Progress 09/01/04 to 08/31/09
Outputs
OUTPUTS: We have completed a 10.4X draft sequence covering approximately 54 Mb, (>98% of the genome in contigs) in approximately 1,523 scaffolds with an average size of ~85 kbp. Despite having an unusually low GC content of only 27% (compared to the free-living nematode C. elegans at 36%), much of the genome (87%) represents unique sequence. Most of the repetitive sequences (~12%) are in the moderately repetitive DNA class (low complexity sequence); only 1% is highly repetitive class. Consequently, the VW9 strain of M. hapla has proven to be an extremely tractable system for genomic analysis. Using Glimmer and FgenesH (both independently trained on ~1,400 hand curated M. hapla gene models) for ab initio gene predictions from genomic sequence identified 14,494 protein-coding genes (annotation freeze Mh1.1g) in M. hapla. More than 3,000 of these have been experimentally validated using EST data. As noted above, this is in stark contrast to C. elegans and may reflect a diminished need for the parasite to carry as full a gene complement as free-living species, due to dependence on the host to provide essential resources. The average intron and exon sizes (53/145, respectively) are very similar to those in C. elegans. One intriguing feature of the C. elegans genome is that approximately 25% of the genes are organized into operons. Because of the small genome size, M. hapla genes tend to be close together and intergenic regions tend to be short. A comparison to the M. hapla gene repertoire has revealed that the single largest gene family in C. elegans, the G-protein coupled receptor family (GPCR: 1,011 genes), is drastically reduced in M. hapla (184 genes). Perhaps this reduced gene count represents the gene loss observed during niche specialization to become an internal parasite of plants (a homeostatic environment compared to soil), or alternatively, may reflect gene expansion in C. elegans for its unique niche. In contrast, the number of genes in the nuclear steroid hormone receptor family (170 genes, C. elegans) is about the same in M. hapla; to date we have identified 86 genes, but this is likely an underestimate because compared to the GPCRs this is a more divergent family and thus one can be less confident of identifying orthologs between M. hapla and C. elegans. Nuclear steroid hormone receptors likely play roles in nematode development, a process that is core to parasitic and free-living species alike. Not surprisingly, almost half of the genes to which we can ascribe function in M. hapla show the highest similarities to C. elegans genes. Because of their potential acquisition from bacteria via horizontal gene transfer, we also are very interested in those M. hapla genes with matches to bacterial genes. One intriguing example is provided by the pectate lyase genes, of which M. hapla has 22 copies. The distribution and sequence homology of these genes is consistent with multiple acquisition events from bacteria, plus duplication within the nematode. PARTICIPANTS: Nothing significant to report during this reporting period. TARGET AUDIENCES: All scientists interested in parasitism, general evolutionary mechanisms, nematode development, and horizontal gene transfer. PROJECT MODIFICATIONS: Not relevant to this project.
Impacts
The results from this project confirm that Meloidogyne hapla is the premier model parasitic system. In addition, this sequence represents the smallest multicellular animal genome sequenced to date. We developed an automated annotation system for parasitic nematodes that may become the model for other parasitic species. We have discovered potential gene family expansion that relates to parasitic ability and have described potential evolutionary mechanisms for this event. In addition, we have found a radically reduced gene number compared to free-living nematodes. Remarkably, M. hapla has 6,000 fewer genes than its free-living counterpart, Caenorhabditis elegans. By identifying the differences, key clues to the evolution of parasitism may be uncovered. The genetic system we developed in conjunction with our sequencing project has made M. hapla one of the 3 best characterized nematodes, and certainly the best understood plant-parasitic nematode. Finally, the genome sequence is being used by industry to identify potential novel targets for nematode control.
Publications
- Cromer, J., Opperman, C.H., and Bird, D.McK. 2009. Bioinformatic discovery of pathogenic effectors in Meloidogyne hapla. Submitted, Molecular Plant Pathology.
