Discovery of Genes Related to Witches Broom Disease in <i>Paulownia tomentosa × Paulownia fortunei</i> by a <i>De Novo</i> Assembled Transcriptome

In spite of its economic importance, very little molecular genetics and genomic research has been targeted at the family Paulownia spp. The little genetic information on this plant is a big obstacle to studying the mechanisms of its ability to resist Paulownia Witches’ Broom (PaWB) disease. Analysis of the Paulownia transcriptome and its expression profile data are essential to extending the genetic resources on this species, thus will greatly improves our studies on Paulownia. In the current study, we performed the de novo assembly of a transcriptome on P. tomentosa × P. fortunei using the short-read sequencing technology (Illumina). 203,664 unigenes with a mean length of 1,328 bp was obtained. Of these unigenes, 32,976 (30% of all unigenes) containing complete structures were chosen. Eukaryotic clusters of orthologous groups, gene orthology, and the Kyoto Encyclopedia of Genes and Genomes annotations were performed of these unigenes. Genes related to PaWB disease resistance were analyzed in detail. To our knowledge, this is the first study to elucidate the genetic makeup of Paulownia. This transcriptome provides a quick way to understanding Paulownia, increases the number of gene sequences available for further functional genomics studies and provides clues to the identification of potential PaWB disease resistance genes. This study has provided a comprehensive insight into gene expression profiles at different states, which facilitates the study of each gene’s roles in the developmental process and in PaWB disease resistance.尽管泡桐属（Paulownia spp.）植物具有重要经济价值，但针对该类群的分子遗传学与基因组学研究却相对匮乏。该物种可用的遗传信息极少，这成为解析其抗泡桐丛枝病（Paulownia Witches’ Broom, PaWB）机制的重大阻碍。对泡桐转录组及其表达谱数据的分析，是丰富该物种遗传资源的关键途径，也将极大推动泡桐相关研究的进展。本研究采用短读长测序技术（Illumina），对毛泡桐×白花泡桐（P. tomentosa × P. fortunei）的转录组进行了从头组装，最终获得203,664条平均长度为1328 bp的单基因（unigene）序列。其中，选取了32,976条（占总单基因数的30%）具备完整结构的单基因序列，并对这些序列开展了真核生物同源蛋白簇（Eukaryotic clusters of orthologous groups, KOG）、基因同源性注释以及京都基因与基因组百科全书（Kyoto Encyclopedia of Genes and Genomes, KEGG）功能注释。针对与泡桐丛枝病抗性相关的基因进行了详细分析。据我们所知，本研究是首个解析泡桐属植物遗传构成的相关研究。该转录组数据为快速解析泡桐属植物提供了便捷途径，扩充了可用于后续功能基因组学研究的基因序列数量，并为潜在抗泡桐丛枝病基因的筛选提供了重要线索。本研究全面解析了不同状态下的基因表达谱，为探究各基因在植物发育过程及泡桐丛枝病抗性中的功能提供了有力支撑。