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Genome deterioration: Loss of repeated sequences and accumulation of junk DNA
Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolutionary Biology, Molecular Evolution.
Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolutionary Biology, Molecular Evolution.
Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolutionary Biology, Molecular Evolution.
2002 (English)In: Genetica, ISSN 0016-6707, E-ISSN 1573-6857, Vol. 115, no 1, 1-12 p.Article in journal (Refereed) Published
Abstract [en]

A global survey of microbial genomes reveals a correlation between genome size, repeat content and lifestyle. Free-living bacteria have large genomes with a high content of repeated sequences and self-propagating DNA, such as transposons and bacteriophages. In contrast, obligate intracellular bacteria have small genomes with a low content of repeated sequences and no or few genetic parasites. In extreme cases, such as in the 650 kb-genomes of aphid endosymbionts of the genus Buchnera all repeated sequences above 200bp have been eliminated. We speculate that the initial downsizing of the genomes of obligate symbionts and parasites occurred by homologous recombination at repeated genes, leading to the loss of large blocks of DNA as well as to the consumption of repeated sequences. Further sequence elimination in these small genomes seems primarily to result from the accumulation of short deletions within genic sequences. This process may lead to temporary increases in the genomic content of pseudogenes and 'junk' DNA. We discuss causes and long-term consequences of extreme genome size reductions in obligate intracellular bacteria.

Place, publisher, year, edition, pages
2002. Vol. 115, no 1, 1-12 p.
National Category
Biochemistry and Molecular Biology
Identifiers
URN: urn:nbn:se:uu:diva-89693PubMedID: 12188042OAI: oai:DiVA.org:uu-89693DiVA: diva2:161379
Available from: 2002-03-06 Created: 2002-03-06 Last updated: 2017-12-14Bibliographically approved
In thesis
1. Patterns and Processes of Molecular Evolution in Rickettsia
Open this publication in new window or tab >>Patterns and Processes of Molecular Evolution in Rickettsia
2002 (English)Doctoral thesis, comprehensive summary (Other academic)
Abstract [en]

Species of the genus Rickettsia are obligate intracellular parasites of the a-proteobacterial subdivision. It has been suggested that obligate intracellular bacteria have evolved from free-living bacteria with much larger genome sizes. Transitions to intracellular growth habitats are normally associated with radical genomic alterations, particularly genome rearrangements and gene losses.

This thesis presents a comparative study of evolutionary processes such as gene rearrangements, deletions and duplications in a variety of Rickettsia species. The results show that early intrachromosomal recombination events mediated by duplicated genes and short repeats have resulted in deletions as well as rearrangements. For example, an exceptional organization of the elongation factor genes was found in all species examined, suggesting that this rearrangement event occurred at the early stage of the evolution of Rickettsia. Likewise, it was found that a repetitive element, the so-called Rickettsia Palindromic Element (RPE) flourished prior to species divergence in Rickettsia. Finally, a phylogenetic analysis shows that the duplication events that gave rise to the five genes encoding ATP/ADP transporters occurred long before the divergence of the two major groups of Rickettsia. Taken together, this suggests that Rickettsia have been intracellular parasites for an extensive period of time.

A detailed analysis of the patterns of nucleotide changes in genes and intergenic regions among the different species provides evidence for a gradual accumulation of short deletions. This suggests that different distributions of genes and repeated sequences in modern Rickettsia species reflect species-specific differences in rates of deterioration rather than variation in rates of intra-genomic sequence proliferation.

Place, publisher, year, edition, pages
Uppsala: Acta Universitatis Upsaliensis, 2002. 40 p.
Series
Comprehensive Summaries of Uppsala Dissertations from the Faculty of Science and Technology, ISSN 1104-232X ; 689
Keyword
Developmental biology, Utvecklingsbiologi
National Category
Developmental Biology
Research subject
Molecular Biology
Identifiers
urn:nbn:se:uu:diva-1789 (URN)91-554-5248-5 (ISBN)
Public defence
2002-03-22, Lindahlsalen, Uppsala, 10:00
Opponent
Available from: 2002-03-06 Created: 2002-03-06Bibliographically approved

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