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Genomics and Proteomics

DNA Sequence Duplication in Rhodobacter sphaeroides 2.4.1: Evidence of an Ancient Partnership between Chromosomes I and II

Madhusudan Choudhary, Yun-Xin Fu, Chris Mackenzie, Samuel Kaplan
Madhusudan Choudhary
1Department of Microbiology and Molecular Genetics
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Yun-Xin Fu
2Computational Genomic Section, Human Genetics Center, The University of Texas Health Science Center, Houston, Texas 77030
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Chris Mackenzie
1Department of Microbiology and Molecular Genetics
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Samuel Kaplan
1Department of Microbiology and Molecular Genetics
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  • For correspondence: Samuel.Kaplan@uth.tmc.edu
DOI: 10.1128/JB.186.7.2019-2027.2004
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ABSTRACT

The complex genome of Rhodobacter sphaeroides 2.4.1, composed of chromosomes I (CI) and II (CII), has been sequenced and assembled. We present data demonstrating that the R. sphaeroides genome possesses an extensive amount of exact DNA sequence duplication, 111 kb or ∼2.7% of the total chromosomal DNA. The chromosomal DNA sequence duplications were aligned to each other by using MUMmer. Frequency and size distribution analyses of the exact DNA duplications revealed that the interchromosomal duplications occurred prior to the intrachromosomal duplications. Most of the DNA sequence duplications in the R. sphaeroides genome occurred early in species history, whereas more recent sequence duplications are rarely found. To uncover the history of gene duplications in the R. sphaeroides genome, 44 gene duplications were sampled and then analyzed for DNA sequence similarity against orthologous DNA sequences. Phylogenetic analysis revealed that ∼80% of the total gene duplications examined displayed type A phylogenetic relationships; i.e., one copy of each member of a duplicate pair was more similar to its orthologue, found in a species closely related to R. sphaeroides, than to its duplicate, counterpart allele. The data reported here demonstrate that a massive level of gene duplications occurred prior to the origin of the R. sphaeroides 2.4.1 lineage. These findings lead to the conclusion that there is an ancient partnership between CI and CII of R. sphaeroides 2.4.1.

  • Copyright © 2004 American Society for Microbiology
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DNA Sequence Duplication in Rhodobacter sphaeroides 2.4.1: Evidence of an Ancient Partnership between Chromosomes I and II
Madhusudan Choudhary, Yun-Xin Fu, Chris Mackenzie, Samuel Kaplan
Journal of Bacteriology Mar 2004, 186 (7) 2019-2027; DOI: 10.1128/JB.186.7.2019-2027.2004

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DNA Sequence Duplication in Rhodobacter sphaeroides 2.4.1: Evidence of an Ancient Partnership between Chromosomes I and II
Madhusudan Choudhary, Yun-Xin Fu, Chris Mackenzie, Samuel Kaplan
Journal of Bacteriology Mar 2004, 186 (7) 2019-2027; DOI: 10.1128/JB.186.7.2019-2027.2004
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KEYWORDS

Bacterial Proteins
Chromosomes, Bacterial
Evolution, Molecular
gene duplication
Rhodobacter sphaeroides

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