title: Comparative genomics of Brassica oleracea and Arabidopsis thaliana reveal gene loss, fragmentation, and dispersal after polyploidy.
abstract: We sequenced 2.2 Mb representing triplicated genome segments of Brassica oleracea, which are each paralogous with one another and homologous with a segmentally duplicated region of the Arabidopsis thaliana genome. Sequence annotation identified 177 conserved collinear genes in the B. oleracea genome segments. Analysis of synonymous base substitution rates indicated that the triplicated Brassica genome segments diverged from a common ancestor soon after divergence of the Arabidopsis and Brassica lineages. This conclusion was corroborated by phylogenetic analysis of protein families. Using A. thaliana as an outgroup, 35% of the genes inferred to be present when genome triplication occurred in the Brassica lineage have been lost, most likely via a deletion mechanism, in an interspersed pattern. Genes encoding proteins involved in signal transduction or transcription were not found to be significantly more extensively retained than those encoding proteins classified with other functions, but putative proteins predicted in the A. thaliana genome were underrepresented in B. oleracea. We identified one example of gene loss from the Arabidopsis lineage. We found evidence for the frequent insertion of gene fragments of nuclear genomic origin and identified four apparently intact genes in noncollinear positions in the B. oleracea and A. thaliana genomes.
authors.affiliation: The Institute for Genomic Research, Rockville, Maryland 20850, USA.
authors.forename: Christopher D
authors.initials: CD
authors.lastname: Town
authors.forename: Foo
authors.initials: F
authors.lastname: Cheung
authors.forename: Rama
authors.initials: R
authors.lastname: Maiti
authors.forename: Jonathan
authors.initials: J
authors.lastname: Crabtree
authors.forename: Brian J
authors.initials: BJ
authors.lastname: Haas
authors.forename: Jennifer R
authors.initials: JR
authors.lastname: Wortman
authors.forename: Erin E
authors.initials: EE
authors.lastname: Hine
authors.forename: Ryan
authors.initials: R
authors.lastname: Althoff
authors.forename: Tamara S
authors.initials: TS
authors.lastname: Arbogast
authors.forename: Luke J
authors.initials: LJ
authors.lastname: Tallon
authors.forename: Marielle
authors.initials: M
authors.lastname: Vigouroux
authors.forename: Martin
authors.initials: M
authors.lastname: Trick
authors.forename: Ian
authors.initials: I
authors.lastname: Bancroft
mesh_terms: D017360:Arabidopsis / Q000235:genetics*; D001937:Brassica / Q000235:genetics*; D017124:Conserved Sequence / Q000235:genetics; D020451:Contig Mapping; D004251:DNA Transposable Elements / Q000235:genetics; D017353:Gene Deletion; D020440:Gene Duplication; D017343:Genes, Plant / Q000235:genetics*; D018745:Genome, Plant; D023281:Genomics; D020411:Oligonucleotide Array Sequence Analysis; D010802:Phylogeny; D011123:Polyploidy; D016415:Sequence Alignment
chemical_list: D004251:DNA Transposable Elements