Transcript profiling of Populus tomentosa genes in normal, tension, and opposite wood by RNA-seq.
Transcript profiling of Populus tomentosa genes in normal, tension, and opposite wood by RNA-seq.
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DOI：
10.1186/s12864-015-1390-y
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发表时间：
2015-03-10
期刊：
影响因子：
4.4
通讯作者：
Zhang D
中科院分区：
文献类型：
--
作者：
Chen J;Chen B;Zhang D
木材的形成影响木材的化学和物理特性，从而影响其作为建筑材料或生物燃料、纸浆和纸张原料的效用。为了获得木材形成中转录组变化和调控网络的全基因组见解，我们使用高通量RNA测序来表征工业树种毛白杨中张力木（TW），对生木（OW）和正常木（NW）成熟木质部的cDNA文库。我们的测序产生了140，978，316（TW）、128，972，228（OW）和117，672，362（NW）读段，对应于10，127（TW）、10，129（OW）和10，129（NW）独特基因。其中，361个基因在TW和OW之间差异转录（log 2FC ≥ 1或≤-1，FDR < 0.05），2，658个基因在OW和NW之间差异，2，417个基因在TW和NW之间差异。这表明NW与树枝中的木材显著不同; GO术语分析也表明OW经历了更多的转录组重塑。差异表达的基因包括97个转录因子（TF）编码基因、40个激素信号转导相关基因、33个木质素生物合成相关基因、21个类黄酮生物合成相关基因和43个细胞壁代谢相关基因，其中纤维素合成酶、蔗糖合成酶和COBRA基因的差异表达量最大。超过一半的差异表达的TF表现出超过4倍的低转录水平相比，在西北TW或OW，表明TF丰度差异显着不同的木材类型，并可能有重要的作用，在反应木材的形成。此外，与TW相比，OW中参与木质素生物合成的大多数基因的转录本更丰富，与OW中较高的木质素含量一致。基于不同基因的共表达模式，我们构建了两个调控木质素和纤维素生物合成的转录组网络，包括转录因子。最后，我们使用逆转录定量PCR来验证所鉴定的差异表达基因。在这里，我们确定了全球模式和TW，OW和NW之间的基因表达差异，并构建了两个转录调控网络参与TW形成的毛白杨。本研究还为杨树木材品质的分子育种提供了候选基因，为揭示杨树木材形成的分子机制奠定了基础。本文的在线版本（doi：10.1186/s12864-015-1390-y）包含补充材料，可供授权用户使用。
Wood formation affects the chemical and physical properties of wood, and thus affects its utility as a building material or a feedstock for biofuels, pulp and paper. To obtain genome-wide insights on the transcriptome changes and regulatory networks in wood formation, we used high-throughput RNA sequencing to characterize cDNA libraries of mature xylem from tension wood (TW), opposite wood (OW), and normal wood (NW), in the industrial tree species Populus tomentosa. Our sequencing generated 140,978,316 (TW), 128,972,228 (OW), and 117,672,362 (NW) reads, corresponding to 10,127 (TW), 10,129 (OW), and 10,129 (NW) unique genes. Of these, 361 genes were differentially transcribed between TW and OW (log2FC ≥ 1 or ≤ -1, FDR < 0.05), 2,658 differed between OW and NW, and 2,417 differed between TW and NW. This indicates that NW differs significantly from the wood in branches; GO term analysis also indicated that OW experienced more transcriptome remodeling. The differentially expressed genes included 97 encoding transcription factors (TFs), 40 involved in hormone signal transduction, 33 in lignin biosynthesis, 21 in flavonoid biosynthesis, and 43 in cell wall metabolism, including cellulose synthase, sucrose synthase, and COBRA. More than half of the differentially expressed TF showed more than 4-fold lower transcript levels in NW compared with TW or OW, indicating that TF abundances differed dramatically in different wood types and may have important roles in the formation of reaction wood. In addition, transcripts of most of the genes involved in lignin biosynthesis were more abundant in OW compared with TW, consistent with the higher lignin content of OW. We constructed two transcriptomic networks for the regulation of lignin and cellulose biosynthesis, including TFs, based on the co-expression patterns of different genes. Lastly, we used reverse transcription quantitative PCR to validate the differentially expressed genes identified. Here, we identified the global patterns and differences in gene expression among TW, OW, and NW, and constructed two transcriptomic regulatory networks involved in TW formation in P. tomentosa. We also identified candidate genes for molecular breeding of wood quality, and provided a starting point to decipher the molecular mechanisms of wood formation in Populus. The online version of this article (doi:10.1186/s12864-015-1390-y) contains supplementary material, which is available to authorized users.
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1.8
作者：
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DOI：
10.1073/pnas.0900188106
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2009-04-07
影响因子：
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通讯作者：
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