Data - Attack of the clones: population genetics reveals clonality of Colletotrichum lupini, the causal agent of lupin anthracnose

<em>Colletotrichum lupini</em>, causing lupin anthracnose, is one of the worst pathogens to lupin cultivation worldwide. Understanding its population structure and evolutionary potential is crucial to design successful disease management strategies. The objective of this study was to employ population genetics to investigate the genetic diversity, evolutionary dynamics and molecular basis of host-speciation of this notorious lupin pathogen. A collection of globally representative <em>C. lupini </em>isolates was genotyped through triple digest restriction-site associated DNA sequencing (3D-RADseq), resulting in a dataset of unparalleled resolution. Phylogenetic and structural analysis could distinguish four (I – IV) independent lineages. The strong population structure, low recombination rate and slow linkage decay strongly indicate that <em>C. lupini</em> reproduces clonally. Different morphologies and virulence patterns on white and Andean lupin were observed between and within clonal lineages. Lineage II isolates were shown to have a mini chromosome which was also partly present in lineage III and IV, but not in lineage I isolates. Variation in the presence of this mini-chromosome could indicate a function related to virulence or host-speciation. All four lineages were present in the South American Andes region, which is concluded to be the center of origin of this species. Only members of lineage II have been found outside South America since the 1990s, indicating it as the current pandemic population. As a seed-borne pathogen, <em>C. lupini</em> has mainly spread through infected but symptomless seeds, stressing the importance of phytosanitary measures to prevent future outbreaks of strains that are yet confined to South America.羽扇豆炭疽病菌（Colletotrichum lupini）是引发羽扇豆炭疽病的病原菌之一，也是全球范围内对羽扇豆种植危害最严重的病原物之一。解析该菌的种群结构与演化潜力，对于制定高效的病害防控策略至关重要。本研究旨在利用种群遗传学方法，探究这一臭名昭著的羽扇豆病原菌的遗传多样性、演化动态以及寄主专化的分子基础。研究团队收集了具有全球代表性的羽扇豆炭疽病菌分离株，通过三酶切限制性位点关联DNA测序（3D-RADseq）进行基因分型，获得了分辨率空前的数据集。系统发育与种群结构分析可将该菌划分为4个独立演化支（I~IV）。显著的种群结构特征、较低的重组率以及缓慢的连锁衰变现象，均强烈表明羽扇豆炭疽病菌以无性繁殖方式繁衍。在无性演化支之间及内部，均可观察到其在白羽扇豆与安第斯羽扇豆上的形态特征与致病模式存在差异。研究发现，演化支II的分离株携带微型染色体，该染色体在演化支III与IV中也有部分存在，但未在演化支I的分离株中检测到。该微型染色体携带情况的差异，可能与其致病力或寄主专化功能相关。南美洲安第斯山脉区域存在全部4个演化支，据此可推断该区域为羽扇豆炭疽病菌的起源中心。自20世纪90年代以来，仅有演化支II的菌株在南美洲以外区域被检出，表明该演化支为当前的大流行种群。作为一种种传病原菌，羽扇豆炭疽病菌主要通过带菌但无明显症状的种子进行传播，这凸显了植物检疫措施的重要性，可有效防范此前仅局限于南美洲的菌株引发未来的病害暴发。