The genome of Nectria haematococca

Contribution of supernumerary chromosomes to gene expansion

Jeffrey J. Coleman, Steve D. Rounsley, Marianela Rodriguez-Carres, Alan Kuo, Catherine C. Wasmann, Jane Grimwood, Jeremy Schmutz, Masatoki Taga, Gerard J. White, Shiguo Zhou, David C. Schwartz, Michael Freitag, Li Jun Ma, Etienne G.J. Danchin, Bernard Henrissat, Pedro M. Coutinho, David Nelson, Dave Straney, Carolyn A. Napoli, Bridget M. Barker & 19 others Michael Gribskov, Martijn Rep, Scott Kroken, István Molnár, Christopher Rensing, John C. Kennell, Jorge Zamora, Mark L. Farman, Eric U. Selker, Asaf Salamov, Harris Shapiro, Jasmyn Pangilinan, Erika Lindquist, Casey Lamers, Igor V. Grigoriev, David M. Geiser, Sarah F. Covert, Esteban Temporini, Hans D. Vanetten

Research output: Contribution to journalArticle

236 Citations (Scopus)

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.

Original languageEnglish (US)
Article numbere1000618
JournalPLoS genetics
Volume5
Issue number8
DOIs
StatePublished - Aug 1 2009

Fingerprint

Nectria
Fusarium eumartii
chromosome
genome
Chromosomes
Genome
gene
Genes
genes
chromosomes
Fusarium
Genome Size
Chromosomes, Human, Pair 17
Fungi
Fusarium solani
fungus
fungi
Ecosystem
B chromosomes
Chromosomes, Human, Pair 15

All Science Journal Classification (ASJC) codes

  • Ecology, Evolution, Behavior and Systematics
  • Molecular Biology
  • Genetics
  • Genetics(clinical)
  • Cancer Research

Cite this

Coleman, J. J., Rounsley, S. D., Rodriguez-Carres, M., Kuo, A., Wasmann, C. C., Grimwood, J., ... Vanetten, H. D. (2009). The genome of Nectria haematococca: Contribution of supernumerary chromosomes to gene expansion. PLoS genetics, 5(8), [e1000618]. https://doi.org/10.1371/journal.pgen.1000618

The genome of Nectria haematococca : Contribution of supernumerary chromosomes to gene expansion. / Coleman, Jeffrey J.; Rounsley, Steve D.; Rodriguez-Carres, Marianela; Kuo, Alan; Wasmann, Catherine C.; Grimwood, Jane; Schmutz, Jeremy; Taga, Masatoki; White, Gerard J.; Zhou, Shiguo; Schwartz, David C.; Freitag, Michael; Ma, Li Jun; Danchin, Etienne G.J.; Henrissat, Bernard; Coutinho, Pedro M.; Nelson, David; Straney, Dave; Napoli, Carolyn A.; Barker, Bridget M.; Gribskov, Michael; Rep, Martijn; Kroken, Scott; Molnár, István; Rensing, Christopher; Kennell, John C.; Zamora, Jorge; Farman, Mark L.; Selker, Eric U.; Salamov, Asaf; Shapiro, Harris; Pangilinan, Jasmyn; Lindquist, Erika; Lamers, Casey; Grigoriev, Igor V.; Geiser, David M.; Covert, Sarah F.; Temporini, Esteban; Vanetten, Hans D.

In: PLoS genetics, Vol. 5, No. 8, e1000618, 01.08.2009.

Research output: Contribution to journalArticle

Coleman, JJ, Rounsley, SD, Rodriguez-Carres, M, Kuo, A, Wasmann, CC, Grimwood, J, Schmutz, J, Taga, M, White, GJ, Zhou, S, Schwartz, DC, Freitag, M, Ma, LJ, Danchin, EGJ, Henrissat, B, Coutinho, PM, Nelson, D, Straney, D, Napoli, CA, Barker, BM, Gribskov, M, Rep, M, Kroken, S, Molnár, I, Rensing, C, Kennell, JC, Zamora, J, Farman, ML, Selker, EU, Salamov, A, Shapiro, H, Pangilinan, J, Lindquist, E, Lamers, C, Grigoriev, IV, Geiser, DM, Covert, SF, Temporini, E & Vanetten, HD 2009, 'The genome of Nectria haematococca: Contribution of supernumerary chromosomes to gene expansion', PLoS genetics, vol. 5, no. 8, e1000618. https://doi.org/10.1371/journal.pgen.1000618
Coleman JJ, Rounsley SD, Rodriguez-Carres M, Kuo A, Wasmann CC, Grimwood J et al. The genome of Nectria haematococca: Contribution of supernumerary chromosomes to gene expansion. PLoS genetics. 2009 Aug 1;5(8). e1000618. https://doi.org/10.1371/journal.pgen.1000618
Coleman, Jeffrey J. ; Rounsley, Steve D. ; Rodriguez-Carres, Marianela ; Kuo, Alan ; Wasmann, Catherine C. ; Grimwood, Jane ; Schmutz, Jeremy ; Taga, Masatoki ; White, Gerard J. ; Zhou, Shiguo ; Schwartz, David C. ; Freitag, Michael ; Ma, Li Jun ; Danchin, Etienne G.J. ; Henrissat, Bernard ; Coutinho, Pedro M. ; Nelson, David ; Straney, Dave ; Napoli, Carolyn A. ; Barker, Bridget M. ; Gribskov, Michael ; Rep, Martijn ; Kroken, Scott ; Molnár, István ; Rensing, Christopher ; Kennell, John C. ; Zamora, Jorge ; Farman, Mark L. ; Selker, Eric U. ; Salamov, Asaf ; Shapiro, Harris ; Pangilinan, Jasmyn ; Lindquist, Erika ; Lamers, Casey ; Grigoriev, Igor V. ; Geiser, David M. ; Covert, Sarah F. ; Temporini, Esteban ; Vanetten, Hans D. / The genome of Nectria haematococca : Contribution of supernumerary chromosomes to gene expansion. In: PLoS genetics. 2009 ; Vol. 5, No. 8.
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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.",
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