Transcriptomic Analysis of Multipurpose Timber Yielding Tree Neolamarckia cadamba during Xylogenesis Using RNA-Seq.
Transcriptomic Analysis of Multipurpose Timber Yielding Tree Neolamarckia cadamba during Xylogenesis Using RNA-Seq.
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使用 RNA-Seq 对多用途木材生产树 Neolamarckia cadamba 木质化过程中的转录组分析
DOI：
10.1371/journal.pone.0159407
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发表时间：
2016
期刊：
影响因子：
3.7
通讯作者：
Chen X
中科院分区：
文献类型：
--
作者：
Ouyang K;Li J;Zhao X;Que Q;Li P;Huang H;Deng X;Singh SK;Wu AM;Chen X
Neolamarkia cadamba是一种生长迅速的热带硬木树，广泛用于胶合板和纸浆生产，轻型家具制造，建筑材料，并作为制备某些土著药物的原料。基因组资源的缺乏阻碍了这一多用途树种的分子育种和遗传改良的进展。在这项研究中，转录组分析的分化茎进行了解N。卡丹巴木发生了N.使用Illumina配对末端测序技术对cadamba转录组进行测序。这产生了42.49 G的原始数据，然后重新组装成55，432个平均长度为803.2bp的UniGenes。大约47.8%的UniGenes（26，487）针对生物学上可用的蛋白质数据库进行了注释，其中21，699和7，754个UniGenes分别被分配到基因本体类别（GO）和直系亲属组簇（COG）。使用京都基因和基因组百科全书（KEGG）通路数据库，5，589个UniGenes可以被映射到116个通路上。在木质发生期间表现出差异表达的6，202个UniGenes中，与顶端茎段相比，1，634个在基部和中部茎段中表现出显著更高的表达水平。这些基因包括与次生细胞壁生物合成相关的NAC和MYB转录因子、与木质素生物合成的大多数代谢步骤相关的基因以及与纤维素生物合成相关的CesA基因。本研究为进一步筛选与烟草木质部发生相关的关键基因奠定了基础。cadamba，以及提高我们对速生树木的木质化机制的理解。
Neolamarckia cadamba is a fast-growing tropical hardwood tree that is used extensively for plywood and pulp production, light furniture fabrication, building materials, and as a raw material for the preparation of certain indigenous medicines. Lack of genomic resources hampers progress in the molecular breeding and genetic improvement of this multipurpose tree species. In this study, transcriptome profiling of differentiating stems was performed to understand N. cadamba xylogenesis. The N. cadamba transcriptome was sequenced using Illumina paired-end sequencing technology. This generated 42.49 G of raw data that was then de novo assembled into 55,432 UniGenes with a mean length of 803.2bp. Approximately 47.8% of the UniGenes (26,487) were annotated against publically available protein databases, among which 21,699 and 7,754 UniGenes were assigned to Gene Ontology categories (GO) and Clusters of Orthologous Groups (COG), respectively. 5,589 UniGenes could be mapped onto 116 pathways using the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway database. Among 6,202 UniGenes exhibiting differential expression during xylogenesis, 1,634 showed significantly higher levels of expression in the basal and middle stem segments compared to the apical stem segment. These genes included NAC and MYB transcription factors related to secondary cell wall biosynthesis, genes related to most metabolic steps of lignin biosynthesis, and CesA genes involved in cellulose biosynthesis. This study lays the foundation for further screening of key genes associated with xylogenesis in N. cadamba as well as enhancing our understanding of the mechanism of xylogenesis in fast-growing trees.