- Mbeunkui, F., Scholl, E. S., Blackburn, K., Opperman, C. H., Goshe, M. B. and Bird, D. McK. 2009. Computational and experimental determination of the northern root-knot nematode (Meloidogyne hapla) proteome. Submitted, Molecular and Cellular Proteomics.
- Schaff, J.E., Mauchline, T., Opperman, C.H., and Davies, K.G. 2009. Exploiting the genomes of root-knot nematode and Pasteuria penetrans to develop novel biocontrol strategies. In: Biological Control of Nematodes. Spiegel, I., and Davies, K.G., eds.
- Bird, D.McK., Williamson, V.M., Abad, P., McCarter, J., Danchin, E., Castagnone-Serrano, P., and Opperman, C.H. 2009. Genome analyis of sedentary endoparasitic plant-parasitic nematodes. Annual Review of Phytopathology. In press.
- Abad, P., and Opperman, C.H. 2009. The genomes of Meloidogyne incognita and M. hapla. In: Root-Knot Nematodes, Perry, R.N., Moens, M., and Starr, J., eds. CABI. In press.
- Opperman C. H., Bird D. M, Williamson V. M et al. 2008. Sequence and genetic map of Meloidogyne hapla: A compact nematode genome for plant parasitism. Proceedings of the National Academy of Science USA 105: 14802-14807 (supplemental material online).
- Opperman, C.H., Bird, D.M. and Schaff, J.E. 2009. Genome characterization and analysis of root-knot nematodes. Plant Cell Monographs 15: 221-238. Bird, D.M., Opperman, C.H., and Williamson, V.W. 2009. Plant infection by root-knot nematode. Plant Cell Monographs 15: 1-14.
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Progress 10/01/07 to 09/30/08
Outputs
OUTPUTS: We have completed the genome sequence of Meloidogyne hapla from multiple libraries, including 3, 6, and 8 kb shotgun libraries and 40 kb fosmid ends. Our sequence represents a 10.4X coverage of the genome and covers approximately 99% of the M. hapla genome in 1,523 scaffolds. Approximately 53.5 million base pairs of the 54 million base pair genome are present in these assembled scaffolds. Merger of the genetic map with the physical (sequence) map: We are actively merging a genetic (linkage) map with the genome sequence, using co-dominant markers from a VW9xVW8 (avirulent) cross. We have placed over 90% of the co-dominant markers on one or more scaffolds, and thus far, every marker examined has aligned with the sequence. Not only is this assisting with genome assembly, but it also makes cloning genes by genetic mapping readily achievable. Estimation of gene number: our annotations of gene density in the assembled 10.4X genome indicate that M. hapla contains 14,420 genes. This is in stark contrast to C. elegans, which has 20,000+ genes (Wormbase release WS190). This difference may reflect a diminished need for the parasite to carry as full a gene complement as free-living species, due to dependence on the host to provide essential resources. We are extremely interested in what functions M. hapla may have dispensed with (and, of course, what new functions this obligate parasite might have). Analysis further reveals areas of microsynteny between M. hapla and C. elegans, although substantial rearrangements have occurred. Analysis of the genome to date reveals suites of putative parasitism genes clustered in several areas, numerous horizontal gene transfer candidates, and strong coverage of the dauer pathway. We have also re-analyzed 26,000 ESTs previously acquired and have assembled a 5,540 unigene set, representing approximately 46% of the genes in M. hapla. PARTICIPANTS: PARTICIPANTS: C.H. Opperman, NCSU, D.M. Bird, NCSU, D. Rohksar, Joint Genome Institute TARGET AUDIENCES: TARGET AUDIENCES: Nematologists, Ag companies, biologists PROJECT MODIFICATIONS: Nothing significant to report during this reporting period.
Impacts
In addition to the direct impacts on the plant nematology community, the acquisition of this sequence will have a substantial impact on the greater nematode biology community, including the model nematode C. elegans. Phylogenetic and evolutionary studies will be enhanced, as well as the ability to explore horizontal gene transfer and the roots of parasitism.
