Agrobacterium tumefaciens C58 Genome

& Functional Genomics Project


ad Goodner, Professor of Biology, Edward J. Smerek Endowed Chair in Mathematics, the Sciences, & Technology, Hiram College

        Major collaborators on C58 genome: Steve Slater, GLBRC, Univ. Wisconsin;
                Derek Wood, Seattle
Pacific University; Barry Goldman, Mons
anto Co.,
                Joao Setubal, Univ. Sao Paulo; Stephen Farrand, Univ. Illinois;
                Gene Nester, Univ. Washington; Tom Burr, Cornell University
        Major collaborators on C58 functional genomics:
Steve Slater,
                GLBRC, Univ. Wisconsin; Derek Wood, Seattle
Pacific University;
                Katey Houmiel, Seattle Pacific University; David Rhoads, Univ. Arizona

Brief Description of Agrobacterium tumefaciens C58:
    A. tumefaciens C58 is the most heavily studied member of the genus Agrobacterium. Members of this genus are commonly found in soils all over the world as a aerobic heterotroph that can use a wide variety of carbon sources. However, most people know Agrobacterium because some strains can do something that no other cellular pathogen does - inject a piece of its own DNA into a plant cell altering how that plant cell works. Scientists know a lot now about virulent Agrobacterium strains do this and have worked out methods to use this natural DNA transformation process to introduce novel genes into plants and even fungi for agricultural, medical, and biotechnological purposes.
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Summary of Research Program and Progress:
    My lab was involved in the genetic/physically mapping and sequencing of the A. tumefaciens C58 genome (Goodner et al., 1999; Goodner et al., 2001; Wood et al., 2001). Over the past 12+ years, my undergrads and I have worked to update the annotation of the C58 genome and to connect genes to cellular functions through a variety of functional genomic approaches (Slater et al., 2012).
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Student Annotation Tally (as of March 2013):
Prior to IMG-ACT
  • Number of open reading frames (ORFs) annotated in this organism:  94 (all involved in pathways)
  • Number of biochemical pathways annotated in this organism: 7
  • Number of ORFs annotated in this organism:  184 (all hypotheticals)

Student Functional Genomics Tally (as of March 2013):

  • Number of ORFs connected to cellular functions by transposon mutagenesis: 103
  • Number of ORFs connected to cellular functions by targeted gene disruptions: 97
  • Number of ORFs connected to cellular functions by functional complementation: 18

Are you interested in joining the Interpret a Genome program?  More information and the opportunity to receive training can be found at the DOE/JGI Interpret a Genome Program and the Microbial Genome Annotation Network (MGAN) websites (See navigation bar). 

This program is a collaboration with the Department of Energy (DOE) Joint Genome Institute (JGI) as part of the Genomic Encyclopedia for Bacteria and Archaea (GEBA) project using the Integrated Microbial Genomes Annotation Collaboration Tool (IMG-ACT).

 The Design of this website template was funded by NSF (RCN-UBE-DBI 0954829)