Simple sequence repeat markers that identify Claviceps species and strains

Abstract

Background: Claviceps purpurea is a pathogen that infects most members of Pooideae, a subfamily of Poaceae, and causes ergot, a floral disease in which the ovary is replaced with a sclerotium. When the ergot body is accidently consumed by either man or animal in high enough quantities, there is extreme pain, limb loss and sometimes death.Results: This study was initiated to develop simple sequence repeat (SSRs) markers for rapid identification of C. purpurea. SSRs were designed from sequence data stored at the National Center for Biotechnology Information database. The study consisted of 74 ergot isolates, from four different host species, Lolium perenne, Poa pratensis, Bromus inermis, and Secale cereale plus three additional Claviceps species, C. pusilla, C. paspali and C. fusiformis. Samples were collected from six different counties in Oregon and Washington over a 5-year period. Thirty-four SSR markers were selected, which enabled the differentiation of each isolate from one another based solely on their molecular fingerprints. Discriminant analysis of principle components was used to identify four isolate groups, CA Group 1, 2, 3, and 4, for subsequent cluster and molecular variance analyses. CA Group 1 consisting of eight isolates from the host species P. pratensis, was separated on the cluster analysis plot from the remaining three groups and this group was later identified as C. humidiphila. The other three groups were distinct from one another, but closely related. These three groups contained samples from all four of the host species. These SSRs are simple to use, reliable and allowed clear differentiation of C. humidiphila from C. purpurea. Isolates from the three separate species, C. pusilla, C. paspali and C. fusiformis, also amplified with these markers. Conclusions:The SSR markers developed in this study will be helpful in defining the population structure and genetics of Claviceps strains. They will also provide valuable tools for plant breeders needing to identify resistance in crops or for researchers examining fungal movements across environments.

Updating genome annotation for the microbial cell factoryAspergillus nigerusing gene co-expression networks

“…The transcriptional activation of secondary metabolite (SM) gene clusters in different filamentous fungi is one current focus of the fungal research community (16) as >60% of currently approved clinical drugs are derived from natural products (59). A. niger stands out due to its exceptional high number of predicted SM gene clusters in its genome (n = 78), harboring 81 core enzymes in total, such as NRPS and PKS (39).…”

“…More recent sequencing of additional A. niger strains and other genomes from the genus Aspergillus (4–9), combined with refinement of online genome analyses portals (10–12), and comparative genomic studies amongst the Aspergilli (5,13–15), have not significantly increased the percentage of A. niger genes that have functional predictions. While the exact number of ‘hypothetical’ genes varies between databases and A. niger genomes, recent estimates suggest that between 40 and 50% of the genes still remain hypothetical (1,16). Furthermore, only 2% of its genes (n = 247) have a verified function in the Aspergillus Genome Database (AspGD (17)).…”

“…Even for the gold-standard model organism Saccharomyces cerevisiae , 21% of its predicted genes have dubious functional predictions (18), despite its high genetic tractability and a research community with >1,800 research labs worldwide. Indeed, gene functional predictions for A. nidulans, A. fumigatus, A. oryze and other Aspergilli typically cover 40–50% of the genome (16,17).…”

New Draft Genome Sequence of the Ergot Disease Fungus Claviceps paspali

“…C. paspali ILB432 was isolated from sclerotia obtained from Paspalum urvillei -infected inflorescences collected near Portezuelo, Maldonado, Uruguay (global positioning system coordinates 34.888591S, 55.030316W), using a previously reported C. paspali isolation procedure ( 5 ). ILB432 was cultured at 26°C on Claviceps medium containing 36 g/liter potato dextrose agar, 2 g/liter yeast extract, 10 g/liter malt extract, 10 g/liter sucrose, and 5 g/liter agar ( 6 ). Phylogenetic analysis based on the partial gene coding for the second largest subunit of RNA polymerase subunit II ( RPB2 ) showed that ILB432, like reference isolate RRC-1481, belongs to the most frequent lineage of C. paspali ( 5 ).…”

Genomewide identification and development of microsatellite markers for Marssonina brunnea and their applications in two populations

“…Primer development for SSRs is easy and is commonly used between individuals because the flanking regions of microsatellites are well conserved (Vieira et al, 2016). To date, SSRs of various plant pathogens, including several fungal species with biphasic life cycles, have been developed for genetic studies (Della, Eyre, Danti, & Garbelotto, 2011;Devkota, Cornejo, Werth, Chaudhary, & Scheidegger, 2014;Gilmore et al, 2016;Zhang, Chen, Yuan, & Meng, 2015). This study focused on developing microsatellite markers based on the availability of the whole genome sequence of M. brunnea.…”