Gene expression analysis of bud burst process in European hazelnut (Corylus avellana L.) using RNA-Seq

Physiology and Molecular Biology of Plants : an International Journal of Functional Plant Biology
Musa KavasHüseyin İrfan Balık

Abstract

The control of bud burst process depending on temperature is crucial factor in woody perennial plants to survive in unfavorable ecological conditions. Although it has important economic and agronomic values, little information is available on the molecular mechanism of the bud burst process in Corylus avellana. Here for the first time, we conducted a de novo transcriptome-based experiment using eco-dormant leaf bud tissues. Four transcriptome libraries were constructed from the leaf bud tissues and sequenced via Illumina platform. Transcriptome analysis revealed 86,394 unigenes with a mean length of 1189 nt and an N50 of 1916 nt. Among these unigenes, 63,854 (73.78%) of them were annotated by at least one database. De novo assembled transcripts were enriched in phenylpropanoid metabolism, phytohormone biosynthesis and signal transduction pathways. Analyses of phytohormone-associated genes revealed important changes during bud burst, in response to gibberellic acid, auxin, and brassinosteroids. Approximately 2163 putative transcription factors were predicted, of which the largest number of unique transcripts belonged to the MYB transcription factor family. These results contribute to a better understanding of the regulation of b...Continue Reading

References

Sep 1, 1997·Nucleic Acids Research·S F AltschulD J Lipman
Jul 1, 1997·The Plant Journal : for Cell and Molecular Biology·A L SilverstoneT P Sun
Oct 24, 1997·Science·R L TatusovD J Lipman
Oct 10, 1998·Plant Physiology·T GuilfoyleJ Murfett
Mar 6, 1999·Current Opinion in Plant Biology·B Weisshaar, G I Jenkins
Jan 25, 2000·Plant Molecular Biology·H Jin, C Martin
May 3, 2002·Journal of Plant Growth Regulation·José Luis García-Martinez, Joan Gil
Apr 6, 2004·Trends in Plant Science·Muthugapatti K KandasamyRichard B Meagher
May 11, 2006·The New Phytologist·Jérémy DeroryAntoine Kremer
Jan 25, 2007·Journal of Experimental Botany·Luca MazzitelliMark A Taylor
Feb 9, 2007·BMC Bioinformatics·Diego Mauricio Riaño-PachónBernd Mueller-Roeber
Feb 19, 2008·Plant Molecular Biology·Stefan SchwarzPeter Huijser
Jun 13, 2008·Nature Protocols·Thomas D Schmittgen, Kenneth J Livak
Mar 6, 2009·Genome Biology·Ben LangmeadSteven L Salzberg
Mar 7, 2009·Journal of Experimental Botany·Effie Mutasa-Göttgens, Peter Hedden
Aug 26, 2009·Plant Signaling & Behavior·Antje von SchaewenHisashi Koiwa
Dec 26, 2009·Molecular Plant·Thomas Vogt
Sep 16, 2010·BMC Plant Biology·Peter E HedleyRex Brennan
May 17, 2011·Nature Biotechnology·Manfred G GrabherrAviv Regev
Aug 4, 2011·Journal of Thrombosis and Haemostasis : JTH·J A Huntington
Oct 22, 2011·Journal of Experimental Botany·John GardinerJan Marc
Dec 18, 2014·Genome Biology·Michael I LoveSimon Anders
Jun 11, 2015·Bioinformatics·Felipe A SimãoEvgeny M Zdobnov
Jan 1, 2014·Horticulture Research·Donghwan ShimKyung-Hwan Han

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Citations

Oct 23, 2020·Physiology and Molecular Biology of Plants : an International Journal of Functional Plant Biology·Baopeng DingLiulin Li

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Methods Mentioned

BETA
RNA-Seq

Software Mentioned

BUSCO
DeSeq 2 R
TIGR Gene Indices TGICL
BLAST
GetORF
RSEM
Open ORFs ) finder
Trinity
BLASTx
ESTScan

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