Publications
- Opperman C. H., Bird D. M, Williamson V. M et al. 2008. Sequence and genetic map of Meloidogyne hapla: A compact nematode genome for plant parasitism. Proceedings of the National Academy of Science USA 105: 14802-14807 (supplemental material online).
- Opperman, C.H., Bird, D.M. and Schaff, J.E. 2008. Genome characterization and analysis of root-knot nematodes. in: Cell Biology of Plant-Nematode Interactions, R. H. Berg and C. G. Taylor (Eds), Springer, Heidelberg, in press.
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Progress 10/01/06 to 09/30/07
Outputs
OUTPUTS: We have completed the primary genome sequence of Meloidogyne hapla from multiple libraries, including 3, 6, and 8 kb shotgun libraries and 40 kb fosmid ends. Our sequence represents a 10.4X draft of the genome and covers approximately 97% of the M. hapla genome in 1,523 scaffolds. Approximately 54 million base pairs of the 56 million base pair genome are present in these assembled scaffolds. Merger of the genetic map with the physical (sequence) map: We are actively merging a genetic (linkage) map with the genome sequence, using co-dominant markers from a VW9xVW8 (avirulent) cross. We have placed over 90% of the co-dominant markers on one or more scaffolds, and thus far, every marker examined has aligned with the sequence. Not only is this assisting with genome assembly, but it also makes cloning genes by genetic mapping readily achievable. Estimation of gene number: We previously used a computational approach (SPECRICH) originally designed by ecologists to estimate species
abundance and diversity based on sampling distributions in the wild to predict the M. hapla gene number from our ~26,000 EST dateset. Much to our surprise, SPECRICH calculations suggested that M. hapla possesses fewer than 13,000 genes; our initial annotations of gene density in the assembled 10.4X genome support this estimate. This is in stark contrast to C. elegans, which has 23,000+ genes (Wormbase release WS178). This difference may reflect a diminished need for the parasite to carry as full a gene complement as free-living species, due to dependence on the host to provide essential resources. We are extremely interested in what functions M. hapla may have dispensed with (and, of course, what new functions this obligate parasite might have). Analysis further reveals areas of microsynteny between M. hapla and C. elegans, although substantial rearrangements have occurred. Analysis of the genome to date reveals suites of putative parasitism genes clustered in several areas, numerous
horizontal gene transfer candidates, and strong coverage of the dauer pathway. We have also re-analyzed 26,000 ESTs previously acquired and have assembled a 5,540 unigene set, representing approximately 46% of the genes in M. hapla.
PARTICIPANTS: C.H. Opperman, NCSU, D.M. Bird, NCSU, D. Rohksar, Joint Genome Institute
TARGET AUDIENCES: Nematologists, Ag companies, biologists
Impacts
In addition to the direct impacts on the plant nematology community, the acquisition of this sequence will have a substantial impact on the greater nematode biology community, including the model nematode C. elegans. Phylogenetic and evolutionary studies will be enhanced, as well as the ability to explore horizontal gene transfer and the roots of parasitism.
Publications
- No publications reported this period
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Progress 10/01/05 to 09/30/06
Outputs
The first draft of the Meloidogyne hapla genome has been completed at the CBNP and by our partner, the Joint Genome Institute (JGI). Preliminary analysis of the sequence data strongly indicates that the plant-parasitic M. hapla carries substantially fewer genes (12,000) than the free-living nematode, Caenorhabditis elegans (19,500). Although typical of obligate pathogenic bacteria, this is the first indication that the gene loss phenomenon occurs in a multicellular, eukaryotic obligate parasite. Understanding what genes and pathways have been lost might say as much about parasitism as does the genes retained.
