Comparative genomics provides new insights into the evolution of Colletotrichum

Colletotrichum is an economically important pathogen with a worldwide distribution associated with a wide range of plant hosts.Characterization of the genomic profiles of Colletotrichum can generate new insights to understand its speciation, diversity, and pathogenicity potential.Although some genomic studies on this genus have been reported, a systematic comparative genomic analysis of the genus has so far been lacking.In this study, we first compared genome completeness generated by second-and third-generation sequencing platforms and confirmed the effectiveness of second-generation sequencing techniques for genomic studies.We then integrated the taxonomic concept of Colletotrichum species complexes into the comparative genomic analysis and depicted the genomic features of 102 Colletotrichum genomes from 39 species across ten species complexes and two singletons.Genome sizes of Colletotrichum species vary tremendously (44.15-109.66Mb), and the average genome sizes of species complexes are significantly different.Repetitive sequences are the key drivers for genome size and GC content variation.The number of predicted genes of each genome (10,809) is positively correlated to the size of non-repeat genome sequences.Phylogenetically close strains consist of similar composition of secretomes, however, the number of major components is significantly different between different species complexes.The C. gloeosporioides species complex possessed the most abundant CAZymes, which may be responsible for its diverse distribution and higher pathogenicity.A total of 7,971 putative SMGCs covering 20 types were detected in these genomes, suggesting their immense biosynthetic potential to produce natural products.We further constructed a genomescale TimeTree of Colletotrichum and investigated the evolution of gene families.The result suggested that gene gain and loss are both important for environmental adaption but less useful in delineating species complexes.Our study characterized the genomes of Colletotrichum species from different perspectives, providing insights into the genomic evolution of Colletotrichum species.