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Gene discovery by genome-wide CDS re-prediction and microarray-based transcriptional analysis in phytopathogen Xanthomonas campestris
BACKGROUND: One of the major tasks of the post-genomic era is "reading" genomic sequences in order to extract all the biological information contained in them. Although a wide variety of techniques is used to solve the gene finding problem and a number of prokaryotic gene-finding software...
Autores principales: | , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
BioMed Central
2011
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3142249/ https://www.ncbi.nlm.nih.gov/pubmed/21745409 http://dx.doi.org/10.1186/1471-2164-12-359 |
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author | Zhou, Lian Vorhölter, Frank-Jörg He, Yong-Qiang Jiang, Bo-Le Tang, Ji-Liang Xu, Yuquan Pühler, Alfred He, Ya-Wen |
author_facet | Zhou, Lian Vorhölter, Frank-Jörg He, Yong-Qiang Jiang, Bo-Le Tang, Ji-Liang Xu, Yuquan Pühler, Alfred He, Ya-Wen |
author_sort | Zhou, Lian |
collection | PubMed |
description | BACKGROUND: One of the major tasks of the post-genomic era is "reading" genomic sequences in order to extract all the biological information contained in them. Although a wide variety of techniques is used to solve the gene finding problem and a number of prokaryotic gene-finding software are available, gene recognition in bacteria is far from being always straightforward. RESULTS: This study reported a thorough search for new CDS in the two published Xcc genomes. In the first, putative CDSs encoded in the two genomes were re-predicted using three gene finders, resulting in the identification of 2850 putative new CDSs. In the second, similarity searching was conducted and 278 CDSs were found to have homologs in other bacterial species. In the third, oligonucleotide microarray and RT-PCR analysis identified 147 CDSs with detectable mRNA transcripts. Finally, in-frame deletion and subsequent phenotype analysis of confirmed that Xcc_CDS002 encoding a novel SIR2-like domain protein is involved in virulence and Xcc_CDS1553 encoding a ArsR family transcription factor is involved in arsenate resistance. CONCLUSIONS: Despite sophisticated approaches available for genome annotation, many cellular transcripts have remained unidentified so far in Xcc genomes. Through a combined strategy involving bioinformatic, postgenomic and genetic approaches, a reliable list of 306 new CDSs was identified and a more thorough understanding of some cellular processes was gained. |
format | Online Article Text |
id | pubmed-3142249 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2011 |
publisher | BioMed Central |
record_format | MEDLINE/PubMed |
spelling | pubmed-31422492011-07-23 Gene discovery by genome-wide CDS re-prediction and microarray-based transcriptional analysis in phytopathogen Xanthomonas campestris Zhou, Lian Vorhölter, Frank-Jörg He, Yong-Qiang Jiang, Bo-Le Tang, Ji-Liang Xu, Yuquan Pühler, Alfred He, Ya-Wen BMC Genomics Research Article BACKGROUND: One of the major tasks of the post-genomic era is "reading" genomic sequences in order to extract all the biological information contained in them. Although a wide variety of techniques is used to solve the gene finding problem and a number of prokaryotic gene-finding software are available, gene recognition in bacteria is far from being always straightforward. RESULTS: This study reported a thorough search for new CDS in the two published Xcc genomes. In the first, putative CDSs encoded in the two genomes were re-predicted using three gene finders, resulting in the identification of 2850 putative new CDSs. In the second, similarity searching was conducted and 278 CDSs were found to have homologs in other bacterial species. In the third, oligonucleotide microarray and RT-PCR analysis identified 147 CDSs with detectable mRNA transcripts. Finally, in-frame deletion and subsequent phenotype analysis of confirmed that Xcc_CDS002 encoding a novel SIR2-like domain protein is involved in virulence and Xcc_CDS1553 encoding a ArsR family transcription factor is involved in arsenate resistance. CONCLUSIONS: Despite sophisticated approaches available for genome annotation, many cellular transcripts have remained unidentified so far in Xcc genomes. Through a combined strategy involving bioinformatic, postgenomic and genetic approaches, a reliable list of 306 new CDSs was identified and a more thorough understanding of some cellular processes was gained. BioMed Central 2011-07-12 /pmc/articles/PMC3142249/ /pubmed/21745409 http://dx.doi.org/10.1186/1471-2164-12-359 Text en Copyright ©2011 Zhou et al; licensee BioMed Central Ltd. http://creativecommons.org/licenses/by/2.0 This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. |
spellingShingle | Research Article Zhou, Lian Vorhölter, Frank-Jörg He, Yong-Qiang Jiang, Bo-Le Tang, Ji-Liang Xu, Yuquan Pühler, Alfred He, Ya-Wen Gene discovery by genome-wide CDS re-prediction and microarray-based transcriptional analysis in phytopathogen Xanthomonas campestris |
title | Gene discovery by genome-wide CDS re-prediction and microarray-based transcriptional analysis in phytopathogen Xanthomonas campestris |
title_full | Gene discovery by genome-wide CDS re-prediction and microarray-based transcriptional analysis in phytopathogen Xanthomonas campestris |
title_fullStr | Gene discovery by genome-wide CDS re-prediction and microarray-based transcriptional analysis in phytopathogen Xanthomonas campestris |
title_full_unstemmed | Gene discovery by genome-wide CDS re-prediction and microarray-based transcriptional analysis in phytopathogen Xanthomonas campestris |
title_short | Gene discovery by genome-wide CDS re-prediction and microarray-based transcriptional analysis in phytopathogen Xanthomonas campestris |
title_sort | gene discovery by genome-wide cds re-prediction and microarray-based transcriptional analysis in phytopathogen xanthomonas campestris |
topic | Research Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3142249/ https://www.ncbi.nlm.nih.gov/pubmed/21745409 http://dx.doi.org/10.1186/1471-2164-12-359 |
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