title: Evidence of neutral transcriptome evolution in plants.
abstract: * The transcriptome of an organism is its set of gene transcripts (mRNAs) at a defined spatial and temporal locus. Because gene expression is affected markedly by environmental and developmental perturbations, it is widely assumed that transcriptome divergence among taxa represents adaptive phenotypic selection. This assumption has been challenged by neutral theories which propose that stochastic processes drive transcriptome evolution. * To test for evidence of neutral transcriptome evolution in plants, we quantified 18 494 gene transcripts in nonsenescent leaves of 14 taxa of Brassicaceae using robust cross-species transcriptomics which includes a two-step physical and in silico-based normalization procedure based on DNA similarity among taxa. * Transcriptome divergence correlates positively with evolutionary distance between taxa and with variation in gene expression among samples. Results are similar for pseudogenes and chloroplast genes evolving at different rates. Remarkably, variation in transcript abundance among root-cell samples correlates positively with transcriptome divergence among root tissues and among taxa. * Because neutral processes affect transcriptome evolution in plants, many differences in gene expression among or within taxa may be nonfunctional, reflecting ancestral plasticity and founder effects. Appropriate null models are required when comparing transcriptomes in space and time.
authors.affiliation: School of Biosciences, University of Nottingham, Sutton Bonington, Loughborough LE12 5RD, UK.
authors.forename: M R
authors.initials: MR
authors.lastname: Broadley
authors.affiliation: SCRI, Invergowrie, Dundee DD2 5DA, UK.
authors.forename: P J
authors.initials: PJ
authors.lastname: White
authors.affiliation: University of Warwick, Wellesbourne, Warwick CV35 9EF, UK.
authors.forename: J P
authors.initials: JP
authors.lastname: Hammond
authors.affiliation: School of Biosciences, University of Nottingham, Sutton Bonington, Loughborough LE12 5RD, UK.
authors.forename: N S
authors.initials: NS
authors.lastname: Graham
authors.affiliation: University of Warwick, Wellesbourne, Warwick CV35 9EF, UK.
authors.forename: H C
authors.initials: HC
authors.lastname: Bowen
authors.affiliation: School of Biosciences, University of Nottingham, Sutton Bonington, Loughborough LE12 5RD, UK.
authors.forename: Z F
authors.initials: ZF
authors.lastname: Emmerson
authors.affiliation: School of Biosciences, University of Nottingham, Sutton Bonington, Loughborough LE12 5RD, UK.
authors.forename: R G
authors.initials: RG
authors.lastname: Fray
authors.affiliation: SCRI, Invergowrie, Dundee DD2 5DA, UK.
authors.forename: P P M
authors.initials: PPM
authors.lastname: Iannetta
authors.affiliation: SCRI, Invergowrie, Dundee DD2 5DA, UK.
authors.forename: J W
authors.initials: JW
authors.lastname: McNicol
authors.affiliation: School of Biosciences, University of Nottingham, Sutton Bonington, Loughborough LE12 5RD, UK.
authors.forename: S T
authors.initials: ST
authors.lastname: May
mesh_terms: D017360:Arabidopsis / Q000235:genetics*; D029681:Arabidopsis Proteins / Q000235:genetics; D019607:Brassicaceae / Q000235:genetics*; D015342:DNA Probes; D019143:Evolution, Molecular; D015870:Gene Expression; D020869:Gene Expression Profiling; D017343:Genes, Plant; D040961:Genetic Drift; D014644:Genetic Variation; D054628:Genome, Chloroplast; D018398:Homeodomain Proteins / Q000235:genetics; D008957:Models, Genetic; D010802:Phylogeny; D018517:Plant Roots / Q000235:genetics; D011544:Pseudogenes; D012333:RNA, Messenger / Q000235:genetics; D013269:Stochastic Processes; D014157:Transcription Factors / Q000235:genetics
chemical_list: D029681:Arabidopsis Proteins; D015342:DNA Probes; D018398:Homeodomain Proteins; C092852:KNAT5 protein, Arabidopsis; D012333:RNA, Messenger; D014157:Transcription Factors
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