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. 2013 Feb;79(4):1414-7.
doi: 10.1128/AEM.03192-12. Epub 2012 Dec 14.

Reconciliation of sequence data and updated annotation of the genome of Agrobacterium tumefaciens C58, and distribution of a linear chromosome in the genus Agrobacterium

Steven Slater  1 , João C Setubal, Brad Goodner, Kathryn Houmiel, Jian Sun, Rajinder Kaul, Barry S Goldman, Stephen K Farrand, Nalvo Almeida Jr, Thomas Burr, Eugene Nester, David M Rhoads, Ryosuke Kadoi, Trucian Ostheimer, Nicole Pride, Allison Sabo, Erin Henry, Erin Telepak, Lindsey Cromes, Alana Harkleroad, Louis Oliphant, Phil Pratt-Szegila, Roy Welch, Derek Wood
Affiliations

Reconciliation of sequence data and updated annotation of the genome of Agrobacterium tumefaciens C58, and distribution of a linear chromosome in the genus Agrobacterium

Steven Slater et al. Appl Environ Microbiol. 2013 Feb.

Abstract

Two groups independently sequenced the Agrobacterium tumefaciens C58 genome in 2001. We report here consolidation of these sequences, updated annotation, and additional analysis of the evolutionary history of the linear chromosome, which is apparently limited to the biovar I group of Agrobacterium.

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Figures

Fig 1
Fig 1
Potential secondary structures for genomic repeat elements. (A) The structure emphasizes the inverted repeats present at each end of the CIR2 full element. (B) An alternative secondary structure for a CIR2 full element that emphasizes the larger overall inverted repeat. The extent of the stem forming above position 44 depends on the sequence of the spacer region. The shaded polygon indicates where a CcrM binding site sits if one is present (it is found in only about one-third of the elements). (C) Potential secondary structure for CIR1 elements. The structure emphasizes the larger overall inverted repeat. The shaded area indicates the usual location of a CcrM binding site, but quite often, a second CcrM binding site exists directly opposite the first location in a full element (the example here does not contain such a second site). (D) Potential secondary structure for KE3 half elements and ends of KE3 full elements.
Fig 2
Fig 2
Genomic transfers between chromosome I and chromosome II associated with the atu2521-atu2523 (telA) region. The top diagram shows genes on the A. vitis S4 chromosome I from avi4581 (tRNA-met) through avi3984 (a conserved hypothetical gene) (16). The lower diagrams show the syntenic regions of the A. tumefaciens C58 genome, with lines connecting orthologous genes of C58 and S4. Note the breakpoints in synteny immediately upstream of avi3961 and downstream of avi3963 in the S4 genome, identifying breakpoints for large genomic transfers between chromosome I and chromosome II in the C58 genome. Protein-coding genes are shown in gray, tRNA genes are shown in black, and rRNA genes are shown in white. Genomic locations of each region correspond to the base pair numbering in the sequence files available at NCBI.
See this image and copyright information in PMC

References

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