Progress 07/01/06 to 09/30/10
Outputs
OUTPUTS: OUTPUTS: The habitat diversity of the fungus Nectria haematococca MPVI has been shown to be due in part to conditionally dispensable (CD) chromosomes that carry habitat-defining genes. Studies at the start of this CRIS project had showed that the N. haematococca PDA1 CD chromosome, which carries the genes for pea pathogenicity (PEP), also has genes for the utilization of homoserine (HUT), an amino acid found in pea root exudates. Transformation, insertional mutagenesis, and bioinformatics were used to identify a cluster of five genes (HUT cluster) on the PDA1 CD chromosome that was responsible for the HUT phenotype in N. haematococca. Additional studies used a newly developed real-time PCR technique that measures the copy number of genes on the normal and CD chromosomes of the fungus and a gene on the plants chromosomes allows a precise measurement of the fungal and plant biomasses. The use of this assay and a competition assay (the deWit replacement series) was used to determine if genes, other than the HUT genes, were on the different CD chromosome that gives the fungus, not only a competitive advantage in the rhizosphere of pea, but increase its ability to colonize the rhizospheres of soybean, tomato and alfalfa. DISSEMINATION:To disseminate the outputs from this and related hatch projects, lab members attended and presented data (talks and posters) at the, 24th, 25th and 26th Fungal Genetics Conference at Asilomar, CA, the American Phytopathology Society, the Western American Society of Plant Biologists
Annual Meeting, the Canadian Phytopathology Society meetings, the Asilomar Model Legume meeting, and the 9TH European Conference on Fungal Genetics in Edinburgh.
PARTICIPANTS: INDIVIDUALS: Hans D. VanEtten as PI. Cathy Wasmann as laboratory manager, Rhodesia Celoy, Marianela Rodriguez-Carres, and Jeff Coleman as graduate students and Gerard White as graduate student and Post Doc worked on this project. COLLABORATORS: All of those individuals that worked on the genomic analysis of Nectria haematococca. Those individuals, other than thus above are: S. D. Rounsley, A. Kuo, J. Grimwood, J. Schmutz, M. Taga, S. Zhou, D. C. Schwartz, M. Freitag, L-J. Ma, E. G. J. Danchin, B. Henrissat, P. M. Coutinho, D. R. Nelson, D. Straney, C. A. Napoli, B. M. Barker, M. Gribskov, M. Rep, S. Kroken, I. Molnar, C. Rensing, J. C. Kennell, J. Zamora, M. L. Farman, E. U. Selker, A. Salamov, H. Shapiro, J. Pangilinan, E. Lindquist, C. Lamers, I.V. Grigoriev, D. M. Geiser, S. F. Covert, and E. Temporini. TARGET AUDIENCES: TARGET AUDIENCES: The audiences for this information are other scientists that work with fungi and soil borne organisms. The main means to reach these individuals is through publications and presentation of our results at scientific meetings. PROJECT MODIFICATIONS: No major changes were made in this project.
Impacts
OUTCOME/IMPACT: Competition experiments comparing HUT+ and HUT- isolates showed that the HUT cluster is responsible for increased competitive ability of HUT+ N. haematococca isolates in the rhizosphere of pea. This finding was supported using competition studies with fluorescent protein-tagged HUT+ and HUT- isolates. Further analyses have demonstrated that two different CD chromosomes confer competitive advantage in the rhizospheres of different plant species. Both the PDA1 and PDA6 CD chromosomes confer a competitive advantage in the rhizosphere of soybean, whereas only the PDA6 CD chromosome confers a competitive advantage in the rhizospheres of tomato and alfalfa, and only the PDA1 CD chromosome confers a competitive advantage in the rhizosphere of pea. These studies suggest the presence of genes on the PDA6 and PDA1 CD chromosomes that enhance the ability of N. haematococca to expand its habitat and support the idea that fungal CD chromosomes are analogous to host-specifying plasmids in plant-associated bacteria. These studies are some of the first to identify rhizosphere competitive genes in fungi.
