Derbyshire Mark C, Newman Toby E, Khentry Yuphin, Michael Pippa J, Bennett Sarita Jane, Rijal Lamichhane Ashmita, Graham-Taylor Carolyn, Chander Subhash, Camplone Claudia, Vicini Simone, Esquivel-Garcia Laura, Coutu Cathy, Hegedus Dwayne, Clarkson John, Lindbeck Kurt, Kamphuis Lars G
Centre for Crop and Disease Management, Curtin University, Perth, WA, Australia.
Department of Genetics and Plant Breeding, Oilseeds Section, CCS Haryana Agricultural University, Hisar-125004, India.
BMC Biol. 2025 Apr 28;23(1):110. doi: 10.1186/s12915-025-02179-x.
An understanding of plant pathogen evolution is important for sustainable management of crop diseases. Plant pathogen populations must maintain adequate heritable phenotypic variability to survive. Polymorphisms ≥ 50 bp, known as structural variants (SVs), could contribute strongly to this variability by disrupting gene activities. SV acquisition is largely driven by mobile genetic elements called transposons, though a less appreciated source of SVs is erroneous meiotic double-strand break repair. The relative impacts of transposons and recombination on SV diversity and the overall contribution of SVs to phenotypic variability is elusive, especially in host generalists.
We use 25 high-quality genomes to create a graphical pan-genome of the globally distributed host-generalist crop pathogen Sclerotinia sclerotiorum. Outcrossing and recombination rates in this self-fertile species have been debated. Using bisulfite sequencing and short-read data from 190 strains, we show that S. sclerotiorum has many hallmarks of eukaryotic meiosis, including recombination hot and cold spots, centromeric and genic recombination suppression, and rapid linkage disequilibrium decay. Using a new statistic that captures average pairwise structural variation, we show that recombination and transposons make distinct contributions to SV diversity. Furthermore, despite only 5% of genes being dispensable, SVs often had a stronger impact than other variants across 14 life history traits measured in 103 distinct strains.
Transposons and recombination make distinct contributions to SV diversity in S. sclerotiorum. Despite limited gene content diversity, SVs may strongly impact phenotypic variability. This sheds light on the genomic forces shaping adaptive flexibility in host generalists.
了解植物病原体的进化对于作物病害的可持续管理至关重要。植物病原体群体必须保持足够的可遗传表型变异性才能生存。长度≥50bp的多态性，即结构变异（SVs），可能通过破坏基因活性对这种变异性产生重大影响。SV的获得很大程度上由称为转座子的移动遗传元件驱动，不过，SVs的一个较少被认识到的来源是减数分裂错误的双链断裂修复。转座子和重组对SV多样性的相对影响以及SVs对表型变异性的总体贡献尚不清楚，尤其是在寄主广适性病原菌中。
我们使用25个高质量基因组构建了全球分布的寄主广适性作物病原菌核盘菌的图形化泛基因组。这种自交可育物种的异交率和重组率一直存在争议。利用亚硫酸氢盐测序和来自190个菌株的短读长数据，我们表明核盘菌具有真核生物减数分裂的许多特征，包括重组热点和冷点、着丝粒和基因重组抑制以及快速的连锁不平衡衰减。使用一种新的统计方法来捕获平均成对结构变异，我们表明重组和转座子对SV多样性有不同的贡献。此外，尽管只有5%的基因是 dispensable，但在103个不同菌株中测量的14个生活史性状上，SVs的影响通常比其他变异更强。
转座子和重组对核盘菌的SV多样性有不同的贡献。尽管基因含量多样性有限，但SVs可能对表型变异性产生强烈影响。这揭示了塑造寄主广适性病原菌适应性灵活性的基因组力量。
