Muterko Alexandr, Surina Tatyana, Dobrovolskaya Oxana
FRC Institute of Cytology and Genetics SB RAS, Lavrentyeva Avenue 10, Novosibirsk, 630090, Russian Federation.
All-Russian Plant Quarantine Center (FGBU VNIIKR), Bykovo, Ramenskoye, Moscow Oblast, Russian Federation.
Appl Microbiol Biotechnol. 2023 Feb;107(4):1311-1327. doi: 10.1007/s00253-023-12370-1. Epub 2023 Jan 18.
Diaporthe caulivora is an economically important fungal pathogen and a causal agent of soybean stem canker and seed decay. Here, the genome of a Russian Far Eastern isolate of D. caulivora was sequenced, assembled, and announced. Assembly quality was enough for advanced annotation, including prediction of potential disease-related genes encoding virulence factors and molecular determinants contributing to pathogen-host selection, interactions, and adaptation. Comparative analysis of 15 Diaporthe species was conducted regarding general genome properties, collinearity, and proteomes, and included detailed investigation of interspersed repeats. A notable feature of this analysis is a high recombinant variability of Diaporthe genomes, determined by the number and distribution of interspersed repeats, which also proved to be responsible for the diversity of GC content and genome size. This variability is assumed the main determinant of the divergence of Diaporthe genomes. A Bayesian multi-gene phylogeny was inferred for the 15 Diaporthe species on the basis of twenty thousand polymorphic sites of > 100 orthologous genes using independently adjusted evolutionary models. This allowed for the most accurate determination of evolutionary relationships and species boundaries for effective reporting about these plant pathogens. The evidence, obtained by different genome analysis techniques, implies the host-independent evolution of Diaporthe species. KEY POINTS: • The genome of a Far Eastern isolate of D. caulivora was announced. • A high degree of recombinant variability determines genomic divergence in Diaporthe genus. • The multi-gene phylogeny implies host-independent evolution of Diaporthe species.
菜生间座壳菌是一种具有重要经济意义的真菌病原体，也是大豆茎溃疡病和种子腐烂病的病原体。在此，对一株俄罗斯远东地区的菜生间座壳菌分离株的基因组进行了测序、组装和公布。组装质量足以进行高级注释，包括预测潜在的与疾病相关的基因，这些基因编码毒力因子以及有助于病原体与宿主选择、相互作用和适应的分子决定因素。对15种间座壳菌的基因组特性、共线性和蛋白质组进行了比较分析，其中包括对散布重复序列的详细研究。该分析的一个显著特征是间座壳菌基因组具有高度的重组变异性，这由散布重复序列的数量和分布决定，同时也被证明是GC含量和基因组大小多样性的原因。这种变异性被认为是间座壳菌基因组分化的主要决定因素。基于一万个多态性位点的超过100个直系同源基因，使用独立调整的进化模型，为15种间座壳菌推断了贝叶斯多基因系统发育树。这使得能够最准确地确定进化关系和物种界限，以便有效地报告这些植物病原体。通过不同基因组分析技术获得的证据表明间座壳菌物种的进化与宿主无关。要点：•公布了远东地区菜生间座壳菌分离株的基因组。•高度的重组变异性决定了间座壳菌属的基因组分化。•多基因系统发育意味着间座壳菌物种的进化与宿主无关。
