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Full-length transcriptome sequencing reveals the low-temperature-tolerance mechanism of Medicago falcata roots
BACKGROUND: Low temperature is one of the main environmental factors that limits crop growth, development, and production. Medicago falcata is an important leguminous herb that is widely distributed worldwide. M. falcata is related to alfalfa but is more tolerant to low temperature than alfalfa. Und...
Autores principales: | , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
BioMed Central
2019
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6925873/ https://www.ncbi.nlm.nih.gov/pubmed/31864302 http://dx.doi.org/10.1186/s12870-019-2192-1 |
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author | Cui, Guowen Chai, Hua Yin, Hang Yang, Mei Hu, Guofu Guo, Mingying Yi, Rugeletu Zhang, Pan |
author_facet | Cui, Guowen Chai, Hua Yin, Hang Yang, Mei Hu, Guofu Guo, Mingying Yi, Rugeletu Zhang, Pan |
author_sort | Cui, Guowen |
collection | PubMed |
description | BACKGROUND: Low temperature is one of the main environmental factors that limits crop growth, development, and production. Medicago falcata is an important leguminous herb that is widely distributed worldwide. M. falcata is related to alfalfa but is more tolerant to low temperature than alfalfa. Understanding the low temperature tolerance mechanism of M. falcata is important for the genetic improvement of alfalfa. RESULTS: In this study, we explored the transcriptomic changes in the roots of low-temperature-treated M. falcata plants by combining SMRT sequencing and NGS technologies. A total of 115,153 nonredundant sequences were obtained, and 8849 AS events, 73,149 SSRs, and 4189 lncRNAs were predicted. A total of 111,587 genes from SMRT sequencing were annotated, and 11,369 DEGs involved in plant hormone signal transduction, protein processing in endoplasmic reticulum, carbon metabolism, glycolysis/gluconeogenesis, starch and sucrose metabolism, and endocytosis pathways were identified. We characterized 1538 TF genes into 45 TF gene families, and the most abundant TF family was the WRKY family, followed by the ERF, MYB, bHLH and NAC families. A total of 134 genes, including 101 whose expression was upregulated and 33 whose expression was downregulated, were differentially coexpressed at all five temperature points. PB40804, PB75011, PB110405 and PB108808 were found to play crucial roles in the tolerance of M. falcata to low temperature. WGCNA revealed that the MEbrown module was significantly correlated with low-temperature stress in M. falcata. Electrolyte leakage was correlated with most genetic modules and verified that electrolyte leakage can be used as a direct stress marker in physiological assays to indicate cell membrane damage from low-temperature stress. The consistency between the qRT-PCR results and RNA-seq analyses confirmed the validity of the RNA-seq data and the analysis of the regulatory mechanism of low-temperature stress on the basis of the transcriptome. CONCLUSIONS: The full-length transcripts generated in this study provide a full characterization of the transcriptome of M. falcata and may be useful for mining new low-temperature stress-related genes specific to M. falcata. These new findings could facilitate the understanding of the low-temperature-tolerance mechanism of M. falcata. |
format | Online Article Text |
id | pubmed-6925873 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2019 |
publisher | BioMed Central |
record_format | MEDLINE/PubMed |
spelling | pubmed-69258732019-12-30 Full-length transcriptome sequencing reveals the low-temperature-tolerance mechanism of Medicago falcata roots Cui, Guowen Chai, Hua Yin, Hang Yang, Mei Hu, Guofu Guo, Mingying Yi, Rugeletu Zhang, Pan BMC Plant Biol Research Article BACKGROUND: Low temperature is one of the main environmental factors that limits crop growth, development, and production. Medicago falcata is an important leguminous herb that is widely distributed worldwide. M. falcata is related to alfalfa but is more tolerant to low temperature than alfalfa. Understanding the low temperature tolerance mechanism of M. falcata is important for the genetic improvement of alfalfa. RESULTS: In this study, we explored the transcriptomic changes in the roots of low-temperature-treated M. falcata plants by combining SMRT sequencing and NGS technologies. A total of 115,153 nonredundant sequences were obtained, and 8849 AS events, 73,149 SSRs, and 4189 lncRNAs were predicted. A total of 111,587 genes from SMRT sequencing were annotated, and 11,369 DEGs involved in plant hormone signal transduction, protein processing in endoplasmic reticulum, carbon metabolism, glycolysis/gluconeogenesis, starch and sucrose metabolism, and endocytosis pathways were identified. We characterized 1538 TF genes into 45 TF gene families, and the most abundant TF family was the WRKY family, followed by the ERF, MYB, bHLH and NAC families. A total of 134 genes, including 101 whose expression was upregulated and 33 whose expression was downregulated, were differentially coexpressed at all five temperature points. PB40804, PB75011, PB110405 and PB108808 were found to play crucial roles in the tolerance of M. falcata to low temperature. WGCNA revealed that the MEbrown module was significantly correlated with low-temperature stress in M. falcata. Electrolyte leakage was correlated with most genetic modules and verified that electrolyte leakage can be used as a direct stress marker in physiological assays to indicate cell membrane damage from low-temperature stress. The consistency between the qRT-PCR results and RNA-seq analyses confirmed the validity of the RNA-seq data and the analysis of the regulatory mechanism of low-temperature stress on the basis of the transcriptome. CONCLUSIONS: The full-length transcripts generated in this study provide a full characterization of the transcriptome of M. falcata and may be useful for mining new low-temperature stress-related genes specific to M. falcata. These new findings could facilitate the understanding of the low-temperature-tolerance mechanism of M. falcata. BioMed Central 2019-12-21 /pmc/articles/PMC6925873/ /pubmed/31864302 http://dx.doi.org/10.1186/s12870-019-2192-1 Text en © The Author(s). 2019 Open AccessThis article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated. |
spellingShingle | Research Article Cui, Guowen Chai, Hua Yin, Hang Yang, Mei Hu, Guofu Guo, Mingying Yi, Rugeletu Zhang, Pan Full-length transcriptome sequencing reveals the low-temperature-tolerance mechanism of Medicago falcata roots |
title | Full-length transcriptome sequencing reveals the low-temperature-tolerance mechanism of Medicago falcata roots |
title_full | Full-length transcriptome sequencing reveals the low-temperature-tolerance mechanism of Medicago falcata roots |
title_fullStr | Full-length transcriptome sequencing reveals the low-temperature-tolerance mechanism of Medicago falcata roots |
title_full_unstemmed | Full-length transcriptome sequencing reveals the low-temperature-tolerance mechanism of Medicago falcata roots |
title_short | Full-length transcriptome sequencing reveals the low-temperature-tolerance mechanism of Medicago falcata roots |
title_sort | full-length transcriptome sequencing reveals the low-temperature-tolerance mechanism of medicago falcata roots |
topic | Research Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6925873/ https://www.ncbi.nlm.nih.gov/pubmed/31864302 http://dx.doi.org/10.1186/s12870-019-2192-1 |
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