Genome reconstruction of the non-culturable spinach downy mildew Peronospora effusa by metagenome filtering

作者：Joel D. Klein, Manon Neilen, Marcel C. Van Verk, Guido Van den Ackerveken, Bas E. Dutilh · 发表于：bioRxiv (Cold Spring Harbor Laboratory) · 年份：2019 · DOI：10.1101/842658 · 被引用次数：4 · 研究领域：Plant Pathogens and Resistance、Plant Pathogens and Fungal Diseases、Plant-Microbe Interactions and Immunity

Peronospora effusa (previously known as P. farinosa f. sp. spinaciae , and here referred to as Pfs ) is an obligate biotrophic oomycete that causes downy mildew on spinach ( Spinacia oleracea ). To combat this destructive disease resistant cultivars are continually bred. However, new Pfs races rapidly break the employed resistance genes. To get insight into the gene repertoire of Pfs and identify infection-related genes, the genome of the first reference race, Pfs1 , was sequenced, assembled, and annotated. Due to the obligate biotrophic nature of this pathogen, material for DNA isolation can only be collected from infected spinach leaves that, however, also contain many other microorganisms. The obtained sequences are, therefore, considered a metagenome. To filter and obtain Pfs sequences we utilized the CAT tool to taxonomically annotate ORFs residing on long sequences of a genome pre-assembly. This study is the first to show that CAT filtering performs well on eukaryotic contigs. Based on the taxonomy, determined on multiple ORFs, contaminating long sequences and corresponding reads were removed. Filtered reads were re-assembled to provide a clean and improved Pfs genome sequence of 32.40 Mbp consisting of 8,635 scaffolds. Transcript sequencing of a range of infection time points aided the prediction of a total of 13,277 gene models, including 99 RXLR(-like) effector, and 14 putative Crinkler genes. Comparative analysis identified common features in the secretomes of diffe...