The genome and transcriptome of Pyronema confluens - a window into fungal evolution

该项目的目的是(A)获得子囊霉菌的基因组序列和全面的转录组，(B)将其用于比较基因组学研究，以揭示丝状真菌的进化起源和发育原理。对于丝状子囊菌的几个主要类群(丝状菌纲、丝状菌纲、欧洲菌纲和丝状菌纲)，基因组序列已经可用；然而，只有一个基因组(松露)从丝状子囊菌的一个成员中被测序，该类群相对于其他丝状子囊菌位于系统发育树的底部。因此，对另外一个平菇菌类的基因组和转录组的分析可以得出子囊菌从简单形式到更复杂形式进化的结论。合生青霉是青霉属中的一员，具有典型的单子实体(无果皮)。此外，合流假单胞菌的生活周期很短，并且易于利用分子技术。在该项目中，将使用下一代测序技术(Roche/454和Illumina/Solexa)对P.confluens基因组进行测序。此外，来自不同发育阶段和生长条件的cDNA将通过Solexa技术(RNA-seq)进行测序，以获得融合P.confluens的全面转录组，以帮助对基因组进行注释。基因组序列和预测的基因和转录本将与其他真菌的基因组序列和预测基因和转录本进行比较。这种比较方法将为丝状子囊菌基因组结构、基因家族和基因表达的进化提供新的见解。

The aims of this project are (a) to obtain the genome sequence and a comprehensive transcriptome of the ascomycete Pyronema confluens and (b) their use for comparative genomics studies to unravel evolutionary origins and developmental principles of filamentous fungi. For several of the major groups of filamentous ascomycetes (Sordariomycetes, Leotiomycetes, Eurotiomycetes, and Dothideomycetes), genome sequences are available already; however, only one genome (truffle) has been sequenced yet from a member of the Pezizomycetes, a group that is situated at the base of the phylogenetic tree relative to the other filamentous ascomycetes. The analysis of an additional Pezizomycete genome and transcriptome will therefore allow conclusions about the evolution of ascomycetes from simple to more complex forms. P. confluens is a member of the Pezizomycetes with a typical simple fruiting body (apothecium). Furthermore, P. confluens has a well-described, short life cycle and is amenable to molecular techniques. Within the project, the P. confluens genome will be sequenced using next-generation sequencing techniques (Roche/454 and Illumina/Solexa). Additionally, cDNAs from different developmental stages and growth conditions will be sequenced by Solexa techniques (RNA-seq) to obtain a comprehensive transcriptome from P. confluens to aid in the annotation of the genome. The genome sequence and predicted genes and transcripts will be compared to those from other fungi. This comparative approach will lead to new insights into the evolution of genome structure, gene families and gene expression in filamentous ascomycetes.