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 R. Nelson; Dave Straney; Carolyn A. Napoli; Bridget M. Barker; 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

doi:10.1371/journal.pgen.1000618

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 R. Nelson, Dave Straney, Carolyn A. Napoli, Bridget M. BarkerMichael 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 journal › Article › peer-review

361 Scopus citations

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 language	English (US)
Article number	e1000618
Journal	PLoS genetics
Volume	5
Issue number	8
DOIs	https://doi.org/10.1371/journal.pgen.1000618
State	Published - Aug 2009

All Science Journal Classification (ASJC) codes

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

Access to Document

10.1371/journal.pgen.1000618

Cite this

Coleman, J. J., Rounsley, S. D., Rodriguez-Carres, M., Kuo, A., Wasmann, C. C., Grimwood, J., Schmutz, J., Taga, M., White, G. J., Zhou, S., Schwartz, D. C., Freitag, M., Ma, L. J., Danchin, E. G. J., Henrissat, B., Coutinho, P. M., Nelson, D. R., Straney, D., Napoli, C. A., ... Vanetten, H. D. (2009). The genome of Nectria haematococca: Contribution of supernumerary chromosomes to gene expansion. PLoS genetics, 5(8), Article e1000618. https://doi.org/10.1371/journal.pgen.1000618

@article{e02a95b739264663b064174398490e77,

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.",

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

year = "2009",

month = aug,

doi = "10.1371/journal.pgen.1000618",

language = "English (US)",

volume = "5",

journal = "PLoS genetics",

issn = "1553-7390",

publisher = "Public Library of Science",

number = "8",

}

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, DR, 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

TY - JOUR

T1 - The genome of Nectria haematococca

T2 - Contribution of supernumerary chromosomes to gene expansion

AU - Coleman, Jeffrey J.

AU - Rounsley, Steve D.

AU - Rodriguez-Carres, Marianela

AU - Kuo, Alan

AU - Wasmann, Catherine C.

AU - Grimwood, Jane

AU - Schmutz, Jeremy

AU - Taga, Masatoki

AU - White, Gerard J.

AU - Zhou, Shiguo

AU - Schwartz, David C.

AU - Freitag, Michael

AU - Ma, Li Jun

AU - Danchin, Etienne G.J.

AU - Henrissat, Bernard

AU - Coutinho, Pedro M.

AU - Nelson, David R.

AU - Straney, Dave

AU - Napoli, Carolyn A.

AU - Barker, Bridget M.

AU - Gribskov, Michael

AU - Rep, Martijn

AU - Kroken, Scott

AU - Molnár, István

AU - Rensing, Christopher

AU - Kennell, John C.

AU - Zamora, Jorge

AU - Farman, Mark L.

AU - Selker, Eric U.

AU - Salamov, Asaf

AU - Shapiro, Harris

AU - Pangilinan, Jasmyn

AU - Lindquist, Erika

AU - Lamers, Casey

AU - Grigoriev, Igor V.

AU - Geiser, David M.

AU - Covert, Sarah F.

AU - Temporini, Esteban

AU - Vanetten, Hans D.

PY - 2009/8

Y1 - 2009/8

N2 - 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.

AB - 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.

UR - http://www.scopus.com/inward/record.url?scp=70149110707&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=70149110707&partnerID=8YFLogxK

U2 - 10.1371/journal.pgen.1000618

DO - 10.1371/journal.pgen.1000618

M3 - Article

C2 - 19714214

AN - SCOPUS:70149110707

SN - 1553-7390

VL - 5

JO - PLoS genetics

JF - PLoS genetics

IS - 8

M1 - e1000618

ER -

The genome of Nectria haematococca: Contribution of supernumerary chromosomes to gene expansion

Abstract

All Science Journal Classification (ASJC) codes

Access to Document

Other files and links

Fingerprint

Cite this