title: A Colletotrichum graminicola mutant deficient in the establishment of biotrophy reveals early transcriptional events in the maize anthracnose disease interaction.
abstract: BACKGROUND
  Colletotrichum graminicola is a hemibiotrophic fungal pathogen that causes maize anthracnose disease. It progresses through three recognizable phases of pathogenic development in planta: melanized appressoria on the host surface prior to penetration; biotrophy, characterized by intracellular colonization of living host cells; and necrotrophy, characterized by host cell death and symptom development. A "Mixed Effects" Generalized Linear Model (GLM) was developed and applied to an existing Illumina transcriptome dataset, substantially increasing the statistical power of the analysis of C. graminicola gene expression during infection and colonization. Additionally, the in planta transcriptome of the wild-type was compared with that of a mutant strain impaired in the establishment of biotrophy, allowing detailed dissection of events occurring specifically during penetration, and during early versus late biotrophy.
  
  
  RESULTS
  More than 2000 fungal genes were differentially transcribed during appressorial maturation, penetration, and colonization. Secreted proteins, secondary metabolism genes, and membrane receptors were over-represented among the differentially expressed genes, suggesting that the fungus engages in an intimate and dynamic conversation with the host, beginning prior to penetration. This communication process probably involves reception of plant signals triggering subsequent developmental progress in the fungus, as well as production of signals that induce responses in the host. Later phases of biotrophy were more similar to necrotrophy, with increased production of secreted proteases, inducers of plant cell death, hydrolases, and membrane bound transporters for the uptake and egress of potential toxins, signals, and nutrients.
  
  
  CONCLUSIONS
  This approach revealed, in unprecedented detail, fungal genes specifically expressed during critical phases of host penetration and biotrophic establishment. Many encoded secreted proteins, secondary metabolism enzymes, and receptors that may play roles in host-pathogen communication necessary to promote susceptibility, and thus may provide targets for chemical or biological controls to manage this important disease. The differentially expressed genes could be used as 'landmarks' to more accurately identify developmental progress in compatible versus incompatible interactions involving genetic variants of both host and pathogen.
authors.affiliation: Department of Plant Pathology, University of Kentucky, 201F Plant Science Building, 1405 Veterans Drive, Lexington, KY, 40546-0312, USA. mft2002@qatar-med.cornell.edu.|Present Address: Functional Genomics Laboratory, Weill Cornell Medical College, Cornell University, Qatar Foundation - Education City, Doha, Qatar. mft2002@qatar-med.cornell.edu.
authors.forename: Maria F
authors.initials: MF
authors.lastname: Torres
authors.affiliation: AgriLife Genomics and Bioinformatics, Texas A&M AgriLife Research, Texas A&M University, College Station, TX, 77845, USA. nghaffari@tamu.edu.
authors.forename: Noushin
authors.initials: N
authors.lastname: Ghaffari
authors.affiliation: Department of Plant Pathology, University of Kentucky, 201F Plant Science Building, 1405 Veterans Drive, Lexington, KY, 40546-0312, USA. esterbuiate@uky.edu.|Present Address: Monsanto Company Brazil, Uberlândia, Minas Gerais, Brazil. esterbuiate@uky.edu.
authors.forename: Ester A S
authors.initials: EA
authors.lastname: Buiate
authors.affiliation: Department of Computer Science, University of Kentucky, Davis Marksbury Building, 328 Rose Street, Lexington, KY, 40506-0633, USA. neil@cs.uky.edu.
authors.forename: Neil
authors.initials: N
authors.lastname: Moore
authors.affiliation: AgriLife Genomics and Bioinformatics, Texas A&M AgriLife Research, Texas A&M University, College Station, TX, 77845, USA. scott.schwartz@utexas.edu.|Present Address: Department of Integrative Biology, University of Texas, Austin, TX, 78712, USA. scott.schwartz@utexas.edu.
authors.forename: Scott
authors.initials: S
authors.lastname: Schwartz
authors.affiliation: AgriLife Genomics and Bioinformatics, Texas A&M AgriLife Research, Texas A&M University, College Station, TX, 77845, USA. charlie@ag.tamu.edu.
authors.forename: Charles D
authors.initials: CD
authors.lastname: Johnson
authors.affiliation: Department of Plant Pathology, University of Kentucky, 201F Plant Science Building, 1405 Veterans Drive, Lexington, KY, 40546-0312, USA. vaillan@uky.edu.|Present Address: Department of Integrative Biology, University of Texas, Austin, TX, 78712, USA. vaillan@uky.edu.
authors.forename: Lisa J
authors.initials: LJ
authors.lastname: Vaillancourt
mesh_terms: D020231:Colletotrichum / Q000235:genetics* / Q000472:pathogenicity; D015966:Gene Expression Regulation, Fungal; D005800:Genes, Fungal; D054884:Host-Pathogen Interactions; D016014:Linear Models; D010935:Plant Diseases / Q000382:microbiology*; D012331:RNA, Fungal / Q000235:genetics; D064210:Secondary Metabolism; D017423:Sequence Analysis, RNA; D059467:Transcriptome; D003313:Zea mays / Q000382:microbiology
chemical_list: D012331:RNA, Fungal