Dipartimento di Biotecnologie, Università degli Studi di Verona, Verona, Italy.
Consiglio per la ricerca in agricoltura e l'analisi dell'economia agraria, Research Centre for Plant Protection and Certification, Rome, Italy.
PLoS One. 2018 Jul 6;13(7):e0200217. doi: 10.1371/journal.pone.0200217. eCollection 2018.
The first draft genome sequencing of the non-model fungal pathogen Pyrenochaeta lycopersici showed an expansion of gene families associated with heterokaryon incompatibility and lacking of mating-type genes, providing insights into the genetic basis of this "imperfect" fungus which lost the ability to produce the sexual stage. However, due to the Illumina short-read technology, the draft genome was too fragmented to allow a comprehensive characterization of the genome, especially of the repetitive sequence fraction. In this work, the sequencing of another P. lycopersici isolate using long-read Single Molecule Real-Time sequencing technology was performed with the aim of obtaining a gapless genome. Indeed, a gapless genome assembly of 62.7 Mb was obtained, with a fraction of repetitive sequences representing 30% of the total bases. The gene content of the two P. lycopersici isolates was very similar, and the large difference in genome size (about 8 Mb) might be attributable to the high fraction of repetitive sequences detected for the new sequenced isolate. The role of repetitive elements, including transposable elements, in modulating virulence effectors is well established in fungal plant pathogens. Moreover, transposable elements are of fundamental importance in creating and re-modelling genes, especially in imperfect fungi. Their abundance in P. lycopersici, together with the large expansion of heterokaryon incompatibility genes in both sequenced isolates, suggest the presence of possible mechanisms alternative to gene re-assorting mediated by sexual recombination. A quite large fraction (~9%) of repetitive elements in P. lycopersici, has no homology with known classes, strengthening this hypothesis. The availability of a gapless genome of P. lycopersici allowed the in-depth analysis of its genome content, by annotating functional genes and TEs. This goal will be an important resource for shedding light on the evolution of the reproductive and pathogenic behaviour of this soilborne pathogen and the onset of a possible speciation within this species.
非模式真菌病原体番茄溃疡病菌的首个基因组草图测序结果显示，与异核体不亲和性相关的基因家族发生扩张，而缺乏交配型基因，这为了解这种失去产生有性阶段能力的“不完美”真菌的遗传基础提供了线索。然而，由于 Illumina 短读测序技术的限制，该草图基因组过于碎片化，无法全面描述基因组，尤其是重复序列部分。在这项工作中，使用长读长单分子实时测序技术对另一个番茄溃疡病菌分离株进行了测序，目的是获得无间隙基因组。实际上，获得了一个无间隙的 62.7Mb 基因组组装，重复序列部分占总碱基的 30%。两个番茄溃疡病菌分离株的基因内容非常相似，而基因组大小的巨大差异（约 8 Mb）可能归因于新测序分离株中检测到的高重复序列部分。重复元件（包括转座元件）在调节真菌植物病原体毒力效应子中的作用已得到充分证实。此外，转座元件在创造和重新构建基因方面具有重要意义，尤其是在不完美真菌中。它们在番茄溃疡病菌中的丰富度，以及在两个测序分离株中异核体不亲和性基因的大量扩张，表明可能存在替代有性重组介导基因重排的可能机制。在番茄溃疡病菌中，约 9%的重复元件具有与已知类别没有同源性，这进一步支持了这一假设。番茄溃疡病菌无间隙基因组的可用性允许对其基因组内容进行深入分析，包括注释功能基因和 TEs。这一目标将为揭示这种土壤病原体生殖和致病行为的进化以及该物种内可能发生的物种形成提供重要资源。
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