The process of genome shrinkage in the obligate symbiont Buchnera aphidicola

Persistent Link:
http://hdl.handle.net/10150/610142
Title:
The process of genome shrinkage in the obligate symbiont Buchnera aphidicola
Author:
Moran, Nancy; Mira, Alex
Affiliation:
Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ 85721, USA
Issue Date:
2001
Publisher:
BioMed Central
Citation:
Genome Biology 2001, 2(12):research0054.1–0054.12 http://genomebiology.com/2001/2/12/research/0054
Journal:
Genome Biology
Rights:
© 2001 Moran and Mira, licensee BioMed Central Ltd
Collection Information:
This item is part of the UA Faculty Publications collection. For more information this item or other items in the UA Campus Repository, contact the University of Arizona Libraries at repository@u.library.arizona.edu.
Abstract:
BACKGROUND:Very small genomes have evolved repeatedly in eubacterial lineages that have adopted obligate associations with eukaryotic hosts. Complete genome sequences have revealed that small genomes retain very different gene sets, raising the question of how final genome content is determined. To examine the process of genome reduction, the tiny genome of the endosymbiont Buchnera aphidicola was compared to the larger ancestral genome, reconstructed on the basis of the phylogenetic distribution of gene orthologs among fully sequenced relatives of Escherichia coli and Buchnera.RESULTS:The reconstructed ancestral genome contained 2,425 open reading frames (ORFs). The Buchnera genome, containing 564 ORFs, consists of 153 fragments of 1-34 genes that are syntenic with reconstructed ancestral regions. On the basis of this reconstruction, 503 genes were eliminated within syntenic fragments, and 1,403 genes were lost from the gaps between syntenic fragments, probably in connection with genome rearrangements. Lost regions are sometimes large, and often span functionally unrelated genes. In addition, individual genes and regulatory regions have been lost or eroded. For the categories of DNA repair genes and rRNA genes, most lost loci fall in regions between syntenic fragments. This history of gene loss is reflected in the sequences of intergenic spacers at positions where genes were once present.CONCLUSIONS:The most plausible interpretation of this reconstruction is that Buchnera lost many genes through the fixation of large deletions soon after the acquisition of an obligate endosymbiotic lifestyle. An implication is that final genome composition may be partly the chance outcome of initial deletions and that neighboring genes influence the likelihood of loss of particular genes and pathways.
DOI:
10.1186/gb-2001-2-12-research0054
Version:
Final published version
Additional Links:
http://genomebiology.biomedcentral.com/articles/10.1186/gb-2001-2-12-research0054

Full metadata record

DC FieldValue Language
dc.contributor.authorMoran, Nancyen
dc.contributor.authorMira, Alexen
dc.date.accessioned2016-05-20T08:59:29Z-
dc.date.available2016-05-20T08:59:29Z-
dc.date.issued2001en
dc.identifier.citationGenome Biology 2001, 2(12):research0054.1–0054.12 http://genomebiology.com/2001/2/12/research/0054en
dc.identifier.doi10.1186/gb-2001-2-12-research0054en
dc.identifier.urihttp://hdl.handle.net/10150/610142-
dc.description.abstractBACKGROUND:Very small genomes have evolved repeatedly in eubacterial lineages that have adopted obligate associations with eukaryotic hosts. Complete genome sequences have revealed that small genomes retain very different gene sets, raising the question of how final genome content is determined. To examine the process of genome reduction, the tiny genome of the endosymbiont Buchnera aphidicola was compared to the larger ancestral genome, reconstructed on the basis of the phylogenetic distribution of gene orthologs among fully sequenced relatives of Escherichia coli and Buchnera.RESULTS:The reconstructed ancestral genome contained 2,425 open reading frames (ORFs). The Buchnera genome, containing 564 ORFs, consists of 153 fragments of 1-34 genes that are syntenic with reconstructed ancestral regions. On the basis of this reconstruction, 503 genes were eliminated within syntenic fragments, and 1,403 genes were lost from the gaps between syntenic fragments, probably in connection with genome rearrangements. Lost regions are sometimes large, and often span functionally unrelated genes. In addition, individual genes and regulatory regions have been lost or eroded. For the categories of DNA repair genes and rRNA genes, most lost loci fall in regions between syntenic fragments. This history of gene loss is reflected in the sequences of intergenic spacers at positions where genes were once present.CONCLUSIONS:The most plausible interpretation of this reconstruction is that Buchnera lost many genes through the fixation of large deletions soon after the acquisition of an obligate endosymbiotic lifestyle. An implication is that final genome composition may be partly the chance outcome of initial deletions and that neighboring genes influence the likelihood of loss of particular genes and pathways.en
dc.language.isoenen
dc.publisherBioMed Centralen
dc.relation.urlhttp://genomebiology.biomedcentral.com/articles/10.1186/gb-2001-2-12-research0054en
dc.rights© 2001 Moran and Mira, licensee BioMed Central Ltden
dc.titleThe process of genome shrinkage in the obligate symbiont Buchnera aphidicolaen
dc.typeArticleen
dc.contributor.departmentDepartment of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ 85721, USAen
dc.identifier.journalGenome Biologyen
dc.description.collectioninformationThis item is part of the UA Faculty Publications collection. For more information this item or other items in the UA Campus Repository, contact the University of Arizona Libraries at repository@u.library.arizona.edu.en
dc.eprint.versionFinal published versionen
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