Lifestyle Transitions in Fusarioid Fungi are Frequent and Lack Clear Genomic Signatures.
Lifestyle Transitions in Fusarioid Fungi are Frequent and Lack Clear Genomic Signatures.
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类镰孢真菌的生活方式转变频繁，缺乏明确的基因组特征。
DOI：
10.1093/molbev/msac085
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发表时间：
2022-04-11
影响因子：
10.7
通讯作者：
Gaya, Ester
中科院分区：
文献类型：
--
作者：
Hill, Rowena;Buggs, Richard J. A.;Dang Toan Vu;Gaya, Ester
真菌镰刀菌属(子囊菌门)包括已知的植物病原菌，它们与世界各地的疾病有关，其中许多已经被基因组测序。该属还包括其他不同的生活方式，包括无处不在的无症状植物居住者(内生植物)物种。在这里，我们为五个内生镰刀菌菌株制作了结构注释的基因组组件，包括第一个赤霉镰刀菌的全基因组数据。镰刀菌属和亲缘关系密切的属的系统基因组重建揭示了多次和频繁的生活方式转变，主要的例外是互惠共生的单系昆虫分支。不同的密码子使用偏向和增加的密码子优化将狭义镰刀菌从近缘属中分离出来。我们对可能参与宿主-真菌相互作用的候选分泌效应蛋白(CSEP)和碳水化合物活性酶(CAZymes)进行了计算预测，并寻找它们的频率可以预测生活方式的证据。然而，系统发育距离比生活方式更好地描述了基因变异。虽然我们确实发现了一些证据表明基因拷贝数变异可能与致病性有关，但植物病原菌和内生菌的CSEP、CAZyme或基因谱系没有显著差异。大量的附属CSEP(即，存在于一个以上的分类群中，但不是全部)和相对较少的菌株特异性CSEP表明，与植物相关的镰刀菌物种之间存在有限的专化性。我们还发现了一半的核心基因处于正选择之下，并确定了特定的CSEP和CAZyme，这些基因预计在某些谱系上是正选择的。我们的研究结果将镰刀菌类真菌描述为多产的通用型真菌，并突出了预测该群体的致病潜力的难度。
The fungal genus Fusarium (Ascomycota) includes well-known plant pathogens that are implicated in diseases worldwide, and many of which have been genome sequenced. The genus also encompasses other diverse lifestyles, including species found ubiquitously as asymptomatic-plant inhabitants (endophytes). Here, we produced structurally annotated genome assemblies for five endophytic Fusarium strains, including the first whole-genome data for Fusarium chuoi. Phylogenomic reconstruction of Fusarium and closely related genera revealed multiple and frequent lifestyle transitions, the major exception being a monophyletic clade of mutualist insect symbionts. Differential codon usage bias and increased codon optimisation separated Fusarium sensu stricto from allied genera. We performed computational prediction of candidate secreted effector proteins (CSEPs) and carbohydrate-active enzymes (CAZymes)—both likely to be involved in the host–fungal interaction—and sought evidence that their frequencies could predict lifestyle. However, phylogenetic distance described gene variance better than lifestyle did. There was no significant difference in CSEP, CAZyme, or gene repertoires between phytopathogenic and endophytic strains, although we did find some evidence that gene copy number variation may be contributing to pathogenicity. Large numbers of accessory CSEPs (i.e., present in more than one taxon but not all) and a comparatively low number of strain-specific CSEPs suggested there is a limited specialisation among plant associated Fusarium species. We also found half of the core genes to be under positive selection and identified specific CSEPs and CAZymes predicted to be positively selected on certain lineages. Our results depict fusarioid fungi as prolific generalists and highlight the difficulty in predicting pathogenic potential in the group.
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影响因子：
3.7
作者：
Álvarez-Loayza P;White JF Jr;Torres MS;Balslev H;Kristiansen T;Svenning JC;Gil N
通讯作者：
Gil N
影响因子：
2.7
作者：
Borowiec ML
通讯作者：
Borowiec ML
影响因子：
1.7
作者：
Ampt, Eline A.;Bush, Daniel S.;Berenbaum, May R.
通讯作者：
Berenbaum, May R.
影响因子：
2.5
作者：
Bilal, Lubna;Asaf, Sajjad;Hussain, Anwar
通讯作者：
Hussain, Anwar
影响因子：
4.5
作者：
Coleman JJ;Rounsley SD;Rodriguez-Carres M;Kuo A;Wasmann CC;Grimwood J;Schmutz J;Taga M;White GJ;Zhou S;Schwartz DC;Freitag M;Ma LJ;Danchin EG;Henrissat B;Coutinho PM;Nelson DR;Straney D;Napoli CA;Barker BM;Gribskov M;Rep M;Kroken S;Molnár I;Rensing C;Kennell JC;Zamora J;Farman ML;Selker EU;Salamov A;Shapiro H;Pangilinan J;Lindquist E;Lamers C;Grigoriev IV;Geiser DM;Covert SF;Temporini E;Vanetten HD
通讯作者：
Vanetten HD