The multi-speed genome of Fusarium oxysporum reveals association of histone modifications with sequence divergence and footprints of past horizontal chromosome transfer events

作者：Like Fokkens, Shermineh Shahi, Lanelle Connolly, Remco Stam, Sarah M. Schmidt, Kristina Smith, Michael Freitag, Martijn Rep · 发表于：bioRxiv (Cold Spring Harbor Laboratory) · 年份：2018 · DOI：10.1101/465070 · 被引用次数：74 · 研究领域：Plant Pathogens and Fungal Diseases、Plant-Microbe Interactions and Immunity、Plant Disease Resistance and Genetics

Abstract Fusarium oxysporum is an economically important pathogen causing wilting or rotting disease symptoms in a large number of crops. It is proposed to have a structured, “two-speed” genome: i.e. regions containing genes involved in pathogenicity cluster with transposons on separate accessory chromosomes. This is hypothesized to enhance evolvability. Given the continuum of adaptation of all the genes encoded in a genome, however, one would expect a more complex genome structure. By comparing the genome of reference strain Fol4287 to those of 58 other Fusarium oxysporum strains, we found that some Fol4287 accessory chromosomes are lineage-specific, while others occur in multiple lineages with very high sequence similarity - but only in strains that infect the same host as Fol4287. This indicates that horizontal chromosome transfer has been instrumental in past host-switches. Unexpectedly, we found that the sequence of the three smallest core chromosomes (Chr. 11, 12 and 13) is more divergent than that of the other core chromosomes. Moreover, these chromosomes are enriched in genes involved in metabolism and transport and genes that are differentially regulated during infection. Interestingly, these chromosomes are –like the accessory chromosomes– marked by histone H3 lysine 27 trimethylation (H3K27me3) and depleted in histone H3 lysine 4 dimethylation (H3K4me2). Detailed genomic analyses revealed a complex, “multi-speed genome” structure in Fusarium oxysporum . We found a ...