Deep sequencing-based characterization of transcriptome of trifoliate orange Poncirus trifoliata L. Raf. in response to cold stressReportar como inadecuado




Deep sequencing-based characterization of transcriptome of trifoliate orange Poncirus trifoliata L. Raf. in response to cold stress - Descarga este documento en PDF. Documentación en PDF para descargar gratis. Disponible también para leer online.

BMC Genomics

, 16:555

First Online: 29 July 2015Received: 12 February 2015Accepted: 12 May 2015DOI: 10.1186-s12864-015-1629-7

Cite this article as: Wang, M., Zhang, X. & Liu, JH. BMC Genomics 2015 16: 555. doi:10.1186-s12864-015-1629-7

Abstract

BackgroundTrifoliate 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.

ResultsMore 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.

ConclusionsThis 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.

KeywordsPoncirus trifoliata RNA-seq Cold stress Transcriptome profiling Digital gene expression Citrus AbbreviationsACSAminocyclopropane carboxylic acid ACC synthase

ADCArginine decarboxylase

CACold acclimation

CBFC-repeat CRT-binding factor

CDSsCoding sequences

COGClusters of orthologous groups

CORCold-regulated

DEGsDifferentially expressed genes

DREB1Dehydration-responsive element-binding factors 1

FPKMFragments per kb per million fragments

GOGene ontology

HPLCHigh-performance liquid chromatography

KEGGKyoto encyclopedia of genes and genomes

MAPKMitogen-activated protein kinase

qPCRQuantitative real-time RT-PCR

ODCOrnithine decarboxylase

ROSReactive oxygen species

SAMDCS-adenosylmethionine decarboxylase

SPDSSpermidine synthase

SPMSSpermine synthase

TFTranscription factor

Electronic supplementary materialThe 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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Autor: Min Wang - Xiaona Zhang - Ji-Hong Liu

Fuente: https://link.springer.com/







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