The complete genome sequence of the phytopathogenic fungus Sclerotinia sclerotiorum reveals insights into the genome architecture of broad host range pathogens.
The complete genome sequence of the phytopathogenic fungus Sclerotinia sclerotiorum reveals insights into the genome architecture of broad host range pathogens.
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植物病原真菌核盘菌的完整基因组序列揭示了对广泛宿主范围病原体的基因组结构的见解。
DOI：
10.1093/gbe/evx030
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发表时间：
2017-03
影响因子：
3.3
通讯作者：
Oliver R
中科院分区：
文献类型：
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作者：
Derbyshire M;Denton-Giles M;Hegedus D;Seifbarghy S;Rollins J;van Kan J;Seidl MF;Faino L;Mbengue M;Navaud O;Raffaele S;Hammond-Kosack K;Heard S;Oliver R
核盘菌（Sclerotinia sclerotiorum）是一种植物病原真菌，有400多种寄主，包括许多重要的栽培种。这与许多经济上具有破坏性的病原体形成对比，这些病原体仅表现出单一或很少的宿主。许多植物病原体表现出“双速”基因组。之所以这样描述，是因为它们的基因组包含交替的基因丰富，重复稀疏和基因贫乏，重复丰富的区域。在真菌中，富含重复序列的区域可能经历称为重复序列诱导的点突变（RIP）的过程。重复序列活性和RIP被认为在分泌的毒力蛋白（称为效应子）的进化中起重要作用。我们提供了一个完整的基因组序列。使用单分子实时测序技术生成核盘菌的RNA序列，其具有使用广泛的RNA测序数据集产生的高度准确的注释。我们确定了70个效应候选人，并强调了他们在植物表达谱。此外，我们还对S.与表现出“双速”基因组的植物病原体相比，核盘菌的基因组更强。我们发现，分泌蛋白的位置和具有高RIP指数的区域在S。但我们没有检测到分泌蛋白比例与GC含量之间的相关性。我们也没有检测到CDS含量和分泌蛋白比例之间的负相关。核盘菌基因组我们的结论是S.核盘菌表现出由于转座和RIP活性而在特定基因组区室中分泌蛋白突变增强的微妙特征。然而，这些特征在全基因组规模上是不可观察的。
Sclerotinia sclerotiorum is a phytopathogenic fungus with over 400 hosts including numerous economically important cultivated species. This contrasts many economically destructive pathogens that only exhibit a single or very few hosts. Many plant pathogens exhibit a “two-speed” genome. So described because their genomes contain alternating gene rich, repeat sparse and gene poor, repeat-rich regions. In fungi, the repeat-rich regions may be subjected to a process termed repeat-induced point mutation (RIP). Both repeat activity and RIP are thought to play a significant role in evolution of secreted virulence proteins, termed effectors. We present a complete genome sequence of S. sclerotiorum generated using Single Molecule Real-Time Sequencing technology with highly accurate annotations produced using an extensive RNA sequencing data set. We identified 70 effector candidates and have highlighted their in planta expression profiles. Furthermore, we characterized the genome architecture of S. sclerotiorum in comparison to plant pathogens that exhibit “two-speed” genomes. We show that there is a significant association between positions of secreted proteins and regions with a high RIP index in S. sclerotiorum but we did not detect a correlation between secreted protein proportion and GC content. Neither did we detect a negative correlation between CDS content and secreted protein proportion across the S. sclerotiorum genome. We conclude that S. sclerotiorum exhibits subtle signatures of enhanced mutation of secreted proteins in specific genomic compartments as a result of transposition and RIP activity. However, these signatures are not observable at the whole-genome scale.