The genome of Nectria haematococca: contribution of supernumerary chromosomes to gene expansion.
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.
Coleman
Jeffrey J
JJ
Department of Plant Sciences, University of Arizona, Tucson, Arizona, United States of America.
Rounsley
Steve D
SD
Rodriguez-Carres
Marianela
M
Kuo
Alan
A
Wasmann
Catherine C
CC
Grimwood
Jane
J
Schmutz
Jeremy
J
Taga
Masatoki
M
White
Gerard J
GJ
Zhou
Shiguo
S
Schwartz
David C
DC
Freitag
Michael
M
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Li-Jun
LJ
Danchin
Etienne G J
EG
Henrissat
Bernard
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Coutinho
Pedro M
PM
Nelson
David R
DR
Straney
Dave
D
Napoli
Carolyn A
CA
Barker
Bridget M
BM
Gribskov
Michael
M
Rep
Martijn
M
Kroken
Scott
S
Molnár
István
I
Rensing
Christopher
C
Kennell
John C
JC
Zamora
Jorge
J
Farman
Mark L
ML
Selker
Eric U
EU
Salamov
Asaf
A
Shapiro
Harris
H
Pangilinan
Jasmyn
J
Lindquist
Erika
E
Lamers
Casey
C
Grigoriev
Igor V
IV
Geiser
David M
DM
Covert
Sarah F
SF
Temporini
Esteban
E
Vanetten
Hans D
HD
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