Abstract
The majority of plant pathogens are fungi and many of these adversely affect food security. This minireview aims to provide an analysis of the plant pathogenic fungi for which genome sequences are publicaNy available, to assess their general genome characteristics, and to consider how genomics has impacted plant pathology. A list of sequenced fungal species was assembled, the taxonomy of all species verified, and the potential reason for sequencing each of the species considered. The genomes of 1090 fungal species are currently (October 2016) in the public domain and this number is rapidly rising. Pathogenic species comprised the largest category (35.5 %) and, amongst these, plant pathogens are predominant. Of the 191 plant pathogenic fungal species with available genomes, 61.3 % cause diseases on food crops, more than half of which are staple crops. The genomes of plant pathogens are slightly larger than those of other fungal species sequenced to date and they contain fewer coding sequences in relation to their genome size. Both of these factors can be attributed to the expansion of repeat elements. Sequenced genomes of plant pathogens provide blueprints from which potential virulence factors were identified and from which genes associated with different pathogenic strategies could be predicted. Genome sequences have also made it possible to evaluate adaptability of pathogen genomes and genomic regions that experience selection pressures. Some genomic patterns, however, remain poorly understood and plant pathogen genomes alone are not sufficient to unravel complex pathogen-host interactions. Genomes, therefore, cannot replace experimental studies that can be complex and tedious. Ultimately, the most promising application lies in using fungal plant pathogen genomics to inform disease management and risk assessment strategies. This will ultimately minimize the risks of future disease outbreaks and assist in preparation for emerging pathogen outbreaks.
Highlights
Sequencing of fungal genomes is being driven by various groups of scientists having different interests and needs from genomic data
We assessed whether pathogens are highly sequenced by FRQVXOWLQJ UHFHQW VFLHQWL¿F OLWHUDWXUH ZKHUH DYDLODEOH RQ each fungal species on the genome list and categorising WKHP DFFRUGLQJ WR WKHLU VLJQL¿FDQFH DQG UHDVRQ IRU EHLQJ VHTXHQFHG 7KH ODUJHVW FDWHJRU\ FRQVLVWHG RI pathogenic fungi and fungi of medical importance (Fig. 4), of which plant pathogens were the most prevalent group &XUUHQWO\ SODQW SDWKRJHQLF VSHFLHV KDYH publically available genomes (Supplementary File 2) and all belong to Dikarya
$V IDU DV ZH DUH DZDUH WKLV UHYLHZ LQFOXGHV WKH ¿UVW comprehensive list of plant pathogenic fungal genomes that KDYH EHHQ VHTXHQFHG WR GDWH :H WKHUHIRUH EULHÀ\ SUHVHQW an overview of the genome characteristics of these species in FRPSDULVRQ WR RWKHU VHTXHQFHG IXQJDO VSHFLHV :H VSHFL¿FDOO\ looked at genome size and the numbers of genes encoded, because previous studies have revealed a link between plant pathogenicity and genome size and gene content (Duplessis et al 2011, Ohm et al 2012, Spanu et al 2010)
Summary
Sequencing of fungal genomes is being driven by various groups of scientists having different interests and needs from genomic data. Mycologists desire genome data to understand how fungi live and evolve, while industries require information on how to improve metabolic pathways RU KRZ WR ¿QG QHZ VRXUFHV RI QDWXUDO SURGXFWV 7KH PHGLFDO and plant pathology sectors need this information to understand diseases, improve diagnoses, understand how they function, and prevent or at least manage disease outbreaks (Kelman 1985).
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