RNA-Seq analysis of differential gene expression in Betula luminifera xylem during the early stages of tension wood formation

PeerJ
Miaomiao CaiMuyuan Zhu

Abstract

Betula luminifera H. Winkler, which is widely distributed in southern China, is an economically important broadleaf tree species. However, little genomic information of B. luminifera is available, and little is known about the molecular mechanisms of wood formation in this species. Meanwhile, few efforts have focused on investigating the early transcriptional changes during tension wood formation in woody plants. A reference transcriptome dataset was first generated containing 45,700 Unigenes, and 35,135 (76.9%) Unigenes were annotated by a BLAST similarity search against four public databases. Then, based on an anatomical investigation, the global gene expression changes during the early stages of tension wood formation were analyzed. Gene expression profiling showed that a total of 13,273 Unigenes were differentially regulated during the early stages of tension wood formation. Most genes involved in cellulose and lignin biosynthesis were highlighted to reveal their biological importance in tension wood formation. In addition, the transcription levels of many genes involved in the auxin response pathway were significantly changed during the early stages of tension wood formation. Furthermore, 18 TFs co-expressed with key enzym...Continue Reading

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Datasets Mentioned

BETA
FJ410442

Methods Mentioned

BETA
RNA-Seq
scanning electron microscopy
fluorescence microscopy
cDNA
PCR
Illumina sequencing

Software Mentioned

Trinity
SOAPaligner
AlignX
BLAST
Blast2GO
BLASTX
WEGO
Cytoscape
MATLAB
SPSS

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