RNA-seq-Based Gene Annotation and Comparative Genomics of Four Fungal Grass Pathogens in the Genus Zymoseptoria Identify Novel Orphan Genes and Species-Specific Invasions of Transposable Elements.
RNA-seq-Based Gene Annotation and Comparative Genomics of Four Fungal Grass Pathogens in the Genus Zymoseptoria Identify Novel Orphan Genes and Species-Specific Invasions of Transposable Elements.
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DOI：
10.1534/g3.115.017731
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发表时间：
2015-04-27
期刊：
影响因子：
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通讯作者：
Stukenbrock EH
中科院分区：
文献类型：
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作者：
Grandaubert J;Bhattacharyya A;Stukenbrock EH
小麦酵母菌（Zymoseptoria tritici）是小麦的主要病原菌。分离物IPO323的参考基因组是装配最好的真核生物基因组之一，编码超过10,000个预测基因。然而，之前标注的基因模型有很大一部分是不完整的，要么没有开始密码子，要么没有停止密码子。RNA-seq数据的可用性可以更好地预测基因结构。本研究使用两种不同的RNA-seq数据集、从头开始转录组组装、基于同源性的比较和训练从头开始的基因调用者来生成小麦籽粒IPO323的新基因注释。该方法还应用于3个亲缘关系较近的小麦种（Z. pseudotritici， Z. ardabiliae， Z. brevis）的基因组重测序。通过对四种酵母菌的预测基因模型进行比较分析，发现了一组具有物种特异性的孤儿基因，这些孤儿基因富含致病性相关基因，编码可能在毒力和宿主特异性中起重要作用的小分泌蛋白。从头开始重复鉴定使我们能够证明在Zymoseptoria物种之间共享的转座元件很少，而我们观察到许多物种特异性的入侵和扩展。本文提供的注释数据为今后研究小麦霉及其姊妹种提供了高质量的资源，并为植物真菌病原体的基因和基因组进化提供了详细的见解。
The fungal pathogen Zymoseptoria tritici (synonym Mycosphaerella graminicola) is a prominent pathogen of wheat. The reference genome of the isolate IPO323 is one of the best-assembled eukaryotic genomes and encodes more than 10,000 predicted genes. However, a large proportion of the previously annotated gene models are incomplete, with either no start or no stop codons. The availability of RNA-seq data allows better predictions of gene structure. We here used two different RNA-seq datasets, de novo transcriptome assemblies, homology-based comparisons, and trained ab initio gene callers to generate a new gene annotation of Z. tritici IPO323. The annotation pipeline was also applied to re-sequenced genomes of three closely related species of Z. tritici: Z. pseudotritici, Z. ardabiliae, and Z. brevis. Comparative analyses of the predicted gene models using the four Zymoseptoria species revealed sets of species-specific orphan genes enriched with putative pathogenicity-related genes encoding small secreted proteins that may play essential roles in virulence and host specificity. De novo repeat identification allowed us to show that few families of transposable elements are shared between Zymoseptoria species while we observe many species-specific invasions and expansions. The annotation data presented here provide a high-quality resource for future studies of Z. tritici and its sister species and provide detailed insight into gene and genome evolution of fungal plant pathogens.