Genomes and Genes
Affiliation: University of Arizona
- Evolutionary origins of genomic repertoires in bacteriaEmmanuelle Lerat
Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, Arizona, USA
PLoS Biol 3:e130. 2005..Although our analyses are limited to the gamma-Proteobacteria, these results resolve a long-standing paradox-i.e., the ability to make robust phylogenetic inferences in light of substantial LGT...
- The evolutionary history of quorum-sensing systems in bacteriaEmmanuelle Lerat
Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ, USA
Mol Biol Evol 21:903-13. 2004..Gene phylogenies for the main LuxI/R family in Pseudomonas species imply a complex history of lateral transfer, ancestral duplication, and gene loss within the genus...
- Examining bacterial species under the specter of gene transfer and exchangeHoward Ochman
Department of Biochemistry and Molecular Biophysics, University of Arizona, Tucson, 85721, USA
Proc Natl Acad Sci U S A 102:6595-9. 2005..Taken as a whole, the results derived from the analysis of complete gene inventories support several of the current means to recognize and define bacterial species...
- From gene trees to organismal phylogeny in prokaryotes: the case of the gamma-ProteobacteriaEmmanuelle Lerat
Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, USA
PLoS Biol 1:E19. 2003....
- A bunch of fun-guys: the whole-genome view of yeast evolutionHoward Ochman
Department of Biochemistry and Molecular Biophysics, University of Arizona, Tucson, AZ 87521, USA
Trends Genet 21:1-3. 2005..The pattern of genome evolution in yeast differs from that in bacteria apparently as a result of stronger selective constraints on bacterial chromosomes...
- The source of laterally transferred genes in bacterial genomesVincent Daubin
Laboratoire de Biometrie et Biologie Evolutive, UMR CNRS 5558, Universite Claude Bernard Lyon 1, Cedex, France
Genome Biol 4:R57. 2003....
- Recognizing the pseudogenes in bacterial genomesEmmanuelle Lerat
Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ 87521, USA
Nucleic Acids Res 33:3125-32. 2005....
- Psi-Phi: exploring the outer limits of bacterial pseudogenesEmmanuelle Lerat
Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, Arizona 87521, USA
Genome Res 14:2273-8. 2004..Almost all (>95%) pseudogenes are restricted to only one of the genomes and are of relatively recent origin, suggesting that these bacteria possess active mechanisms to eliminate nonfunctional genes...
- Codon usage by transposable elements and their host genes in five speciesEmmanuelle Lerat
Laboratoire Biométrie et Biologie Evolutive, UMR CNRS 5558, Universite Lyon 1, 69622 Villeurbanne Cedex, France
J Mol Evol 54:625-37. 2002..melanogaster, however, the bias in codon usage of the TEs clearly differed from that of weakly expressed genes. These findings suggest that selection acts on TEs and that TEs may display specific behavior within the host genomes...
- Maintenance in the chicken genome of the retroviral-like cENS gene family specifically expressed in early embryosEmmanuelle Lerat
Laboratoire de Biometrie et Biologie Evolutive, Universite de Lyon, Universite Lyon 1, CNRS, UMR 5558, Villeurbanne, France
J Mol Evol 65:215-27. 2007..Taken together, these findings suggest a function sustained by a neogene of retroviral origin during the early stages of chicken development...
- Hypervariable and highly divergent intron-exon organizations in the chordate Oikopleura dioicaRolf B Edvardsen
Sars Centre for Marine Molecular Biology, Bergen High Technology Centre, Thormoehlensgt 55, 5020 Bergen, Norway
J Mol Evol 59:448-57. 2004..We also speculate that introns placed at gene-specific positions may contribute to suppressing these exchanges and thereby favor their own persistence...
- Sequence divergence within transposable element families in the Drosophila melanogaster genomeEmmanuelle Lerat
Laboratoire de Biometrie et Biologie Evolutive, Universite Lyon 1, 69622 Villeurbanne Cedex, France
Genome Res 13:1889-96. 2003..This clearly demonstrates that the TEs are highly active within the genome,suggesting that the genetic variability of the Drosophila genome is still being renewed by the action of TEs...
- The relative abundance of dinucleotides in transposable elements in five speciesEmmanuelle Lerat
Mol Biol Evol 19:964-7. 2002
- Losing helena: the extinction of a drosophila line-like elementRita Rebollo
Université de Lyon Université Lyon 1 CNRS UMR 5558, Laboratoire de Biometrie et Biologie Evolutive, Villeurbanne F 69622, France
BMC Genomics 9:149. 2008..simulans, we analyzed the DNA sequences of copies of this element in samples of various natural populations of these two species...