TITLE:
Transcriptome Analysis of Reaction Wood in Gymnosperms by Next-Generation Sequencing
AUTHORS:
Saori Sato, Masato Yoshida, Hideto Hiraide, Kunio Ihara, Hiroyuki Yamamoto
KEYWORDS:
Compression Wood, De Novo Assembly, Differentiating Xylem, RNA-Seq, Transcriptome
JOURNAL NAME:
American Journal of Plant Sciences,
Vol.5 No.18,
August
27,
2014
ABSTRACT: Special xylem tissue called “compression wood” is formed on the lower
side of inclined stems when gymnosperms grow on a slope. We investigated the
molecular mechanism of compression wood formation. Transcriptome analysis by
next-generation sequencing (NGS) was applied to the xylem of Chamaecyparis obtusa to develop a
catalog of general gene expression in differentiating xylem during compression
and normal wood formation. The sequencing output generated 234,924,605 reads
and 40,602 contigs (mean size = 529 bp). Based on a sequence similarity search
with known proteins, 54.2% (22,005) of the contigs showed homology with
sequences in the databases. Of these annotated contigs, 19,293 contigs were
assigned to Gene Ontology categories. Differential gene expression between
the compression and normal wood libraries was analyzed by mapping the reads
from each library to the assembled contigs. In total, 2875 contigs were
identified as differentially expressed, including 1207 that were up-regulated
and 1668 that were down-regulated in compression wood. We selected 30 genes and
compared the transcript abundance between compression and normal wood by
quantitative polymerase chain reaction analysis to validate the NGS results. We
found that 27 of the 30 genes showed the same expression patterns as the
original NGS results.