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Deep sequencing-based characterization of transcriptome of trifoliate orange (Poncirus trifoliata (L.) Raf.) in response to cold stress

BACKGROUND: Trifoliate orange (Poncirus trifoliata (L.) Raf.) is extremely cold hardy after a full acclimation; however the underlying molecular mechanisms underlying this economically valuable trait remain poorly understood. In this study, global transcriptome profiles of trifoliate orange under co...

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Autores principales: Wang, Min, Zhang, Xiaona, Liu, Ji-Hong
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2015
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4518522/
https://www.ncbi.nlm.nih.gov/pubmed/26219960
http://dx.doi.org/10.1186/s12864-015-1629-7
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author Wang, Min
Zhang, Xiaona
Liu, Ji-Hong
author_facet Wang, Min
Zhang, Xiaona
Liu, Ji-Hong
author_sort Wang, Min
collection PubMed
description BACKGROUND: Trifoliate orange (Poncirus trifoliata (L.) Raf.) is extremely cold hardy after a full acclimation; however the underlying molecular mechanisms underlying this economically valuable trait remain poorly understood. In this study, global transcriptome profiles of trifoliate orange under cold conditions (4 °C) over a time course were generated by high-throughput sequencing. RESULTS: More than 68 million high-quality reads were produced and assembled into a non-redundant data of 77,292 unigenes with an average length of 1112 bp (N50 = 1778 bp). Of these, 23,846 had significant sequence similarity to known genes and these were assigned to 61 gene ontology (GO) categories and 25 clusters of orthologous groups (COG) involved in 128 KEGG pathways. Sequences derived from cold-treated and control plants were mapped to the assembled transcriptome, resulting in the identification of 5549 differentially expressed genes (DEGs). These comprised 600 (462 up-regulated, 138 down-regulated), 2346 (1631 up-regulated, 715 down-regulated), and 5177 (2702 up-regulated, 2475 down-regulated) genes from the cold-treated samples at 6, 24 and 72 h, respectively. The accuracy of the RNA-seq derived transcript expression data was validated by analyzing the expression patterns of 17 DEGs by qPCR. Plant hormone signal transduction, plant-pathogen interaction, and secondary metabolism were the most significantly enriched GO categories amongst in the DEGs. A total of 60 transcription factors were shown to be cold responsive. In addition, a number of genes involved in the catabolism and signaling of hormones, such as abscisic acid, ethylene and gibberellin, were affected by the cold stress. Meanwhile, levels of putrescine progressively increased under cold, which was consistent with up-regulation of an arginine decarboxylase gene. CONCLUSIONS: This dataset provides valuable information regarding the trifoliate orange transcriptome changes in response to cold stress and may help guide future identification and functional analysis of genes that are importnatn for enhancing cold hardiness. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s12864-015-1629-7) contains supplementary material, which is available to authorized users.
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spelling pubmed-45185222015-07-30 Deep sequencing-based characterization of transcriptome of trifoliate orange (Poncirus trifoliata (L.) Raf.) in response to cold stress Wang, Min Zhang, Xiaona Liu, Ji-Hong BMC Genomics Research Article BACKGROUND: Trifoliate orange (Poncirus trifoliata (L.) Raf.) is extremely cold hardy after a full acclimation; however the underlying molecular mechanisms underlying this economically valuable trait remain poorly understood. In this study, global transcriptome profiles of trifoliate orange under cold conditions (4 °C) over a time course were generated by high-throughput sequencing. RESULTS: More than 68 million high-quality reads were produced and assembled into a non-redundant data of 77,292 unigenes with an average length of 1112 bp (N50 = 1778 bp). Of these, 23,846 had significant sequence similarity to known genes and these were assigned to 61 gene ontology (GO) categories and 25 clusters of orthologous groups (COG) involved in 128 KEGG pathways. Sequences derived from cold-treated and control plants were mapped to the assembled transcriptome, resulting in the identification of 5549 differentially expressed genes (DEGs). These comprised 600 (462 up-regulated, 138 down-regulated), 2346 (1631 up-regulated, 715 down-regulated), and 5177 (2702 up-regulated, 2475 down-regulated) genes from the cold-treated samples at 6, 24 and 72 h, respectively. The accuracy of the RNA-seq derived transcript expression data was validated by analyzing the expression patterns of 17 DEGs by qPCR. Plant hormone signal transduction, plant-pathogen interaction, and secondary metabolism were the most significantly enriched GO categories amongst in the DEGs. A total of 60 transcription factors were shown to be cold responsive. In addition, a number of genes involved in the catabolism and signaling of hormones, such as abscisic acid, ethylene and gibberellin, were affected by the cold stress. Meanwhile, levels of putrescine progressively increased under cold, which was consistent with up-regulation of an arginine decarboxylase gene. CONCLUSIONS: This dataset provides valuable information regarding the trifoliate orange transcriptome changes in response to cold stress and may help guide future identification and functional analysis of genes that are importnatn for enhancing cold hardiness. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s12864-015-1629-7) contains supplementary material, which is available to authorized users. BioMed Central 2015-07-29 /pmc/articles/PMC4518522/ /pubmed/26219960 http://dx.doi.org/10.1186/s12864-015-1629-7 Text en © Wang et al. 2015 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 work is properly credited. 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
Wang, Min
Zhang, Xiaona
Liu, Ji-Hong
Deep sequencing-based characterization of transcriptome of trifoliate orange (Poncirus trifoliata (L.) Raf.) in response to cold stress
title Deep sequencing-based characterization of transcriptome of trifoliate orange (Poncirus trifoliata (L.) Raf.) in response to cold stress
title_full Deep sequencing-based characterization of transcriptome of trifoliate orange (Poncirus trifoliata (L.) Raf.) in response to cold stress
title_fullStr Deep sequencing-based characterization of transcriptome of trifoliate orange (Poncirus trifoliata (L.) Raf.) in response to cold stress
title_full_unstemmed Deep sequencing-based characterization of transcriptome of trifoliate orange (Poncirus trifoliata (L.) Raf.) in response to cold stress
title_short Deep sequencing-based characterization of transcriptome of trifoliate orange (Poncirus trifoliata (L.) Raf.) in response to cold stress
title_sort deep sequencing-based characterization of transcriptome of trifoliate orange (poncirus trifoliata (l.) raf.) in response to cold stress
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4518522/
https://www.ncbi.nlm.nih.gov/pubmed/26219960
http://dx.doi.org/10.1186/s12864-015-1629-7
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