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Title: The Diaporthe sojae species complex: phylogenetic re-assessment of pathogens associated with soybean, cucurbits and other field crops

Author
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 Biology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 10/28/2014
Publication Date: 5/1/2015
Citation: Udayanga, D., Castlebury, L.A., Rossman, A.Y., Chukeatirote, E., Hyde, K.D. 2015. The Diaporthe sojae species complex: phylogenetic re-assessment of pathogens associated with soybean, cucurbits and other field crops. Fungal Biology. 119(5):383-407.

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 phaseolorum is an important species in this genus as it has been thought to cause diseases of soybeans. It can be isolated from 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 phaselorum, D. sojae and a number of related pathogenic and non-pathogenic species on hosts such as cucumbers, melons 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: Phytopathogenic species of Diaporthe are associated with the serious diseases including seed decay, pod and stem blight and stem canker of soybean leading to considerable loss of crop production worldwide. Accurate identification of the species that cause these diseases has been difficult due to the lack of a recent comprehensive phylogenetic and taxonomic revision. In this study, we revised the phylogenetic placement of the soybean seed decay and pod and stem blight pathogens, D. longicolla and D. sojae, as well as Diaporthe phaseolorum and closely related taxa. Species boundaries of the Diaporthe sojae species complex were determined based on combined phylogenetic analysis of five gene regions: partial sequences of calmodulin (CAL), beta-tubulin (TUB), histone-3 (HIS), translation elongation factor 1-a (EF1-a), and the nuclear ribosomal internal transcribed spacers (ITS). A multi-gene phylogeny inferred for available extype isolates of Diaporthe was used to determine the relative phylogenetic position of the D. sojae species complex with respect to other known Diaporthe species. Phylogenetic analyses revealed that this species complex is comprised of soybean pathogens as well as species associated with hosts in Apiaceae, Asteraceae, Convolvulaceae, Cucurbitaceae, Fabaceae and Solanaceae, including mostly vegetables and other herbaceous field crops and weeds. Diaporthe arctii, D. batatas, D. phaseolorum and D. sojae are epitypified and synonyms are clarified. The seed decay pathogen Diaporthe longicolla was determined to be distinct from D. sojae. Diaporthe phaseolorum associated with stem and leaf blight of Lima bean was not found to be associated with soybean in this study. In addition, Diaporthe cucurbitae, the pathogen causing black rot of cucumbers, was distinguished from D. melonis causing soft rot of cantaloupe. The taxon D. phaseolorum var. brevistylospora, causing concave rot of melon in Japan, is conspecific with D. sojae. A new species, D. ueckerae, associated with Cucumis melo from Oklahoma, is introduced with full description and illustrations.