The Alternaria genomes database: a comprehensive resource for a fungal genus comprised of saprophytes, plant pathogens, and allergenic species

Persistent Link:
http://hdl.handle.net/10150/610283
Title:
The Alternaria genomes database: a comprehensive resource for a fungal genus comprised of saprophytes, plant pathogens, and allergenic species
Author:
Dang, Ha X.; Pryor, Barry; Peever, Tobin; Lawrence, Christopher B.
Affiliation:
Department of Biological Sciences, Virginia Tech; Department of Plant Sciences, University of Arizona; Department of Plant Pathology, Washington State University; Department of Internal Medicine, Division of Oncology, and The Genome Institute, Washington University School of Medicine
Issue Date:
2015
Publisher:
BioMed Central Ltd
Citation:
Dang et al. BMC Genomics (2015) 16:239 DOI 10.1186/s12864-015-1430-7
Journal:
BMC Genomics
Rights:
© 2015 Dang et al.; licensee BioMed Central. . This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0)
Collection Information:
This item is part of the UA Faculty Publications collection. For more information this item or other items in the UA Campus Repository, contact the University of Arizona Libraries at repository@u.library.arizona.edu.
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. 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.
EISSN:
1471-2164
DOI:
10.1186/s12864-015-1430-7
Keywords:
Database; Alternaria; Fungal genome; Sequence; Annotation; Comparative genomics; Plant pathogen; Allergy; Saprophyte
Version:
Final published version
Additional Links:
http://www.biomedcentral.com/1471-2164/16/239

Full metadata record

DC FieldValue Language
dc.contributor.authorDang, Ha X.en
dc.contributor.authorPryor, Barryen
dc.contributor.authorPeever, Tobinen
dc.contributor.authorLawrence, Christopher B.en
dc.date.accessioned2016-05-20T09:03:11Z-
dc.date.available2016-05-20T09:03:11Z-
dc.date.issued2015en
dc.identifier.citationDang et al. BMC Genomics (2015) 16:239 DOI 10.1186/s12864-015-1430-7en
dc.identifier.doi10.1186/s12864-015-1430-7en
dc.identifier.urihttp://hdl.handle.net/10150/610283-
dc.description.abstractBACKGROUND: 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.en
dc.language.isoenen
dc.publisherBioMed Central Ltden
dc.relation.urlhttp://www.biomedcentral.com/1471-2164/16/239en
dc.rights© 2015 Dang et al.; licensee BioMed Central. . This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0)en
dc.subjectDatabaseen
dc.subjectAlternariaen
dc.subjectFungal genomeen
dc.subjectSequenceen
dc.subjectAnnotationen
dc.subjectComparative genomicsen
dc.subjectPlant pathogenen
dc.subjectAllergyen
dc.subjectSaprophyteen
dc.titleThe Alternaria genomes database: a comprehensive resource for a fungal genus comprised of saprophytes, plant pathogens, and allergenic speciesen
dc.typeArticleen
dc.identifier.eissn1471-2164en
dc.contributor.departmentDepartment of Biological Sciences, Virginia Techen
dc.contributor.departmentDepartment of Plant Sciences, University of Arizonaen
dc.contributor.departmentDepartment of Plant Pathology, Washington State Universityen
dc.contributor.departmentDepartment of Internal Medicine, Division of Oncology, and The Genome Institute, Washington University School of Medicineen
dc.identifier.journalBMC Genomicsen
dc.description.collectioninformationThis item is part of the UA Faculty Publications collection. For more information this item or other items in the UA Campus Repository, contact the University of Arizona Libraries at repository@u.library.arizona.edu.en
dc.eprint.versionFinal published versionen
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