The Genome of Nectria haematococca: Contribution of Supernumerary Chromosomes to Gene Expansion

被引：324

作者：

Coleman, Jeffrey J. ^{[1
,2
]}

Rounsley, Steve D. ^{[1
,3
]}

Rodriguez-Carres, Marianela ^{[1
,4
]}

Kuo, Alan ^{[5
]}

Wasmann, Catherine C. ^{[1
]}

Grimwood, Jane ^{[6
,7
]}

Schmutz, Jeremy ^{[6
,7
]}

Taga, Masatoki ^{[8
]}

White, Gerard J. ^{[1
]}

Zhou, Shiguo ^{[9
]}

Schwartz, David C. ^{[9
]}

Freitag, Michael ^{[10
,11
]}

Ma, Li-jun ^{[12
]}

Danchin, Etienne G. J. ^{[13
,14
,15
]}

Henrissat, Bernard ^{[13
,14
]}

Coutinho, Pedro M. ^{[13
,14
]}

Nelson, David R. ^{[16
]}

Straney, Dave ^{[17
]}

Napoli, Carolyn A. ^{[1
]}

Barker, Bridget M. ^{[1
]}

Gribskov, Michael ^{[18
]}

Rep, Martijn ^{[19
]}

Kroken, Scott ^{[1
]}

Molnar, Istvan ^{[20
]}

Rensing, Christopher ^{[21
]}

Kennell, John C. ^{[22
]}

Zamora, Jorge ^{[1
]}

Farman, Mark L. ^{[23
]}

Selker, Eric U. ^{[24
]}

Salamov, Asaf ^{[5
]}

Shapiro, Harris ^{[5
]}

Pangilinan, Jasmyn ^{[5
]}

Lindquist, Erika ^{[5
]}

Lamers, Casey ^{[9
]}

Grigoriev, Igor V. ^{[5
]}

Geiser, David M. ^{[25
]}

Covert, Sarah F. ^{[26
]}

Temporini, Esteban ^{[1
,27
]}

VanEtten, Hans D. ^{[1
]}

机构：

[1] Univ Arizona, Dept Plant Sci, Tucson, AZ 85721 USA

[2] Massachusetts Gen Hosp, Boston, MA 02114 USA

[3] Univ Arizona, Inst BIO5, Tucson, AZ USA

[4] Duke Univ, Dept Biol, Durham, NC USA

[5] Energy Joint Genome Inst, US Dept, Walnut Creek, CA USA

[6] Stanford Human Genome Ctr, Joint Genome Inst, Palo Alto, CA USA

[7] Hudson Alpha Inst Biotechnol, Hudson Alpha Genome Sequencing Ctr, Huntsville, AL USA

[8] Okayama Univ, Dept Biol, Okayama, Japan

[9] Univ Wisconsin, Lab Mol & Computat Genom, Madison, WI USA

[10] Oregon State Univ, Dept Biochem & Biophys, Corvallis, OR 97331 USA

[11] Oregon State Univ, Ctr Genome Res & Biocomp, Corvallis, OR 97331 USA

[12] Broad Inst, Cambridge, MA USA

[13] Univ Aix Marseille 1, CNRS, Architecture & Fonct Macromol Biol, Marseille, France

[14] Univ Aix Marseille 2, CNRS, Architecture & Fonct Macromol Biol, F-13284 Marseille 07, France

[15] Ctr Rech, Inst Natl Rech Agron, Sophia Antipolis, France

[16] Univ Tennessee, Dept Mol Sci, Memphis, TN USA

[17] Univ Maryland, Dept Mol Genet & Cell Biol, College Pk, MD 20742 USA

[18] Purdue Univ, Dept Biol Sci, W Lafayette, IN 47907 USA

[19] Univ Amsterdam, Amsterdam, Netherlands

[20] Univ Arizona, SW Ctr Nat Prod Res & Commercializat, Off Arid Lands Studies, Tucson, AZ USA

[21] Univ Arizona, Dept Soil Water & Environm Sci, Tucson, AZ USA

[22] St Louis Univ, Dept Biol, St Louis, MO 63103 USA

[23] Univ Kentucky, Dept Plant Pathol, Lexington, KY 40546 USA

[24] Univ Oregon, Inst Mol Biol, Eugene, OR 97403 USA

[25] Penn State Univ, Fusarium Res Ctr, Dept Plant Pathol, University Pk, PA 16802 USA

[26] Univ Georgia, Warnell Sch Forestry & Nat Resources, Athens, GA 30602 USA

[27] Vilmorin Inc, Tucson, AZ USA

来源：

PLOS GENETICS | 2009年 / 5卷 / 08期

关键词：

SOLANI SPECIES COMPLEX; PATHOGENICITY PEP GENES; FUSARIUM-SOLANI; NEUROSPORA-CRASSA; FILAMENTOUS FUNGI; IN-VITRO; DISPENSABLE CHROMOSOME; PISATIN DEMETHYLATION; HETERODERA-GLYCINES; HORIZONTAL TRANSFER;

D O I：

10.1371/journal.pgen.1000618

中图分类号：

Q3 [遗传学];

学科分类号：

071007 ; 090102 ;

摘要：

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.

引用

页数：14

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