Department of Soil, Plant and Food Sciences - Plant Pathology Section, University of Bari Aldo Moro, via Amendola 165/A, 70126, Bari, Italy.
BMC Genomics. 2018 Jun 5;19(1):436. doi: 10.1186/s12864-018-4817-4.
Brown rots are important fungal diseases of stone and pome fruits. They are caused by several Monilinia species but M. fructicola, M. laxa and M. fructigena are the most common all over the world. Although they have been intensively studied, the availability of genomic and transcriptomic data in public databases is still scant. We sequenced, assembled and annotated the transcriptomes of the three pathogens using mRNA from germinating conidia and actively growing mycelia of two isolates of opposite mating types per each species for comparative transcriptome analyses.
Illumina sequencing was used to generate about 70 million of paired-end reads per species, that were de novo assembled in 33,861 contigs for M. fructicola, 31,103 for M. laxa and 28,890 for M. fructigena. Approximately, 50% of the assembled contigs had significant hits when blasted against the NCBI non-redundant protein database and top-hits results were represented by Botrytis cinerea, Sclerotinia sclerotiorum and Sclerotinia borealis proteins. More than 90% of the obtained sequences were complete, the percentage of duplications was always less than 14% and fragmented and missing transcripts less than 5%. Orthologous transcripts were identified by tBLASTn analysis using the B. cinerea proteome as reference. Comparative transcriptome analyses revealed 65 transcripts over-expressed (FC ≥ 8 and FDR ≤ 0.05) or unique in M. fructicola, 30 in M. laxa and 31 in M. fructigena. Transcripts were involved in processes affecting fungal development, diversity and host-pathogen interactions, such as plant cell wall-degrading and detoxifying enzymes, zinc finger transcription factors, MFS transporters, cell surface proteins, key enzymes in biosynthesis and metabolism of antibiotics and toxins, and transposable elements.
This is the first large-scale reconstruction and annotation of the complete transcriptomes of M. fructicola, M. laxa and M. fructigena and the first comparative transcriptome analysis among the three pathogens revealing differentially expressed genes with potential important roles in metabolic and physiological processes related to fungal morphogenesis and development, diversity and pathogenesis which need further investigations. We believe that the data obtained represent a cornerstone for research aimed at improving knowledge on the population biology, physiology and plant-pathogen interactions of these important phytopathogenic fungi.
褐腐病是石果和仁果的重要真菌病害。它们由几种链格孢菌引起，但在世界范围内，M. fructicola、M. laxa 和 M. fructigena 最为常见。尽管它们已经被深入研究，但公共数据库中基因组和转录组数据的可用性仍然很少。我们使用每个物种的两种交配型的萌发孢子和生长菌丝的 mRNA 进行测序、组装和注释转录组，用于比较转录组分析。
Illumina 测序用于为每个物种生成约 7000 万条配对末端reads，这些reads被从头组装成 33861 个 contigs，用于 M. fructicola、31103 个用于 M. laxa 和 28890 个用于 M. fructigena。大约 50%的组装 contigs 在对 NCBI 非冗余蛋白质数据库进行 Blast 时具有显著的命中，并且 top-hits 结果由 Botrytis cinerea、Sclerotinia sclerotiorum 和 Sclerotinia borealis 蛋白质代表。获得的序列中超过 90%是完整的，重复率始终小于 14%，碎片化和缺失的转录本小于 5%。使用 B. cinerea 蛋白质组作为参考，通过 tBLASTn 分析鉴定了直系同源转录本。比较转录组分析显示，M. fructicola 中有 65 个转录本过表达（FC≥8，FDR≤0.05）或独特，M. laxa 中有 30 个，M. fructigena 中有 31 个。这些转录本参与影响真菌发育、多样性和宿主-病原体相互作用的过程，例如植物细胞壁降解和解毒酶、锌指转录因子、MFS 转运蛋白、细胞表面蛋白、抗生素和毒素生物合成和代谢的关键酶以及转座元件。
这是首次对 M. fructicola、M. laxa 和 M. fructigena 的完整转录组进行大规模重建和注释，也是首次对这三种病原体进行比较转录组分析，揭示了在真菌形态发生和发育、多样性和发病机制相关的代谢和生理过程中具有潜在重要作用的差异表达基因，这些基因需要进一步研究。我们相信，获得的数据代表了旨在提高对这些重要植物病原真菌种群生物学、生理学和植物-病原体相互作用的认识的研究的基石。
