Abstract
Phytopathogenic Ascomycota are responsible for substantial economic losses each year, destroying valuable crops. The present study aims to provide new insights into phytopathogenicity in Ascomycota from a comparative genomic perspective. This has been achieved by categorizing orthologous gene groups (orthogroups) from 68 phytopathogenic and 24 non-phytopathogenic Ascomycota genomes into three classes: Core, (pathogen or non-pathogen) group-specific, and genome-specific accessory orthogroups. We found that (i) ~20% orthogroups are group-specific and accessory in the 92 Ascomycota genomes, (ii) phytopathogenicity is not phylogenetically determined, (iii) group-specific orthogroups have more enriched functional terms than accessory orthogroups and this trend is particularly evident in phytopathogenic fungi, (iv) secreted proteins with signal peptides and horizontal gene transfers (HGTs) are the two functional terms that show the highest occurrence and significance in group-specific orthogroups, (v) a number of other functional terms are also identified to have higher significance and occurrence in group-specific orthogroups. Overall, our comparative genomics analysis determined positive enrichment existing between orthogroup classes and revealed a prediction of what genomic characteristics make an Ascomycete phytopathogenic. We conclude that genes shared by multiple phytopathogenic genomes are more important for phytopathogenicity than those that are unique in each genome.
Highlights
It is estimated that as many as 5.1 million fungal species exist [1]
The most significant finding is that genes shared by multiple phytopathogenic genomes are more important for phytopathogenicity than those that are unique in each genome, which agrees with our previous finding made in pathogenic bacteria [20]
Our results indicated that horizontal gene transfer (HGT) annotations showed higher significance and higher occurrence in group-specific orthogroups than accessory orthogroups (Figures 3 and 4), and that non-phytopathogenic species had a higher occurrence and average significance than phytopathogenic species (Table 1)
Summary
It is estimated that as many as 5.1 million fungal species exist [1]. These organisms exhibit a diverse range of lifestyles, reproductive methods, and morphological structures [2]. The phylum Ascomycota is one of the most diverse, with over 64,000 species [1,3]. Many of these species are saprotrophic in nature, acquiring nutrients through decaying matter and non-living sources. Several species have been shown to possess the capacity to both infect and damage living plants [4]. Infection and destruction of crops by these pathogens causes severe economic and health impact worldwide [5]
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