title: The Alternaria genomes database: a comprehensive resource for a fungal genus comprised of saprophytes, plant pathogens, and allergenic species.
abstract: BACKGROUND
  Alternaria is considered one of the most common saprophytic fungal genera on the planet. It is comprised of many species that exhibit a necrotrophic phytopathogenic lifestyle. Several species are clinically associated with allergic respiratory disorders although rarely found to cause invasive infections in humans. Finally, Alternaria spp. are among the most well known producers of diverse fungal secondary metabolites, especially toxins.
  
  
  METHODS
  We have recently sequenced and annotated the genomes of 25 Alternaria spp. including but not limited to many necrotrophic plant pathogens such as A. brassicicola (a pathogen of Brassicaceous crops like cabbage and canola) and A. solani (a major pathogen of Solanaceous plants like potato and tomato), and several saprophytes that cause allergy in human such as A. alternata isolates. These genomes were annotated and compared. Multiple genetic differences were found in the context of plant and human pathogenicity, notably the pro-inflammatory potential of A. alternata. The Alternaria genomes database was built to provide a public platform to access the whole genome sequences, genome annotations, and comparative genomics data of these species. Genome annotation and comparison were performed using a pipeline that integrated multiple computational and comparative genomics tools. Alternaria genome sequences together with their annotation and comparison data were ported to Ensembl database schemas using a self-developed tool (EnsImport). Collectively, data are currently hosted using a customized installation of the Ensembl genome browser platform.
  
  
  CONCLUSIONS
  Recent efforts in fungal genome sequencing have facilitated the studies of the molecular basis of fungal pathogenicity as a whole system. The Alternaria genomes database provides a comprehensive resource of genomics and comparative data of an important saprophytic and plant/human pathogenic fungal genus. The database will be updated regularly with new genomes when they become available. The Alternaria genomes database is freely available for non-profit use at http://alternaria.vbi.vt.edu .
authors.affiliation: Department of Biological Sciences, Virginia Tech, Blacksburg, Virginia, 24061, USA. hd@vt.edu.|Current address: Department of Internal Medicine, Division of Oncology, and The Genome Institute, Washington University School of Medicine, St. Louis, MO, 63110, USA. hd@vt.edu.
authors.forename: Ha X
authors.initials: HX
authors.lastname: Dang
authors.affiliation: Department of Plant Sciences, University of Arizona, Tucson, Arizona, 85721, USA. bmpryor@email.arizona.edu.
authors.forename: Barry
authors.initials: B
authors.lastname: Pryor
authors.affiliation: Department of Plant Pathology, Washington State University, Pullman, Washington, 99164, USA. tpeever@wsu.edu.
authors.forename: Tobin
authors.initials: T
authors.lastname: Peever
authors.affiliation: Department of Biological Sciences, Virginia Tech, Blacksburg, Virginia, 24061, USA. cblawren@vt.edu.|Department of Plant Pathology, Washington State University, Pullman, Washington, 99164, USA. cblawren@vt.edu.
authors.forename: Christopher B
authors.initials: CB
authors.lastname: Lawrence
mesh_terms: D000485:Allergens / Q000235:genetics*; D000528:Alternaria / Q000235:genetics* / Q000472:pathogenicity / Q000502:physiology; D030541:Databases, Genetic; D016681:Genome, Fungal
chemical_list: D000485:Allergens