title: The genome of Nectria haematococca: contribution of supernumerary chromosomes to gene expansion.
abstract: 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.
authors.affiliation: Department of Plant Sciences, University of Arizona, Tucson, Arizona, United States of America.
authors.forename: Jeffrey J
authors.initials: JJ
authors.lastname: Coleman
authors.forename: Steve D
authors.initials: SD
authors.lastname: Rounsley
authors.forename: Marianela
authors.initials: M
authors.lastname: Rodriguez-Carres
authors.forename: Alan
authors.initials: A
authors.lastname: Kuo
authors.forename: Catherine C
authors.initials: CC
authors.lastname: Wasmann
authors.forename: Jane
authors.initials: J
authors.lastname: Grimwood
authors.forename: Jeremy
authors.initials: J
authors.lastname: Schmutz
authors.forename: Masatoki
authors.initials: M
authors.lastname: Taga
authors.forename: Gerard J
authors.initials: GJ
authors.lastname: White
authors.forename: Shiguo
authors.initials: S
authors.lastname: Zhou
authors.forename: David C
authors.initials: DC
authors.lastname: Schwartz
authors.forename: Michael
authors.initials: M
authors.lastname: Freitag
authors.forename: Li-Jun
authors.initials: LJ
authors.lastname: Ma
authors.forename: Etienne G J
authors.initials: EG
authors.lastname: Danchin
authors.forename: Bernard
authors.initials: B
authors.lastname: Henrissat
authors.forename: Pedro M
authors.initials: PM
authors.lastname: Coutinho
authors.forename: David R
authors.initials: DR
authors.lastname: Nelson
authors.forename: Dave
authors.initials: D
authors.lastname: Straney
authors.forename: Carolyn A
authors.initials: CA
authors.lastname: Napoli
authors.forename: Bridget M
authors.initials: BM
authors.lastname: Barker
authors.forename: Michael
authors.initials: M
authors.lastname: Gribskov
authors.forename: Martijn
authors.initials: M
authors.lastname: Rep
authors.forename: Scott
authors.initials: S
authors.lastname: Kroken
authors.forename: István
authors.initials: I
authors.lastname: Molnár
authors.forename: Christopher
authors.initials: C
authors.lastname: Rensing
authors.forename: John C
authors.initials: JC
authors.lastname: Kennell
authors.forename: Jorge
authors.initials: J
authors.lastname: Zamora
authors.forename: Mark L
authors.initials: ML
authors.lastname: Farman
authors.forename: Eric U
authors.initials: EU
authors.lastname: Selker
authors.forename: Asaf
authors.initials: A
authors.lastname: Salamov
authors.forename: Harris
authors.initials: H
authors.lastname: Shapiro
authors.forename: Jasmyn
authors.initials: J
authors.lastname: Pangilinan
authors.forename: Erika
authors.initials: E
authors.lastname: Lindquist
authors.forename: Casey
authors.initials: C
authors.lastname: Lamers
authors.forename: Igor V
authors.initials: IV
authors.lastname: Grigoriev
authors.forename: David M
authors.initials: DM
authors.lastname: Geiser
authors.forename: Sarah F
authors.initials: SF
authors.lastname: Covert
authors.forename: Esteban
authors.initials: E
authors.lastname: Temporini
authors.forename: Hans D
authors.initials: HD
authors.lastname: Vanetten
mesh_terms: D001482:Base Composition; D015825:Chromosomes, Fungal / Q000737:chemistry / Q000235:genetics*; D005658:Fungi / Q000145:classification / Q000235:genetics; D020440:Gene Duplication; D016681:Genome, Fungal; D055330:Nectria / Q000737:chemistry / Q000145:classification / Q000235:genetics*; D010802:Phylogeny