Flax Gao, Peng Qiu, Shuqing Ma, Xingliang Parkin, Isobel A. P. Xiang, Daoquan Datla, Raju Plants (Basel) Article Flax (Linum usitatissimum L.) is an important multipurpose crop widely grown for oil and fiber. Despite recent advances in genomics, detailed gene activities during the important reproductive phase of its development are not well defined. In this study, we employed high-throughput RNA-sequencing methods to generate in-depth transcriptome profiles of flax tissues with emphasis on the reproductive phases of five key stages of embryogenesis (globular embryo, heart embryo, torpedo embryo, cotyledon embryo, and mature embryo), mature seed, and vegetative tissues viz. ovary, anther, and root. These datasets were used to establish the co-expression networks covering 36 gene modules based on the expression patterns for each gene through weighted gene co-expression network analysis (WGCNA). Functional interrogation with Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) of dominantly expressed genetic modules in tissues revealed pathways involved in the development of different tissues. Moreover, the essential genes in embryo development and synthesis of storage reserves were identified based on their dynamic expression patterns. Together, this comprehensive dataset for developing embryos, mature seeds and vegetative tissues provides new insights into molecular mechanisms of seed development with potential for flax crop improvement. MDPI 2022-08-04 /pmc/articles/PMC9370790/ /pubmed/35956508 http://dx.doi.org/10.3390/plants11152031 Text en © 2022 by the authors. https://creativecommons.org/licenses/by/4.0/Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/). |
spellingShingle | Article Gao, Peng Qiu, Shuqing Ma, Xingliang Parkin, Isobel A. P. Xiang, Daoquan Datla, Raju Spatiotemporal Transcriptomic Atlas of Developing Embryos and Vegetative Tissues in Flax |
title | Spatiotemporal Transcriptomic Atlas of Developing Embryos and Vegetative Tissues in Flax |
title_full | Spatiotemporal Transcriptomic Atlas of Developing Embryos and Vegetative Tissues in Flax |
title_fullStr | Spatiotemporal Transcriptomic Atlas of Developing Embryos and Vegetative Tissues in Flax |
title_full_unstemmed | Spatiotemporal Transcriptomic Atlas of Developing Embryos and Vegetative Tissues in Flax |
title_short | Spatiotemporal Transcriptomic Atlas of Developing Embryos and Vegetative Tissues in Flax |
title_sort | spatiotemporal transcriptomic atlas of developing embryos and vegetative tissues in flax |
topic | Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9370790/ https://www.ncbi.nlm.nih.gov/pubmed/35956508 http://dx.doi.org/10.3390/plants11152031 |
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