Inter-genome comparison of the Quorn fungus Fusarium venenatum and the closely related plant infecting pathogen Fusarium graminearum.
Inter-genome comparison of the Quorn fungus Fusarium venenatum and the closely related plant infecting pathogen Fusarium graminearum.
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DOI：
10.1186/s12864-018-4612-2
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发表时间：
2018-04-19
期刊：
影响因子：
4.4
通讯作者：
Hammond-Kosack KE
中科院分区：
文献类型：
--
作者：
King R;Brown NA;Urban M;Hammond-Kosack KE
土壤腐坏性非致病性真菌镰刀菌（Fusarium venenatum）在系统发育上与全球重要的谷物和非谷物侵染病原体F. graminearum密切相关，通常用于商业发酵工业。本研究的目的是测序、组装和注释F. venenatum（菌株A3/5）基因组，并将该基因组与F. graminearum进行比较。使用散弹枪测序，将38,660,329 bp的venenatum基因组组装成4条染色体和78,618 bp的线粒体基因组。与F. graminearum相比，13946的预测基因数略低。venenatum的着丝粒比graminearum的小25%。黄颡鱼的染色体长度比黄颡鱼长2.8%，这主要是由于重复元件和转座子的丰度增加，而不是转座子的多样性。在3号染色体上发现了主要的序列重排，但其总体基因含量相对不变。与同thallic graminearum不同，异thallic venenatum具有MAT1-1型位点，但缺乏MAT1-2型位点。与NCBI相比，F. venenatum基因组具有A型trichocene霉菌毒素TRI5簇，而F. graminearum具有b型。据预测，与谷草镰刀菌相比，加注释的镰刀菌基因组具有更多的水解酶编码基因和参与多糖分解的物种特异性基因。两个基因组的比较将先前定义的F. graminearum特异性基因集从741个减少到692个。通过比较禾草镰刀菌和绿足镰刀菌的蛋白质组学，鉴定出15个假定的次级代谢产物基因簇（SMC）、109个分泌蛋白和38个在绿足镰刀菌中未发现的候选效应蛋白。在15个小麦赤霉病特异的SMCs中，有5个在玉米赤霉病基因组中缺失或高度分化，在植物上的表达增加。此外，先前被认为是小麦真菌毒力所必需的两个预测的F. graminearum转录因子缺失或表现出高度序列分化。本研究确定了镰刀菌和谷草镰刀菌基因组之间的差异，这些差异可能导致不同的生活方式，并强调了谷草镰刀菌特异性候选基因和致病机制可能需要的SMCs。本文的在线版本（10.1186/s12864-018-4612-2）包含补充材料，授权用户可以使用。
The soil dwelling saprotrophic non-pathogenic fungus Fusarium venenatum, routinely used in the commercial fermentation industry, is phylogenetically closely related to the globally important cereal and non-cereal infecting pathogen F. graminearum. This study aimed to sequence, assemble and annotate the F. venenatum (strain A3/5) genome, and compare this genome with F. graminearum. Using shotgun sequencing, a 38,660,329 bp F. venenatum genome was assembled into four chromosomes, and a 78,618 bp mitochondrial genome. In comparison to F. graminearum, the predicted gene count of 13,946 was slightly lower. The F. venenatum centromeres were found to be 25% smaller compared to F. graminearum. Chromosome length was 2.8% greater in F. venenatum, primarily due to an increased abundance of repetitive elements and transposons, but not transposon diversity. On chromosome 3 a major sequence rearrangement was found, but its overall gene content was relatively unchanged. Unlike homothallic F. graminearum, heterothallic F. venenatum possessed the MAT1–1 type locus, but lacked the MAT1–2 locus. The F. venenatum genome has the type A trichothecene mycotoxin TRI5 cluster, whereas F. graminearum has type B. From the F. venenatum gene set, 786 predicted proteins were species-specific versus NCBI. The annotated F. venenatum genome was predicted to possess more genes coding for hydrolytic enzymes and species-specific genes involved in the breakdown of polysaccharides than F. graminearum. Comparison of the two genomes reduced the previously defined F. graminearum-specific gene set from 741 to 692 genes. A comparison of the F. graminearum versus F. venenatum proteomes identified 15 putative secondary metabolite gene clusters (SMC), 109 secreted proteins and 38 candidate effectors not found in F. venenatum. Five of the 15 F. graminearum-specific SMCs that were either absent or highly divergent in the F. venenatum genome showed increased in planta expression. In addition, two predicted F. graminearum transcription factors previously shown to be required for fungal virulence on wheat plants were absent or exhibited high sequence divergence. This study identifies differences between the F. venenatum and F. graminearum genomes that may contribute to contrasting lifestyles, and highlights the repertoire of F. graminearum-specific candidate genes and SMCs potentially required for pathogenesis. The online version of this article (10.1186/s12864-018-4612-2) contains supplementary material, which is available to authorized users.
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影响因子：
4.9
作者：
Brown NA;Evans J;Mead A;Hammond-Kosack KE
通讯作者：
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影响因子：
14.9
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