In silico analysis to understand genetic variability, phylogenetic and phylogeographic relationships between Phytophthora capsici isolates infecting various crops

Phytophthora capsici is a major oomycete-based pathogen causing enormous damage to the productivity of peppers and other major crops from different families worldwide by causing fruit rot, root rot and foliar blight diseases. This study utilized molecular signatures present within ITS1-5.8S rRNA-ITS2 and Ras-related GTP binding protein (Ypt1) genes to evaluate haplotype variability and phylogenetic relationships among P. capsici isolates with significant epidemiological implications. Twelve different evolutionary lineages specific to particular hosts and/or geographical regions and differed by SNPs, and 30 haplotypes with maximum diversity in India and Pakistan, were identified by sequence analysis of the ITS regions. It includes country-specific lineages Pc-I and Pc-II in India with multiple host ranges; capsicum-specific lineages Pc-IV, Pc-V and Pc-VIII from Pakistan; papaya-specific lineages Pc-VI from China, and watermelon-specific lineages Pc-VII and Pc-XI from USA. Many lineages showed cross-border infections, such as Pc-III and Pc-X in India and Pakistan, Cocoa-specific lineage Pc-IX in Brazil and Cote d’Ivoire, and Capsicum-specific multi-continental lineage Pc-XII. Similarly, 11 different SNP lineages and 32 haplotypes with maximum diversity in China were identified for the Ypt1 gene. These findings would be very useful for epidemiological surveillance of P. capsici strains worldwide, understanding population and evolutionary dynamics, developing lineage- and haplotype-specific diagnostic assays and disease-resistant varieties.

辣椒疫霉（Phytophthora capsici）是一种主要的卵菌（oomycete）类病原物，可通过引发果实腐烂、根腐与叶枯病，对全球范围内辣椒及其他多科主要作物的产量造成毁灭性损失。本研究借助ITS1-5.8S rRNA-ITS2区间与Ras相关GTP结合蛋白（Ypt1）基因中的分子标记，对具有重要流行病学意义的辣椒疫霉分离株的单倍型多样性及系统发育关系进行了评估。通过对ITS区域的序列分析，共鉴定出12个以单核苷酸多态性（Single Nucleotide Polymorphism, SNP）区分、针对特定宿主或地理区域的独特进化谱系，以及30个单倍型，其中印度与巴基斯坦的单倍型多样性最高。其中包括印度宿主范围广泛的国家特异性谱系Pc-I与Pc-II；巴基斯坦的辣椒特异性谱系Pc-IV、Pc-V与Pc-VIII；中国的木瓜特异性谱系Pc-VI；以及美国的西瓜特异性谱系Pc-VII与Pc-XI。多个进化谱系呈现跨境侵染特征：例如在印度与巴基斯坦均有分布的Pc-III与Pc-X；巴西及科特迪瓦的可可特异性谱系Pc-IX；以及跨大陆分布的辣椒特异性谱系Pc-XII。同理，针对Ypt1基因的序列分析共鉴定出11个不同的SNP谱系与32个单倍型，其中中国的单倍型多样性最高。上述研究结果可为全球辣椒疫霉菌株的流行病学监测、种群与进化动态解析、谱系及单倍型特异性诊断试剂开发以及抗病品种培育提供关键参考依据。