Abstract
Agrobacterium tumefaciens strain C58 is a Gram-negative soil bacterium capable of inducing tumors (crown galls) on many dicotyledonous plants. The genome of A. tumefaciens strain C58 was re-annotated based on the Z-curve method. First, all the ‘hypothetical genes’ were re-identified, and 29 originally annotated ‘hypothetical genes’ were recognized to be non-coding open reading frames (ORFs). Theoretical evidence obtained from principal component analysis, clusters of orthologous groups of proteins occupation, and average length distribution showed that these non-coding ORFs were highly unlikely to encode proteins. Results from the reverse transcription-polymerase chain reaction (RT-PCR) experiments on three different growth stages of A. tumefaciens C58 confirmed that 23 (79%) of the identified non-coding ORFs have no transcripts in these growth stages. In addition, using theoretical prediction, 19 potential protein-coding genes were predicted to be new protein-coding genes. Fifteen (79%) of these genes were verified with RT-PCR experiments. The RT-PCR experimental results confirmed the reliability of our theoretical prediction, indicating that false-positive prediction and missing genes always exist in the annotation of A. tumefaciens C58 genome. The improved annotation will serve as a valuable resource for the research of the lifestyle, metabolism, and pathogenicity of A. tumefaciens C58. The re-annotation of A. tumefaciens C58 can be obtained from http://211.69.128.148/Atum/.
Highlights
Agrobacterium tumefaciens is a Gram-negative bacteria belonging to the Rhizobiaceae family
Most of the gene sequences can be replaced by the transferred DNA (T-DNA), making A. tumefaciens an essential tool for plant transgenic research
Considering that most of the open reading frames (ORFs) are identified by gene-finding programs, but not verified experimentally in the current stage, many false-positive and several falsenegative ORFs always exist in bacterial genome annotation, especially in GC-rich genomes [6,7,8,9,10,11,12,13,14,15]
Summary
Agrobacterium tumefaciens is a Gram-negative bacteria belonging to the Rhizobiaceae family. Most of the A. tumefaciens members are ideal vectors for plant gene-transfer. Most of the gene sequences can be replaced by the T-DNA, making A. tumefaciens an essential tool for plant transgenic research. As a powerful transgenic tool, the detailed genomic study of A. tumefaciens C58 could lead to a directed refinement of plant transformation. The genome of A. tumefaciens C58 is approximately 5.67 Mb and is composed of four replicons, i.e., one circular chromosome, one linear chromosome, and two plasmids, namely, pTiC58 and pAtC58. After the publication of A. tumefaciens C58 genome, the Comprehensive Microbial Resource of The Institute for Genomic Research automatically re-annotated it The four A. tumefaciens C58 replicons were processed by RefSeq pipeline and assigned with a project number (ID: 57865). The annotation of A. tumefaciens C58 in the aforementioned public databases is quite different, indicating that its genome annotation is far from satisfactory
Sign-in/Register to view highlights & summary Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a callDisclaimer: All third-party content on this website/platform is and will remain the property of their respective owners and is provided on "as is" basis without any warranties, express or implied. Use of third-party content does not indicate any affiliation, sponsorship with or endorsement by them. Any references to third-party content is to identify the corresponding services and shall be considered fair use under The CopyrightLaw.
