The prevalence of gene duplications and their ancient origin in <it>Rhodobacter sphaeroides </it>2.4.1
<p>Abstract</p> <p>Background</p> <p><it>Rhodobacter sphaeroides </it>2.4.1 is a metabolically versatile organism that belongs to α-3 subdivision of <it>Proteobacteria</it>. The present study was to identify the extent, history, and role of gene...
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| Format: | Article |
| Language: | English |
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BMC
2010-12-01
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| Series: | BMC Microbiology |
| Online Access: | http://www.biomedcentral.com/1471-2180/10/331 |
| _version_ | 1811287901630103552 |
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| author | Cho Hyuk Peters Anne Schroeder Kristen Lin Lin Bavishi Anish Choudhary Madhusudan |
| author_facet | Cho Hyuk Peters Anne Schroeder Kristen Lin Lin Bavishi Anish Choudhary Madhusudan |
| author_sort | Cho Hyuk |
| collection | DOAJ |
| description | <p>Abstract</p> <p>Background</p> <p><it>Rhodobacter sphaeroides </it>2.4.1 is a metabolically versatile organism that belongs to α-3 subdivision of <it>Proteobacteria</it>. The present study was to identify the extent, history, and role of gene duplications in <it>R. sphaeroides </it>2.4.1, an organism that possesses two chromosomes.</p> <p>Results</p> <p>A protein similarity search (BLASTP) identified 1247 <it>orfs </it>(~29.4% of the total protein coding <it>orfs</it>) that are present in 2 or more copies, 37.5% (234 gene-pairs) of which exist in duplicate copies. The distribution of the duplicate gene-pairs in all Clusters of Orthologous Groups (COGs) differed significantly when compared to the COG distribution across the whole genome. Location plots revealed clusters of gene duplications that possessed the same COG classification. Phylogenetic analyses were performed to determine a tree topology predicting either a Type-A or Type-B phylogenetic relationship. A Type-A phylogenetic relationship shows that a copy of the protein-pair matches more with an ortholog from a species closely related to <it>R. sphaeroides </it>while a Type-B relationship predicts the highest match between both copies of the <it>R. sphaeroides </it>protein-pair. The results revealed that ~77% of the proteins exhibited a Type-A phylogenetic relationship demonstrating the ancient origin of these gene duplications. Additional analyses on three other strains of <it>R. sphaeroides </it>revealed varying levels of gene loss and retention in these strains. Also, analyses on common gene pairs among the four strains revealed that these genes experience similar functional constraints and undergo purifying selection.</p> <p>Conclusions</p> <p>Although the results suggest that the level of gene duplication in organisms with complex genome structuring (more than one chromosome) seems to be not markedly different from that in organisms with only a single chromosome, these duplications may have aided in genome reorganization in this group of eubacteria prior to the formation of <it>R. sphaeroides </it>as gene duplications involved in specialized functions might have contributed to complex genomic development.</p> |
| first_indexed | 2024-04-13T03:27:37Z |
| format | Article |
| id | doaj.art-c4a68984838345679e815fe41963b62d |
| institution | Directory Open Access Journal |
| issn | 1471-2180 |
| language | English |
| last_indexed | 2024-04-13T03:27:37Z |
| publishDate | 2010-12-01 |
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| series | BMC Microbiology |
| spelling | doaj.art-c4a68984838345679e815fe41963b62d2022-12-22T03:04:37ZengBMCBMC Microbiology1471-21802010-12-0110133110.1186/1471-2180-10-331The prevalence of gene duplications and their ancient origin in <it>Rhodobacter sphaeroides </it>2.4.1Cho HyukPeters AnneSchroeder KristenLin LinBavishi AnishChoudhary Madhusudan<p>Abstract</p> <p>Background</p> <p><it>Rhodobacter sphaeroides </it>2.4.1 is a metabolically versatile organism that belongs to α-3 subdivision of <it>Proteobacteria</it>. The present study was to identify the extent, history, and role of gene duplications in <it>R. sphaeroides </it>2.4.1, an organism that possesses two chromosomes.</p> <p>Results</p> <p>A protein similarity search (BLASTP) identified 1247 <it>orfs </it>(~29.4% of the total protein coding <it>orfs</it>) that are present in 2 or more copies, 37.5% (234 gene-pairs) of which exist in duplicate copies. The distribution of the duplicate gene-pairs in all Clusters of Orthologous Groups (COGs) differed significantly when compared to the COG distribution across the whole genome. Location plots revealed clusters of gene duplications that possessed the same COG classification. Phylogenetic analyses were performed to determine a tree topology predicting either a Type-A or Type-B phylogenetic relationship. A Type-A phylogenetic relationship shows that a copy of the protein-pair matches more with an ortholog from a species closely related to <it>R. sphaeroides </it>while a Type-B relationship predicts the highest match between both copies of the <it>R. sphaeroides </it>protein-pair. The results revealed that ~77% of the proteins exhibited a Type-A phylogenetic relationship demonstrating the ancient origin of these gene duplications. Additional analyses on three other strains of <it>R. sphaeroides </it>revealed varying levels of gene loss and retention in these strains. Also, analyses on common gene pairs among the four strains revealed that these genes experience similar functional constraints and undergo purifying selection.</p> <p>Conclusions</p> <p>Although the results suggest that the level of gene duplication in organisms with complex genome structuring (more than one chromosome) seems to be not markedly different from that in organisms with only a single chromosome, these duplications may have aided in genome reorganization in this group of eubacteria prior to the formation of <it>R. sphaeroides </it>as gene duplications involved in specialized functions might have contributed to complex genomic development.</p>http://www.biomedcentral.com/1471-2180/10/331 |
| spellingShingle | Cho Hyuk Peters Anne Schroeder Kristen Lin Lin Bavishi Anish Choudhary Madhusudan The prevalence of gene duplications and their ancient origin in <it>Rhodobacter sphaeroides </it>2.4.1 BMC Microbiology |
| title | The prevalence of gene duplications and their ancient origin in <it>Rhodobacter sphaeroides </it>2.4.1 |
| title_full | The prevalence of gene duplications and their ancient origin in <it>Rhodobacter sphaeroides </it>2.4.1 |
| title_fullStr | The prevalence of gene duplications and their ancient origin in <it>Rhodobacter sphaeroides </it>2.4.1 |
| title_full_unstemmed | The prevalence of gene duplications and their ancient origin in <it>Rhodobacter sphaeroides </it>2.4.1 |
| title_short | The prevalence of gene duplications and their ancient origin in <it>Rhodobacter sphaeroides </it>2.4.1 |
| title_sort | prevalence of gene duplications and their ancient origin in it rhodobacter sphaeroides it 2 4 1 |
| url | http://www.biomedcentral.com/1471-2180/10/331 |
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