Genome sequence and comparative analysis of Colletotrichum gloeosporioides isolated from Liriodendron leaves

First author: Fang-Fang Fu; Affiliations: Nanjing Forestry University (南京林业大学): Nanjing, China

Corresponding author: Jinhui Chen

Colletotrichum gloeosporioides is a hemibiotrophic pathogen causing significant losses to economically important crops and forest trees, including Liriodendron. To explore the interaction between C. gloeosporioides and Liriodendron, and identify the candidate genes determining the pathogenesis, we sequenced and assembled the whole genome of C. gloeosporioides Lc1 (CgLc1) using PacBio and Illumina NGS, and performed a comparative genomic analysis between CgLc1 and Cg01, the latter being a described endophytic species of the C. gloeosporioides complex. Gene structure prediction identified 15,744 protein-coding genes and 837 non-coding RNAs. Species-specific genes were characterized using an ortholog analysis, followed by a pathway enrichment analysis which showed that genes specific to CgLc1 were enriched for the arginine biosynthetic process. Furthermore, genome synteny analysis revealed that most of the protein-coding genes fell into collinear blocks. However, two clusters of polyketide synthase genes were identified to be specific for CgLc1, suggesting they might have an important role in virulence control. Transcriptional regulators co-expressed with polyketide synthase genes were detected through a Weighted Correlation Network Analysis. Taken together, this work provides new insight into the virulence- and pathogenesis-associated genes present in C. gloeosporioides and its possible lifestyle.

胶孢炭疽菌（Colletotrichum gloeosporioides）是一种半活体营养型的病原菌，会造成具有高经济价值的作物和林木的重大损失，其中就包括阔叶树种鹅掌楸。为了探究胶孢炭疽菌与鹅掌楸之间的互作，并鉴定影响胶孢炭疽菌侵染鹅掌楸导致发病的候选基因，作者通过PacBio和Illumina NGS技术测序并组装了来自鹅掌楸叶片中所提取的胶孢炭疽菌（CgLc1）的基因组，并且与胶孢炭疽菌复合物内生物种Cg01进行了比较基因组分析。基因结构预测显示CgLc1基因组编码了15744个蛋白编码基因和837个非编码RNA。通过同源基因分析，作者鉴定了物种特异性基因，并通过通路富集分析揭示了CgLc1基因组特异基因显著富集了精氨酸生物合成通路。此外，基因组共线性分析显示大多数的蛋白都包含在共线性区块内。然而，有两个聚酮合酶（polyketide synthase）基因簇是CgLc1基因组所特有的，说明其可能作用于CgLc1的毒力控制。作者进一步通过WGCNA鉴定了与聚酮合酶基因共表达的转录调控因子。综上，本文的研究为胶孢炭疽菌的毒力和致病相关基因及其可能的生活方式提供了新的见解。

通讯：陈金慧 (http://linxue.njfu.edu.cn/sz/ShowJs.asp?id=259&xb=)

个人简介：1993-1997年，安徽大学，学士；1998-2003年，南京林业大学，博士；2007-2008年，德国弗莱堡大学，博士后。

研究方向：林木细胞工程研究；林木基因编辑及基因工程研究；林木体胚发生的分子机理研究；林木基因组学；林木逆境生理及抗逆基因型育种。

doi: https://doi.org/10.1094/PHYTO-12-19-0452-R

Journal: Phytopathology

Published online: March 23, 2020