Department of Plant Protection, College of Agriculture, Northeast Agricultural University, Harbin, China.
Jiamusi Branch of Heilongjiang Academy of Agricultural Sciences, Jiamusi, China.
BMC Genomics. 2020 Feb 19;21(1):172. doi: 10.1186/s12864-020-6581-5.
Recently, a new strain of Cercospora sojina (Race15) has been identified, which has caused the breakdown of resistance in most soybean cultivars in China. Despite this serious yield reduction, little is known about why this strain is more virulent than others. Therefore, we sequenced the Race15 genome and compared it to the Race1 genome sequence, as its virulence is significantly lower. We then re-sequenced 30 isolates of C. sojina from different regions to identifying differential virulence genes using genome-wide association analysis (GWAS).
The 40.12-Mb Race15 genome encodes 12,607 predicated genes and contains large numbers of gene clusters that have annotations in 11 different common databases. Comparative genomics revealed that although these two genomes had a large number of homologous genes, their genome structures have evolved to introduce 245 specific genes. The most important 5 candidate virulence genes were located on Contig 3 and Contig 1 and were mainly related to the regulation of metabolic mechanisms and the biosynthesis of bioactive metabolites, thereby putatively affecting fungi self-toxicity and reducing host resistance. Our study provides insight into the genomic basis of C. sojina pathogenicity and its infection mechanism, enabling future studies of this disease.
Via GWAS, we identified five candidate genes using three different methods, and these candidate genes are speculated to be related to metabolic mechanisms and the biosynthesis of bioactive metabolites. Meanwhile, Race15 specific genes may be linked with high virulence. The genes highly prevalent in virulent isolates should also be proposed as candidates, even though they were not found in our SNP analysis. Future work should focus on using a larger sample size to confirm and refine candidate gene identifications and should study the functional roles of these candidates, in order to investigate their potential roles in C. sojina pathogenicity.
最近，一种新型的大豆尾孢菌（Race15）已经被鉴定出来，它导致了中国大多数大豆品种的抗性崩溃。尽管这种严重的减产，但对于为什么这种菌株比其他菌株更具毒性知之甚少。因此，我们对 Race15 基因组进行了测序，并将其与 Race1 基因组序列进行了比较，因为它的毒性明显较低。然后，我们对来自不同地区的 30 个大豆尾孢菌分离株进行了重新测序，以使用全基因组关联分析（GWAS）来鉴定差异毒性基因。
40.12-Mb 的 Race15 基因组编码了 12607 个预测基因，并包含大量注释在 11 个不同通用数据库中的基因簇。比较基因组学显示，尽管这两个基因组有大量的同源基因，但它们的基因组结构已经进化到引入了 245 个特定基因。最重要的 5 个候选毒性基因位于 Contig 3 和 Contig 1 上，主要与代谢机制的调节和生物活性代谢物的生物合成有关，从而推测影响真菌的自毒性并降低宿主的抗性。我们的研究提供了对大豆尾孢菌致病性及其感染机制的基因组基础的深入了解，为未来对这种疾病的研究提供了参考。
通过 GWAS，我们使用三种不同的方法鉴定了五个候选基因，这些候选基因推测与代谢机制和生物活性代谢物的生物合成有关。同时，Race15 特异性基因可能与高毒性有关。在毒力分离株中高度流行的基因也应该被提出作为候选基因，即使它们在我们的 SNP 分析中没有发现。未来的工作应该集中在使用更大的样本量来确认和细化候选基因的鉴定，并研究这些候选基因的功能作用，以研究它们在大豆尾孢菌致病性中的潜在作用。
