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Title: Insights into the genus Diaporthe: phylogenetic species delimitation in the D. eres species complex

item UDAYANGA, DHANUSHKA - Mae Fah Luan University
item Castlebury, Lisa
item ROSSMAN, AMY - Retired ARS Employee
item CHUKEATIROTE, EKACHAI - Mae Fah Luan University
item HYDE, KEVIN - Mae Fah Luan University

Submitted to: Fungal Diversity
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 7/15/2014
Publication Date: 8/8/2014
Citation: Udayanga, D., Castlebury, L.A., Rossman, A.Y., Chukeatirote, E., Hyde, K.D. 2014. Insights into the genus Diaporthe: phylogenetic species delimitation in the D. eres species complex. Fungal Diversity. 67(1):203-229.

Interpretive Summary: Fungi in the genus Diaporthe occur on many different plant hosts with some species causing disease and other co-existing with their host plants without causing disease. Because many species in this genus have similar microscopic appearances, they have traditionally been identified based on their host plant. This has led to much confusion as some species are able to infect multiple plant species. Diaporthe eres is an important species in this genus as it is the type species and serves as the reference point for the entire genus. It causes diseases on a number of different host plants and there has been much confusion about its identity over the years. Using DNA sequences and spore characteristics, we were able to accurately determine the species limits for Diaporthe eres and a number of related pathogenic and non-pathogenic species on hosts such as butternut, grapes, blueberries, pears, and soybeans. This research will be used by extension agents, plant breeders, plant pathologists, and plant quarantine officials to implement management strategies for diseases caused by these species and to accurately determine the presence of these species in the United States and other countries.

Technical Abstract: The genus Diaporthe comprises pathogenic, endophytic and saprobic species with both temperate and tropical distributions. Cryptic diversification, phenotypic plasticity and extensive host associations have long complicated accurate identifications of species in this genus. The delimitation of the generic type species Diaporthe eres has been uncertain due to the lack of ex-type cultures. Species limits of numerous fresh collections and cultures of D. eres and closely related species were evaluated using molecular phylogenetic analysis of eight genes including ITS, partial sequences of actin (ACT), DNA-lyase (Apn2), translation elongation factor 1- a (EF1-a), beta-tubulin (TUB), calmodulin (CAL), 60s ribosomal protein L37 (FG1093) and histone-3 (HIS). The criterion of Genealogical Concordance Phylogenetic Species Recognition (GCPSR) was applied to resolve species boundaries based on individual and combined analyses of the genes used. We accept nine distinct phylogenetic species including Diaporthe alleghaniensis, D. alnea, D. bicincta, D. celastrina, D. eres, D. helicis, D. neilliae, D. pulla and D. vaccinii. Epitypes are designated for D. alnea, D. bicincta, D. celastrina, D. eres, D. helicis and D. pulla. Modern descriptions and illustrations are provided for the resolved species. Newly designed primers are introduced to amplify and sequence the Apn2 (DNA- lyase) gene in Diaporthe. Based on phylogenetic informativeness profiles, EF1-a, Apn2 and HIS genes are recognised as the best markers to define species in the D. eres complex.