Publications
- Rodriguez Carres, M., G. White, D. Tsuchiya, M. Taga and H. D. VanEtten. (2008). The supernumerary chromosome of Nectria haematococca that carries pea- pathogenicity genes also carries a trait for rhizosphere competitiveness on pea. Applied and Environmental Microbiology. 74: 3849-3856.
- Coleman, J. J., S. D. Rounsley, M. Rodriguez Carres, A. Kuo, C. C. Wasmann, J. Grimwood, J. Schmutz, M. Taga, G. J. White, S. Zhou, D. C. Schwartz, M. Freitag, L-J. Ma, E. G. J. Danchin, B. Henrissat, P. M. Coutinho, D. R. Nelson, D. Straney, C. A. Napoli, B. M. Barker, M. Gribskov, M. Rep, S. Kroken, I. Molnar, C. Rensing, J. C. Kennell, J. Zamora, M. L. Farman, E. U. Selker, A. Salamov, H. Shapiro, J. Pangilinan, E. Lindquist, C. Lamers, I.V. Grigoriev, D. M. Geiser, S. F. Covert, E. Temporini, H. D. VanEtten. 2009. The Genome of Nectria haematococca: Contribution of Supernumerary Chromosomes to Gene Expansion. PLoS Genet 5: e1000618.
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Progress 01/01/09 to 12/31/09
Outputs
OUTPUTS: OUTPUTS: To disseminate the outputs from this and related hatch projects, a workshop was held and posters presented at the 25th Fungal Genetics Conference at Asilomar, CA March 17 - 22. Also, a talk was given by 2009 American Phytopathology Society meeting in Portland OR, August 1-5 and a poster was presented at the Western American Society of Plant Biologists
Annual Meeting
on April 25 & 26 at Tucson, AZ. New fundamental knowledge that came out of this work is presented in the outcome section below. PARTICIPANTS: Hans D. VanEtten as PI. Cathy Wasmann as laboratory manager Gerard White as Post Doc and Rhodesia Celoy as graduate student. TARGET AUDIENCES: The audience for this information is other scientists that work with fungi and soil borne organisms. The main means to reach these individuals is through publications. PROJECT MODIFICATIONS: No major changes have been made in our basis approach to understanding this biological phenomenon. PARTICIPANTS: The main individuals working on this project are mention in the outputs section (Hans D. VanEtten as PI. Cathy Wasmann as laboratory manager Gerard White as Post Doc and Rhodesia Celoy as graduate student). However, a number of people contributed to the analysis of the genome of Nectria haematococca, which was a part of our Hatch project. Those people are listed as authors on the second publication listed under Publications. Both the rhizospheres studies and the genomic studies gave post docs and graduate studies ample opportunities to learn the new techniques operative in these areas of science. TARGET AUDIENCES: As stated previously the target audience is other research scientists and they are reached through publications and presentations at scientific meetings. PROJECT MODIFICATIONS: Nothing significant to report during this reporting period.
Impacts
Fungi are found in a wide range of environments and the habitat diversity of the fungus Nectria haematococca has been shown to be due in part to unique genes on different supernumerary chromosomes. These chromosomes have been called "conditionally dispensable" (CD) since they are not needed for axenic growth, but are important for expanding the host range of individual isolates. Previous studies have demonstrated that the PDA1 CD chromosome gave this fungus a competitive advantage in the pea rhizosphere and current studies tested the PDA6 CD chromosome for this ability and for the ability of either CD chromosome to confer a competitive advantage in the rhizosphere of soybean, tomato and alfalfa. The PDA1 and PDA6 CD chromosomes conferred a competitive advantage in the rhizosphere of soybean, whereas only the PDA6 CD chromosome confers a competitive advantage in the rhizospheres of tomato and alfalfa, and only the PDA1 CD chromosome confers a competitive advantage in the rhizosphere of pea.
