title: Burkholderia xenovorans LB400 harbors a multi-replicon, 9.73-Mbp genome shaped for versatility.
abstract: Burkholderia xenovorans LB400 (LB400), a well studied, effective polychlorinated biphenyl-degrader, has one of the two largest known bacterial genomes and is the first nonpathogenic Burkholderia isolate sequenced. From an evolutionary perspective, we find significant differences in functional specialization between the three replicons of LB400, as well as a more relaxed selective pressure for genes located on the two smaller vs. the largest replicon. High genomic plasticity, diversity, and specialization within the Burkholderia genus are exemplified by the conservation of only 44% of the genes between LB400 and Burkholderia cepacia complex strain 383. Even among four B. xenovorans strains, genome size varies from 7.4 to 9.73 Mbp. The latter is largely explained by our findings that >20% of the LB400 sequence was recently acquired by means of lateral gene transfer. Although a range of genetic factors associated with in vivo survival and intercellular interactions are present, these genetic factors are likely related to niche breadth rather than determinants of pathogenicity. The presence of at least eleven "central aromatic" and twenty "peripheral aromatic" pathways in LB400, among the highest in any sequenced bacterial genome, supports this hypothesis. Finally, in addition to the experimentally observed redundancy in benzoate degradation and formaldehyde oxidation pathways, the fact that 17.6% of proteins have a better LB400 paralog than an ortholog in a different genome highlights the importance of gene duplication and repeated acquirement, which, coupled with their divergence, raises questions regarding the role of paralogs and potential functional redundancies in large-genome microbes.
authors.affiliation: Center for Microbial Ecology, Michigan State University, East Lansing, MI 48824, USA.
authors.forename: Patrick S G
authors.initials: PS
authors.lastname: Chain
authors.forename: Vincent J
authors.initials: VJ
authors.lastname: Denef
authors.forename: Konstantinos T
authors.initials: KT
authors.lastname: Konstantinidis
authors.forename: Lisa M
authors.initials: LM
authors.lastname: Vergez
authors.forename: Loreine
authors.initials: L
authors.lastname: Agulló
authors.forename: Valeria Latorre
authors.initials: VL
authors.lastname: Reyes
authors.forename: Loren
authors.initials: L
authors.lastname: Hauser
authors.forename: Macarena
authors.initials: M
authors.lastname: Córdova
authors.forename: Luis
authors.initials: L
authors.lastname: Gómez
authors.forename: Myriam
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authors.lastname: González
authors.forename: Miriam
authors.initials: M
authors.lastname: Land
authors.forename: Victoria
authors.initials: V
authors.lastname: Lao
authors.forename: Frank
authors.initials: F
authors.lastname: Larimer
authors.forename: John J
authors.initials: JJ
authors.lastname: LiPuma
authors.forename: Eshwar
authors.initials: E
authors.lastname: Mahenthiralingam
authors.forename: Stephanie A
authors.initials: SA
authors.lastname: Malfatti
authors.forename: Christopher J
authors.initials: CJ
authors.lastname: Marx
authors.forename: J Jacob
authors.initials: JJ
authors.lastname: Parnell
authors.forename: Alban
authors.initials: A
authors.lastname: Ramette
authors.forename: Paul
authors.initials: P
authors.lastname: Richardson
authors.forename: Michael
authors.initials: M
authors.lastname: Seeger
authors.forename: Daryl
authors.initials: D
authors.lastname: Smith
authors.forename: Theodore
authors.initials: T
authors.lastname: Spilker
authors.forename: Woo Jun
authors.initials: WJ
authors.lastname: Sul
authors.forename: Tamara V
authors.initials: TV
authors.lastname: Tsoi
authors.forename: Luke E
authors.initials: LE
authors.lastname: Ulrich
authors.forename: Igor B
authors.initials: IB
authors.lastname: Zhulin
authors.forename: James M
authors.initials: JM
authors.lastname: Tiedje
mesh_terms: D019117:Burkholderia / Q000737:chemistry / Q000235:genetics* / Q000378:metabolism / Q000472:pathogenicity; D002876:Chromosomes, Bacterial; D019143:Evolution, Molecular; D020869:Gene Expression Profiling; D016680:Genome, Bacterial; D015394:Molecular Structure; D020411:Oligonucleotide Array Sequence Analysis; D012093:Replicon