The genome of Nectria haematococca: contribution of supernumerary chromosomes to gene expansion
2009
Coleman , Jeffrey J. (University of ArizonaMassachusetts General Hospital, Tucson AZBoston MA(Etats-Unis). Department of Plant Sciences) | Rounsley , Steve D. (University of Arizona, Tucson AZ(Etats-Unis). Institute and Department of Plant Sciences) | Rodriguez-Carres , Marianela (University of ArizonaDuke University, Tucson AZDurham NC(Etats-Unis). Department of Plant SciencesDepartment of Biology) | Kuo , Alan (Joint Genome Institute, Walnut Creek CA(Etats-Unis).) | Wasmann , Catherine C. (University of Arizona, Tucson AZ(Etats-Unis). Department of Plant Sciences) | Grimwood , Jane (Joint Genome InstituteHudson Alpha Genome Sequencing Center, Palo Alto CAHuntsville AL(Etats-Unis). Stanford Human Genome Center) | Schmutz , Jeremy (Joint Genome InstituteHudson Alpha Genome Sequencing Center, Palo Alto CAHuntsville AL(Etats-Unis).) | Taga , Masatoki (Okayama University, Okayama(Japon).) | White , Gerard J. (University of Arizona, Tucson AZ(Etats-Unis). Department of Plant Sciences) | Zhou , Shiguo (University of Wisconsin-Madison, Madison WI(Etats-Unis). Laboratory for Molecule and Computational Genomics) | Schwartz , David C. (University of Wisconsin-Madison, Madison WI(Etats-Unis). Laboratory for Molecule and Computational Genomics) | Freitag , Michael (Oregon State University, Corvallis OR(Etats-Unis). Department of Biochemistry and Biophysics) | Ma , Li-Jun (Broad Institute, Cambridge MA(Etats-Unis).) | Danchin , Etienne (INRA , Sophia Antipolis (France). UMR 1301 Interactions Biotiques en Santé Végétale ) | Henrissat , Bernard (Centre National de la Recherche ScientifiqueUniversité Aix-Marseille 2, MarseilleMarseille(France). UMR 6098 Architecture et Fonction des Macromolécules Biologiques) | Coutinho , Pedro M. (Centre National de la Recherche ScientifiqueUniversité Aix-Marseille 2, Marseille(France). UMR 6098 Architecture et Fonction des Macromolécules Biologiques) | Nelson , David R. (University of Tennessee, Memphis TN(Etats-Unis). Department of Molecular Sciences) | Straney , Dave (University of Maryland, College Park(Etats-Unis). Department of Cell Biology and Molecular Genetics) | Napoli , Carolyn A. (University of Arizona, Tucson AZ(Etats-Unis). Department of Plant Sciences) | Barker , Bridget M. (University of Arizona, Tucson AZ(Etats-Unis). Department of Plant Sciences) | Gribskov , Michael (Purdue University, West Lafayette IN(Etats-Unis). Department of Biological Sciences) | Rep , Martijn (University of Amsterdam(Pays-Bas). Plant Pathology) | Kroken , Scott (University of Arizona, Tucson AZ(Etats-Unis). Department of Plant Sciences) | Molnár , István (University of Arizona, Tucson AZ(Etats-Unis). South West Center for Natural Products Research and Commercialization) | Rensing , Christopher (University of Arizona, Tucson AZ(Etats-Unis). Department of Soil, Water, and Environmental Science) | Kennell , John C. (Saint Louis University, St Louis MO(Etats-Unis). Department of Biology) | Zamora , Jorge (University of Arizona, Tucson AZ(Etats-Unis). Department of Plant Sciences) | Farman , Mark L. (University of Kentucky, Lexington KY(Etats-Unis). Department of Plant Pathology) | Selker , Eric U. (University of Oregon, Eugene OR(Etats-Unis). Institute of Molecular Biology) | Salamov , Asaf (Joint Genome Institute, Walnut Creek CA(Etats-Unis).) | Shapiro , Harris (Joint Genome Institute, Walnut Creek CA(Etats-Unis).) | Pangilinan , Jasmyn (Joint Genome Institute, Walnut Creek CA(Etats-Unis).) | Lindquist , Erika (Joint Genome Institute, Walnut Creek CA(Etats-Unis).) | Lamers , Casey (University of Wisconsin-Madison, Madison WI(Etats-Unis). Laboratory for Molecule and Computational Genomics) | Grigoriev , Igor V. (Joint Genome Institute, Walnut Creek CA(Etats-Unis).) | Geiser , David M. (Pennsylvania State University, University Park PA(Etats-Unis). Department of Plant Pathology) | Covert , Sarah F. (University of Georgia, Athens GA(Etats-Unis). Warnell School of Forestry and Natural Resources) | Temporini , Esteban (University of Arizona, Tucson AZ(Etats-Unis). Department of Plant Sciences) | VanEtten , Hans D. (University of Arizona, Tucson AZ(Etats-Unis). Department of Plant Sciences)
The ascomycetous fungus Nectria haematococca, (asexual name Fusarium solani), is a member of a group of >50 species known as the "Fusarium solani species complex". Members of this complex have diverse biological properties including the ability to cause disease on >100 genera of plants and opportunistic infections in humans. The current research analyzed the most extensively studied member of this complex, N. haematococca mating population VI (MPVI). Several genes controlling the ability of individual isolates of this species to colonize specific habitats are located on supernumerary chromosomes. Optical mapping revealed that the sequenced isolate has 17 chromosomes ranging from 530 kb to 6.52 Mb and that the physical size of the genome, 54.43 Mb, and the number of predicted genes, 15,707, are among the largest reported for ascomycetes. Two classes of genes have contributed to gene expansion: specific genes that are not found in other fungi including its closest sequenced relative, Fusarium graminearum; and genes that commonly occur as single copies in other fungi but are present as multiple copies in N. haematococca MPVI. Some of these additional genes appear to have resulted from gene duplication events, while others may have been acquired through horizontal gene transfer. The supernumerary nature of three chromosomes, 14, 15, and 17, was confirmed by their absence in pulsed field gel electrophoresis experiments of some isolates and by demonstrating that these isolates lacked chromosome-specific sequences found on the ends of these chromosomes. These supernumerary chromosomes contain more repeat sequences, are enriched in unique and duplicated genes, and have a lower G+C content in comparison to the other chromosomes. Although the origin(s) of the extra genes and the supernumerary chromosomes is not known, the gene expansion and its large genome size are consistent with this species' diverse range of habitats. Furthermore, the presence of unique genes on supernumerary chromosomes might account for individual isolates having different environmental niches
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