Liu Hui, Ma Xiao, Yu Haiqin, Fang Dunhuang, Li Yongping, Wang Xiao, Wang Wen, Dong Yang, Xiao Bingguang
CAS-Max Planck Junior Research Group, State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223 China ; University of Chinese Academy of Sciences, Beijing, 100049 China.
Yunnan Agricultural University, Kunming, 650100 China.
Gigascience. 2016 Jan 28;5:3. doi: 10.1186/s13742-016-0108-7. eCollection 2016.
Black shank is a severe plant disease caused by the soil-borne pathogen Phytophthora nicotianae. Two physiological races of P. nicotianae, races 0 and 1, are predominantly observed in cultivated tobacco fields around the world. Race 0 has been reported to be more aggressive, having a shorter incubation period, and causing worse root rot symptoms, while race 1 causes more severe necrosis. The molecular mechanisms underlying the difference in virulence between race 0 and 1 remain elusive.
We assembled and annotated the genomes of P. nicotianae races 0 and 1, which were obtained by a combination of PacBio single-molecular real-time sequencing and second-generation sequencing (both HiSeq and MiSeq platforms). Gene family analysis revealed a highly expanded ATP-binding cassette transporter gene family in P. nicotianae. Specifically, more RxLR effector genes were found in the genome of race 0 than in that of race 1. In addition, RxLR effector genes were found to be mainly distributed in gene-sparse, repeat-rich regions of the P. nicotianae genome.
These results provide not only high quality reference genomes of P. nicotianae, but also insights into the infection mechanisms of P. nicotianae and its co-evolution with the host plant. They also reveal insights into the difference in virulence between the two physiological races.
黑胫病是一种由土壤传播的病原菌烟草疫霉引起的严重植物病害。烟草疫霉的两个生理小种，0号和1号小种，在世界各地的栽培烟草田中普遍存在。据报道，0号小种更具侵袭性，潜伏期更短，导致更严重的根腐症状，而1号小种则会引起更严重的坏死。0号和1号小种之间毒力差异的分子机制仍然不清楚。
我们组装并注释了烟草疫霉0号和1号小种的基因组，这些基因组是通过PacBio单分子实时测序和第二代测序（HiSeq和MiSeq平台）相结合获得的。基因家族分析显示烟草疫霉中ATP结合盒转运蛋白基因家族高度扩张。具体而言，在0号小种的基因组中发现的RxLR效应子基因比1号小种的更多。此外，发现RxLR效应子基因主要分布在烟草疫霉基因组中基因稀疏、富含重复序列的区域。
这些结果不仅提供了高质量的烟草疫霉参考基因组，还深入了解了烟草疫霉的感染机制及其与寄主植物的共同进化。它们还揭示了两个生理小种之间毒力差异的见解。
