Projects and interests
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How does the organization of genes along chromosomes affect gene family evolution?
One way to approach the question is to examine the distribution of genes in
Arabidopsis, and then to ask how different gene families are distributed.
The image here shows the coding
sequences of the five A. thaliana chromosomes, all blasted against themselves.
Each hit with E value less than 10^-10 is a red dot. Chromosome 1 is top left.
Centromeres show as sparse, gene-poor regions. Portions of the genome that exist
in duplicate are highlighted in blue diagonals (identified using an algorithm of mine).
I created this image using perl and the GD graphics module. See applications of this
information at my gene family evolution page
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How stable are plant genomes, when comparing gene position and order in different taxa?
This is one of the central questions in Nevin Young's lab, which is involved in mapping
and determining correspondences between regions of the soybean and
Medicago truncatula genomes.
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The evolution of traits in plants (such as the flower structures in the legumes
at the top and bottom of my home page page, and the clover image at the top of this page).
By the way, the pictures came from David Smith's Delaware Wildflowers.
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What is the evolutionary history of the largest family of plant disease resistance genes?
These genes are important in helping plants to fight off diseases and pests.
Check here for supplementary material
for the manuscript: "Diversity, Distribution, and Ancient Taxonomic Relationships
within the TIR and non-TIR NBS-LRR Resistance Gene Subfamilies" (Cannon et al., 2002).
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What phylogenetic and analytical methods are suitable for comparing gene family
evolution among multiple gene families and plant taxa?
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Papers
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Johnson JR, Owens KL, Clabots CR, Weissman SJ, Cannon SB (2005)
Phylogenetic Relationships among Clonal Groups of Extraintestinal
Pathogenic Escherichia coli as Assessed by Multi-Locus Sequence Typing.
Submitted.
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Mudge J, Cannon SB, Kalo P, Oldroyd GED, Roe BA, Town CD, Young ND (2005)
Hypersyntenic Regions in the Genomes of Soybean, Medicago truncatula,
and Arabidopsis thaliana. Submitted.
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Cannon SB, Crow JA, Heuer ML, Wang X, Cannon EKS, Dwan C,
Lamblin A, Vasdewani J, Mudge J, Cook A, Cheung F, Kenton S,
Kunau TM, Brown D, Kim D, Cook DR, Roe BA, Town CD,
Young ND, Retzel EF. (2005)
Databases and Information Integration for the Medicago truncatula
Genome and Transcriptome. Plant Physiology, in press.
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Cannon SB, Mitra A, Baumgarten A, Young ND, May G (2004) The roles of
segmental and tandem gene duplication in the evolution of large gene
families in Arabidopsis thaliana. BMC Plant Biology 4:10
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Young ND, Cannon SB, Sato S, Tabata S. (2005) Sequencing the
Genes Spaces of Medicago truncatula and Lotus japonicus.
Plant Physiology, in press.
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Graham MA, Silverstein KAT, Cannon SB, VandenBosch KA (2004)
Computational identification and characterization of novel genes
from legumes. Plant Physiol. 135: 1179-1197.
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Anderson JP, Mueller JL, Rosengren S, Boyle DL, Schaner P,
Cannon SB, Goodyear CS, Hoffman HM (2004)
Structural, expression, and evolutionary
analysis of mouse CIAS1.
Gene 338:25-34.
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Cannon SB, Kozik A, Chan B, Michelmore R, Young ND (2003)
DiagHunter and GenoPix2D: programs for genomic comparisons,
large-scale synteny-discovery, and visualization.
Genome Biology 4:R68.
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MA Graham, KAT Silverstein, SB Cannon, KA VandenBosch (2003)
Computational identification of legume-specific genes.
Stadler Symposium Proceedings.
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Cannon SB (2003)
New tools for understanding plant gene family evolution.
Ph.D. Dissertation, University of Minnesota. December.
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Cannon SB, Young ND (2003)
OrthoParaMap: distinguishing
orthologs from paralogs by integrating comparative genome
data and gene phylogenies. BMC Bioinformatics 4:35.
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Cannon SB, McCombie WR, Sato S, Tabata S, Denny RL, Palmer
L, Katari M, Young ND, Stacey G (2003) Evolution and
microsynteny of the apyrase gene family in three legume
genomes. Mol Genet Genomics 270:347-361.
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Bertioli DJ, Leal-Bertioli SCM, Lion MB, Santos VL, Pappas
Jr G, Cannon SB, Guimar‹es PM (2003) A large scale analysis
of resistance gene homologues in Arachis. Mol Genet Genomics 270:34-45.
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Baumgarten AM, Cannon SB, Spangler R, May G (2003)
Genome-level evolution of NBS-LRR resistance genes in
Arabidopsis thaliana. Genetics 165:309-19.
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Cannon SB, Young ND (2002) The Evolution and Genomic
Architecture of NBS-LRRs. In: Stacey G, Keen NT (eds)
Plant-Microbe Interactions. American Phytopathological
Society, St. Paul, Minnesota, p 81-95.
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Cannon SB, Zhu H, Baumgarten AM, Spangler R, May G, Cook DR,
Young ND (2002) Diversity, distribution, and ancient
taxonomic relationships within the TIR and non-TIR NBS-LRR
resistance gene subfamilies. J Mol Evol 54:548-62.
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Zhu H, Cannon SB, Young ND, Cook DR (2002)
Phylogeny and genomic organization of the TIR and non-TIR NBS-LRR
resistance gene family in Medicago truncatula. Mol Plant
Microbe Interact 15:529-39.
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Cannon SB (1992)
The Garden in the Machine.
M.A. Thesis, Bowling Green State University
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Software
In a previous life, I was an educational game simulation designer
and content specialist for The Learning Company.
- I designed the "event models" for The Oregon Trail, 4th edition and Road Adventures USA
- I was the content specialist for the Princeton Review Math Library, Geometry volume, and a designer for the Math Library as a whole
- I was the content specialist and dialog logic implementer for the Amazon Trail
- I was a content specialist and simulation designer for Explore Yellowstone
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