title: Divergence of RNA polymerase α subunits in angiosperm plastid genomes is mediated by genomic rearrangement.
abstract: Genes for the plastid-encoded RNA polymerase (PEP) persist in the plastid genomes of all photosynthetic angiosperms. However, three unrelated lineages (Annonaceae, Passifloraceae and Geraniaceae) have been identified with unusually divergent open reading frames (ORFs) in the conserved region of rpoA, the gene encoding the PEP α subunit. We used sequence-based approaches to evaluate whether these genes retain function. Both gene sequences and complete plastid genome sequences were assembled and analyzed from each of the three angiosperm families. Multiple lines of evidence indicated that the rpoA sequences are likely functional despite retaining as low as 30% nucleotide sequence identity with rpoA genes from outgroups in the same angiosperm order. The ratio of non-synonymous to synonymous substitutions indicated that these genes are under purifying selection, and bioinformatic prediction of conserved domains indicated that functional domains are preserved. One of the lineages (Pelargonium, Geraniaceae) contains species with multiple rpoA-like ORFs that show evidence of ongoing inter-paralog gene conversion. The plastid genomes containing these divergent rpoA genes have experienced extensive structural rearrangement, including large expansions of the inverted repeat. We propose that illegitimate recombination, not positive selection, has driven the divergence of rpoA.
authors.affiliation: Department of Integrative Biology, University of Texas, Austin, TX 78712, USA.
authors.forename: J Chris
authors.initials: JC
authors.lastname: Blazier
authors.affiliation: Department of Integrative Biology, University of Texas, Austin, TX 78712, USA.
authors.forename: Tracey A
authors.initials: TA
authors.lastname: Ruhlman
authors.affiliation: Department of Integrative Biology, University of Texas, Austin, TX 78712, USA.
authors.forename: Mao-Lun
authors.initials: ML
authors.lastname: Weng
authors.affiliation: Department of Integrative Biology, University of Texas, Austin, TX 78712, USA.
authors.forename: Sumaiyah K
authors.initials: SK
authors.lastname: Rehman
authors.affiliation: Biotechnology Research Group, Department of Biological Science, Faculty of Sciences, King Abdulaziz University, Jeddah 21589, Saudi Arabia.
authors.forename: Jamal S M
authors.initials: JS
authors.lastname: Sabir
authors.affiliation: Department of Integrative Biology, University of Texas, Austin, TX 78712, USA.|Biotechnology Research Group, Department of Biological Science, Faculty of Sciences, King Abdulaziz University, Jeddah 21589, Saudi Arabia.
authors.forename: Robert K
authors.initials: RK
authors.lastname: Jansen
mesh_terms: D060365:Chloroplast Proteins / Q000737:chemistry / Q000235:genetics* / Q000378:metabolism; D017124:Conserved Sequence; D012321:DNA-Directed RNA Polymerases / Q000737:chemistry / Q000235:genetics* / Q000378:metabolism; D019143:Evolution, Molecular; D054627:Genome, Plastid; D042822:Genomic Instability; D019684:Magnoliopsida / Q000201:enzymology / Q000235:genetics*; D016366:Open Reading Frames
chemical_list: D060365:Chloroplast Proteins; D012321:DNA-Directed RNA Polymerases; C113275:RNA polymerase alpha subunit