Genome sequences from Alternaria species in section Alternariae

Authors: Fulcher, Michael; BERGSTROM, GARY - Cornell University

Submitted to: Mycological Society of America
Publication Type: Abstract Only
Publication Acceptance Date: 4/14/2021
Publication Date: N/A
Citation: N/A

Interpretive Summary:

Technical Abstract: Fungi in the genus Alternaria are ubiquitous and associated with a variety of plants, animals, and environments. Because Alternaria spp. range from benign saprophytes to economically and clinically important pathogens, the ability to differentiate between species and to understand the evolution of pathogenicity in the genus is of practical importance to both plant health and human medicine. Whole genome sequences have been used to study species from several taxonomic groups within Alternaria, but no comparative genomics analysis has been conducted for members of the section Infectoriae. There are over 25 species currently defined in Alternaria sect. Infectoriae, and several are known to be plant pathogens with restricted geographic ranges. However, species level identification of these fungi using standard morphological and molecular methods is difficult, and their current taxonomic treatment is uncertain, with most species represented by only a single isolate. We generated the first genome sequences for 15 of these species in order to (1) identify genes or genomic features that may be used to delimit or distinguish between species and (2) compare predicted functional genes between isolates collected from different host plants or substrates. Species in Alternaria sect. Alternariae had similar genome sizes (35,945,444 ± 1,485,548 bp) and little repetitive content (3.78 ± 0.70%). Each genome contained 11,260 ± 295 protein coding genes, and on average, 13.96% of proteins were included in a predicted secretome and 1.76% of genes were identified as potential effectors. Protein coding genes were placed into 11,970 groups of orthologues. Single-copy orthologue groups (n = 6727) present in all genomes were used for phylogenetic inference. Maximum parsimony and maximum likelihood tree building methods produced concordant species topologies with a high degree of node support based on bootstrap values. However, cluster analyses using the presence and number of functionally annotated genes (e.g. carbohydrate associated enzymes, protein family categories, and putative effectors) were not concordant with relationships resolved by genome-wide phylogenies. Ongoing work evaluates species boundaries defined by the concordance of ortholog gene trees and the potential use of genes unique to each species for practical identification of new isolates.