Data from: Utility of internally transcribed spacer region of rDNA (ITS) and β-tubulin gene sequences to infer genetic diversity and migration patterns of Colletotrichum truncatum infecting Capsicum spp.

Anthracnose is among the most economically important diseases affecting pepper (Capsicum spp.) production in the tropics and subtropics. Of the three species of Colletotrichum implicated as causal agents of pepper anthracnose, C. truncatum is considered to be the most destructive in agro-ecosystems worldwide. However, the genetic variation and the migration potential of C. truncatum infecting pepper are not known. Five populations were selected for study and a two-locus (internally transcribed spacer region, ITS1-5.8S-ITS2, and β-tubulin, β-TUB) sequence data set was generated and used in the analyses. Sequences of the ITS region were less informative than β-tubulin gene sequences based on comparisons of DNA polymorphism indices. Trinidad had the highest genetic diversity and also had the largest effective population size in pairwise comparisons with the other populations. The Trinidad population also demonstrated significant genetic differentiation from the other populations. AMOVA and STRUCTURE analyses both suggested significant genetic variation within populations more so than among populations. A consensus Maximum Likelihood tree based on β-TUB gene sequences revealed very little intraspecific diversity for all isolates except for Trinidad. Two clades consisting solely of Trinidad isolates may have diverged earlier than the other isolates. There was also evidence of directional migration among the five populations. These findings may have a direct impact on the development of integrated disease management strategies to control C. truncatum infection in pepper.炭疽病（Anthracnose）是威胁热带与亚热带地区辣椒（Capsicum spp.）生产的最具经济重要性的病害之一。在被鉴定为辣椒炭疽病致病菌的3种炭疽菌属（Colletotrichum）真菌中，平头炭疽菌（C. truncatum）被认为是全球农业生态系统中破坏性最强的致病菌。然而，侵染辣椒的平头炭疽菌的遗传变异与迁移潜力目前仍未明确。本研究选取5个种群开展研究，构建了包含内转录间隔区（internally transcribed spacer region, ITS1-5.8S-ITS2）与β-微管蛋白基因（β-tubulin, β-TUB）两个基因座的序列数据集并用于分析。通过比对DNA多态性指标可知，内转录间隔区序列的信息含量低于β-微管蛋白基因序列。在与其余种群的成对比较中，特立尼达种群的遗传多样性最高，有效种群规模也最大。该种群与其他所有种群均存在显著的遗传分化。分子变异方差分析（AMOVA）与群体结构分析（STRUCTURE）结果均显示，种群内的遗传变异显著高于种群间。基于β-TUB基因序列构建的一致性最大似然树显示，除特立尼达种群的分离菌株外，其余所有分离菌株的种内多样性极低。仅由特立尼达分离菌株构成的两个进化支的分化时间可能早于其余分离菌株。研究同时发现5个种群间存在定向迁移的证据。上述研究结果可为制定防控辣椒平头炭疽菌侵染的综合病害管理策略提供直接依据。