Impacts
THIS IS THE FIRST SEQUENCE OF A PLANT PARASITIC NEMATODE, AND WILL HAVE SUBSTANTIAL IMPACT ON ALL PROGRAMS CONCERNED WITH MANAGEMENT OF THE ROOT-KNOT NEMATODE. IN ADDITION, THE BASIC BIOLOGICAL INFORMATION WILL PROVIDE INFORMATION ON THE EVOLUTION OF NEMATODE PARASITIC ABILITIES.
Publications
- Mitreva, M., Blaxter, M. L., Bird, D. McK., and J. P. McCarter. 2005. Comparative Genomics in Nematodes. Trends in Genetics 21:573-581.
- Bird, D. McK., Blaxter, M. L., McCarter, J. P., Mitreva, M., Sternberg, P. W., and W. K. Thomas. 2005. A white paper on nematode comparative genomics. Journal of Nematology 37:408-416.
- McCarter, J. P., Bird, D. McK., and M. Mitreva. 2005. Nematode gene sequences: Update for December 2005. Journal of Nematology 37:417-421.
- Vanholme, B., Mitreva, M., van Criekinge, W., Logghe, M., Bird, D. McK., McCarter, J. P., and G. Gheysen. 2006. Detection of putative secreted proteins in the plant parasitic nematode Heterodera schachtii. Parasitology Research 98:1-11.
- Opperman, C.H. and Lambert, K. 2006. Genome characterization and analysis of root-knot and cyst nematodes. in: Cell Biology of Plant-Nematode Interactions, R. H. Berg and C. G. Taylor (Eds), Springer, Heidelberg, in press.
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Progress 10/01/04 to 09/30/05
Outputs
We are currently sequencing the genome of the root-knot nematode, Meloidogyne hapla. In this project, libraries have been constructed and prepared for sequencing, in collaboration with Orion Genomics LLC and the Joint Genome Institute. Upon completion of a draft sequence early next year, annotation jamborees will be held at several locations. The primary annotation committee has been formed and preliminary sequencing has commenced.
Impacts
THIS IS THE FIRST SEQUENCE OF A PLANT PARASITIC NEMATODE, AND WILL HAVE SUBSTANTIAL IMPACT ON ALL PROGRAMS CONCERNED WITH MANAGEMENT OF THE ROOT-KNOT NEMATODE. IN ADDITION, THE BASIC BIOLOGICAL INFORMATION WILL PROVIDE INFORMATION ON THE EVOLUTION OF NEMATODE PARASITIC ABILITIES.
Publications
- Diener, S.E., Houfek, T.D., Kalat, S.E., Windham, D.E., Burke, M., Opperman, C.H., and Dean, R.A. 2005. Alkahest NuclearBLAST: a user-friendly BLAST management and analysis system. In press: BMC Bioinformatics 6: (open source online).
- Dong, K., Barker, K. R., and Opperman, C. H. 2005. Virulence Genes in Heterodera glycines: Allele Frequencies and Ror Gene Groups Among Field Isolates and Inbred Lines. Phytopathology 95:186-191.
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Progress 10/01/03 to 09/30/04
Outputs
wE HAVE CONSTRUCTED THE NEEDED LIBRARIES TO BEGIN SEQUENCING THE MELOIDOGYNE HAPLA GENOME. A PHYSICAL MAP PROJECT IS HALFWAY COMPLETED, AND SEQUENCING WILL COMMENCE WITHIN THE NEXT 6 MONTHS.
Impacts
tHIS IS THE FIRST SEQUENCE OF A PLANT PARASITIC NEMATODE, AND WILL HAVE SUBSTANTIAL IMPACT ON ALL PROGRAMS CONCERNED WITH MANAGEMENT OF THE ROOT-KNOT NEMATODE. IN ADDITION, THE BASIC BIOLOGICAL INFORMATION WILL PROVIDE INFORMATION ON THE EVOLUTION OF NEMATODE PARASITIC ABILITIES.
Publications
- No publications reported this period
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