Publications
- Wen, F. , G. J. White, H. D. VanEtten, Z. Xiong, Z. and M. C. Hawes. 2009. Extracellular DNA Is Required for Root Tip Resistance toFungal Infection. Plant Physiology 151:820 to 829.
- Coleman, J. J., S. D. Rounsley, M. Rodriguez-Carres, A. Kuo, C. C. Wasmann, J. Grimwood, J. Schmutz, M. Taga, G. J. White, S. Zhou, D. C. Schwartz, M. Freitag, L-J. Ma, E. G. J. Danchin, B. Henrissat, P. M. Coutinho, D. R. Nelson, D. Straney, C. A. Napoli, B. M. Barker, M. Gribskov, M. Rep, S. Kroken, I. Molnar, C. Rensing, J. C. Kennell, J. Zamora, M. L. Farman, E. U. Selker, A. Salamov, H. Shapiro, J. Pangilinan, E. Lindquist, C. Lamers, I.V. Grigoriev, D. M. Geiser, S. F. Covert, E. Temporini, H. D. VanEtten. 2009. The Genome of Nectria haematococca: Contribution of Supernumerary Chromosomes to Gene Expansion. PLoS Genet 5: e1000618
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Progress 01/01/06 to 12/31/06
Outputs
In the regions flanking the PEP cluster, six additional ORFs have been identified. A comparison of the codon usages of these ORFs, the PEP genes, PDA, and two additional genes (cDNA3 and cDNA4) from the CD chromosomes with the codon usages of 21 genes from the other chromosomes revealed that there is a bias in codon usage that is correlated with the location of the genes. This difference in the codon usage is consistent with the hypothesis that the genes of the CD chromosome have a different origin than the genes from the normal chromosomes and that HGT may have played a role in the evolution of pathogenesis in N. haematococca MPVI. Alternatively, the nonCD chromosomes of N. haematococca MPVI may be heterogeneous in %GC composition, which would suggest an endogenous origin of the CD chromosome and its PEP cluster. This possibility will be evaluated by a genome-wide codon usage analysis when the genomic sequence of N. haematococca is assembled into chromosome-length
supercontigs.
Impacts
The detailed analyses outlined in this proposal should resolve whether it is reasonable to believe that horizontal gene transfer has been a factor in the evolution of new pathogenicity phenotypes in fungi. If horizontal gene transfer appears to have occurred during the evolution of the selected fungi, it has major implications for the contemporary perspective on how quickly fungi with new pathogenic capabilities can appear.
Publications
- Funnell DL, VanEtten HD (2002) Pisatin demethylase genes are on dispensable chromosomes while genes for pathogenicity on carrot and ripe tomato are on other chromosomes in Nectria haematococca. Mol. Plant-Microbe Inter. 15: 840-846.
- Liu X, Inlow M, VanEtten HD (2003) Expression profiles of pea pathogenicity (PEP) genes in vivo and in vitro, characterization of the flanking regions of the PEP cluster and evidence that the PEP cluster region resulted from horizontal gene transfer in the fungal pathogen Nectria haematococca. Cur. Genet. 44: 95-103.
- Temporini E, VanEtten H (2004) An analysis of the phylogenetic distribution of the pea pathogenicity (PEP) genes of Nectria haematococca MPVI supports the hypothesis of their origin by horizontal transfer and uncovers a potentially new pathogen of garden pea: Neocosmospora boniensis. Cur. Genet. 46: 29-36.
- Han Y, Liu X, Benny U, Kistler HC, VanEtten HD (2001) Genes determining pathogenicity to pea are clustered on a supernumerary chromosome in the fungal plant pathogen Nectria haematococca. Plant J. 25: 305-314.
- Temporini E, VanEtten H (2002) Distribution of the pea pathogenicity (PEP) genes in the fungus Nectria haematococca. Cur. Genet. 41:107-114.
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