Transcriptome Analysis of Reaction Wood in Gymnosperms by Next-Generation Sequencing
Transcriptome Analysis of Reaction Wood in Gymnosperms by Next-Generation Sequencing
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DOI：
10.4236/ajps.2014.518295
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发表时间：
2014-08
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影响因子：
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通讯作者：
Saori Sato;Masato Yoshida;Hideto Hiraide;K. Ihara;Hiroyuki Yamamoto
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作者：
Saori Sato;Masato Yoshida;Hideto Hiraide;K. Ihara;Hiroyuki Yamamoto
裸子植物在斜坡上生长时，在倾斜的茎的下侧形成特殊的木质部组织，称为“压缩木材”。我们研究了压缩木材形成的分子机制。应用下一代测序技术(NGS)对木质部进行转录组分析，建立了压缩木质部和正常木材形成过程中木质部分化的通用基因表达谱。测序输出产生234,924,605个读数和40,602个重叠群(平均大小=529个碱基)。根据与已知蛋白质的序列相似性搜索，54.2%(22,005)的重叠群与数据库中的序列具有同源性。在这些注释的重叠群中，19,293个重叠群被分配到基因本体论类别。通过将每个文库的读物映射到组装的重叠群，分析了压缩木材文库和正常木材文库之间的差异基因表达。总共有2875个重叠群被鉴定为差异表达，其中1207个在压缩木材中上调，1668个在压缩木材中下调。我们选择了30个基因，并通过定量聚合酶链式反应比较了压缩木材和正常木材的转录丰度，以验证NGS结果。我们发现，30个基因中有27个与原始NGS结果显示出相同的表达模式。
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.