Sequencing of the genome of Clonostachys rosaea IK726. Clonostachys rosea f. rosea IK726

Clonostachys rosea is a mycoparasitic fungus that can control several important plant diseases. Here we report on the genome sequencing of C. rosea and a comparative genome analysis, in order to resolve the phylogenetic placement of C. rosea and to study the evolution of mycoparasitism as a fungal lifestyle. The genome of C. rosea is estimated to 58.3 Mbp, and contains 14268 predicted genes. A phylogenomic analysis shows that C. rosea clusters as sister taxon to plant pathogenic Fusarium species, with mycoparasitic/saprotrophic Trichoderma species in an ancestral position. A comparative analysis of gene family evolution reveals several distinct differences between the included mycoparasites. C. rosea contains significantly more ATP-binding cassette (ABC) transporters, polyketide synthases, cytochrome P450 monooxygenases, pectin lyases, glucose-methanol-choline oxidoreductases and lytic polysaccharide monooxygenases compared with other fungi in the Hypocreales. Interestingly, the increase of ABC transporter gene number in C. rosea is associated with phylogenetic subgroups B (multidrug resistance proteins) and G (pleiotropic drug resistance transporters), while an increase in subgroup C (multidrug resistance–associated proteins) is evident in T. virens. In contrast with mycoparasitic Trichoderma species, C. rosea contains very few chitinases. Expression of six group B and group G ABC transporter genes were induced in C. rosea during exposure to the Fusarium mycotoxin zearalenone, the fungicide Boscalid or metabolites from the biocontrol bacterium Pseudomonas chlororaphis. The data suggests that tolerance towards secondary metabolites is a prominent feature in the biology of C. rosea.

粉红粘帚霉（Clonostachys rosea）是一种菌寄生真菌，可防控多种重要植物病害。本研究报道了该菌的基因组测序及比较基因组分析结果，旨在明确其系统发育定位，并探究菌寄生作为一类真菌生活方式的演化历程。粉红粘帚霉的基因组大小预估为58.3 Mbp，共预测得到14268个编码基因。系统发育组学分析显示，该菌与植物致病的镰刀菌属（Fusarium）物种构成姊妹群，而菌寄生/腐生的木霉属（Trichoderma）物种则处于更为原始的演化地位。比较基因家族演化分析发现，纳入本研究的各类菌寄生真菌间存在多处显著差异。与肉座菌目（Hypocreales）的其他真菌相比，粉红粘帚霉拥有更多的ATP结合盒（ATP-binding cassette, ABC）转运蛋白、聚酮合酶、细胞色素P450单加氧酶、果胶裂解酶、葡萄糖-甲醇-胆碱氧化还原酶及溶解性多糖单加氧酶。值得注意的是，粉红粘帚霉的ABC转运蛋白基因数量扩增与系统发育亚型B（多药耐药蛋白）及G（多效耐药转运蛋白）密切相关；而深绿木霉（T. virens）中则可见亚型C（多药耐药相关蛋白）基因数量的显著扩增。与菌寄生木霉属物种不同，粉红粘帚霉所含几丁质酶数量极少。当粉红粘帚霉暴露于镰刀菌属真菌产生的毒素玉米赤霉烯酮、杀菌剂啶酰菌胺（Boscalid），或是生防细菌绿针假单胞菌（Pseudomonas chlororaphis）的代谢产物时，其6个B型和G型ABC转运蛋白基因的表达均被诱导上调。本研究数据表明，对次生代谢产物的耐受性是粉红粘帚霉生物学特性中的一项突出特征。