The Alternaria genomes database: a comprehensive resource for a fungal genus comprised of saprophytes, plant pathogens, and allergenic species
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  • 作者：Ha X Dang (1) (4)
    Barry Pryor (2)
    Tobin Peever (3)
    Christopher B Lawrence (1) (3)

    1. Department of Biological Sciences     ; Virginia Tech ; Blacksburg ; Virginia ; 24061 ; USA
    4. Current address     ; Department of Internal Medicine ; Division of Oncology ; and The Genome Institute ; Washington University School of Medicine ; St. Louis ; MO ; 63110 ; USA
    2. Department of Plant Sciences     ; University of Arizona ; Tucson ; Arizona ; 85721 ; USA
    3. Department of Plant Pathology     ; Washington State University ; Pullman ; Washington ; 99164 ; USA
  • 关键词：Database ; Alternaria ; Fungal genome ; Sequence ; Annotation ; Comparative genomics ; Plant pathogen ; Allergy ; Saprophyte
  • 刊名：BMC Genomics
  • 出版年：2015
  • 出版时间：December 2015
  • 年：2015
  • 卷：16
  • 期：1
  • 全文大小：3,253 KB
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  • 刊物主题：Life Sciences, general; Microarrays; Proteomics; Animal Genetics and Genomics; Microbial Genetics and Genomics; Plant Genetics & Genomics;
  • 出版者：BioMed Central
  • ISSN：1471-2164
文摘
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. Description 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. Conclusion 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.

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