苹果源云南链核盘菌近染色体水平基因组图谱构建与基因注释

Construction and gene annotation of a near-chromosome level genomic map of a Monilinia yunnanensis strain infecting apple

褐腐病是核果和仁果等水果作物上的重要真菌病害,可导致采前和采后果实腐烂给生产带来重大损失。褐腐病由链核盘菌属真菌侵染引起,在我国有多个病原种,其中云南链核盘菌Moniliniayunnanensis是地理分布和寄主范围均较广的一个优势种,然而其基因组资源国内外尚未见报道。本研究利用三代PacBioHiFi测序技术,组装了一株苹果源云南链核盘菌的高完整度基因组,并对基因组编码基因进行了注释分析。云南链核盘菌组装基因组大小为43.27Mb,共包含16个scaffolds,N50值为2.61Mb。16个scaffolds中有6个两端均有端粒特征重复序列,9个一端有端粒重复序列,表明组装达到近染色体水平。基因组注释共预测到9569个蛋白编码基因,其中68.7%可被PFAM数据库注释。对云南链核盘菌和其他子囊菌基因组的碳水化合物活性酶(CAZYs)进行了比较分析,发现核盘菌科中半纤维素(木聚糖)水解有关的CAZYs家族(CE4、GH2、GH43)呈现收缩进化特征,果胶利用相关的果胶裂解酶(PLs)呈现收缩进化特征,而多聚半乳糖醛酸酶(果胶水解酶,GH28)呈现扩张进化特征,推测这些基因家族的收缩扩张特征与该类真菌的果胶利用适应性进化有关。交配型位点基因分析支持云南链核盘菌为异宗配合真菌,其基因组还编码一个neosartorin同源的次级代谢物基因簇,推测参与致病或子座休眠过程中微生物间的生态位竞争。本研究首次构建云南链核盘菌的近染色体水平基因组图谱,可为后续深入研究该物种的生物学特征、致病机制及群体遗传多样性奠定重要基础。

Brown rot is an important fungal fruit disease that significantly damages the stone and pome fruit industries,causing pre-and post-harvest fruit rots.In China,multiple Monilinia species can cause brown rot diseases,among which M.yunnanensis is one of the most dominant species in terms of host range and geographic distribution.So far,however,genome resource for M.yunnanensis is still not publicly available.In this study,the generation of a high-quality genome of an apple-derived M.yunnanensis strain is assembled based on the third generation PacBio HiFi sequencing technology.The M.yunnanensis assembly was 43.27 Mb in size,made up of 16 scaffolds,with a N50 value of 2.61 Mb.Among the 16 scaffolds,six contained telomere-characteristic repeats at both ends and nine contained repeats at one end,supporting the near-chromosome level of the assembly.A streamed gene annotation pipeline predicted 9569 protein-coding genes,among which 68.7%could be annotated by the PFAM database.Comparison of CAZYs(carbohydrate-active enzyme contents)among M.yunnanensis and other Ascomycota fungi revealed that several CAZY families related to hemicellulose(xylan)degradation showed characteristics of contracted evolution in Sclerotiniaceae.In the meanwhile,bidirectional evolution pattern was observed for PLs(pectin lyases)and GH28(polygalacturonases)in Sclerotiniaceae,with the former showing contraction pattern and the latter showing expansion pattern.Such bidirectional evolution pattern is in line with elevated capacity of pectin utilization of Sclerotiniaceae fungi.Gene composition of mating type locus supports that M.yunnanensis is a heterothallic fungus and its genome encodes a secondary metabolite biosynthesis gene cluster related to neosartorin,which is presumed to function in ecological niche competition during pathogenesis or stroma survival.In sum,a near-chromosome level genomic map of Monilinia yunnanensis is first constructed and annotated,providing a foundation for further studies related to its biological and pathogenic characteristics,and population genetic diversity.