MBE Advance Access published online on June 27, 2003
Molecular Biology and Evolution, doi:10.1093/molbev/msg175
Molecular Biology and Evolution © Society for Molecular Biology and Evolution 2003; all rights reserved
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1 Department of Molecular Evolution, University of Uppsala, Uppsala, S-751 36 Sweden
* To whom correspondence should be addressed. E-mail: Siv.Andersson{at}ebc.uu.se.
The origin and evolution of the thousands of species-specific genes with unknown functions, the so-called orphans, has been a mystery. Here, we have studied the rates and patterns of orphan sequence evolution, using the Rickettsia as our reference system. 80% of the Rickettsia conorii orphans examined in this study were found to be short gene fragments or fusions of short segments from neighboring genes. We reconstructed the putative sequences of the full-length genes from which the short orphan fragments are thought to have originated. One of the genes thus reconstructed displays weak similarity to the ankyrin-repeat protein family, an identification that is strongly supported by comparative molecular modeling. Studies of the patterns of gene fragmentation underscore the importance of short repeated sequences as targets for recombination events that result in sequence loss and the formation of short, transient ORFs. Our analysis demonstrates that gene sequences present in the common ancestor can be inferred even in cases when no full-length open reading frame is present in any of the contemporary species. Such reconstructions support the identification of lost protein functions and hint at important lifestyle changes. Key Words:
intergenic DNA, molecular evolution, phylogeny, Rickettsia
© 2003 Society for Molecular Biology and Evolution
Original Articles
Birth and Death of Orphan Genes in Rickettsia
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