ArticleScientific reports2016
Divergence of RNA polymerase α subunits in angiosperm plastid genomes is mediated by genomic rearrangement.
Article in Scientific reports, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 28 papers.
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28 citing papers in PubMed, 59 citations in OpenAlex.
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- Elucidating the evolutionary dynamics of parasitism in Cuscuta: in-depth phylogenetic reconstruction and extensive plastomes reduction.BMC genomics · 2025Article
- Phylogenomic analysis and dynamic evolution of chloroplast genomes of Clematis nannophylla.Scientific reports · 2024Article
- Leaf variegation caused by plastome structural variation: an example fromHorticulture research · 2024Article
- Complete chloroplast genomes and comparative analysis of Ligustrum species.Scientific reports · 2023Article
- Towards the plastome evolution and phylogeny of Cycas L. (Cycadaceae): molecular-morphology discordance and gene tree space analysis.BMC plant biology · 2022Article
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- Comparative Plastome Analysis of Three Amaryllidaceae Subfamilies: Insights into Variation of Genome Characteristics, Phylogeny, and Adaptive Evolution.BioMed research international · 2022Article
- Lineage-Specific Variation in IR Boundary Shift Events, Inversions, and Substitution Rates among CaprifoliaceaeInternational journal of molecular sciences · 2021Article
- The chloroplast genome evolution of Venus slipper (Paphiopedilum): IR expansion, SSC contraction, and highly rearranged SSC regions.BMC plant biology · 2021Article
- Chloroplast Genome Evolution in Four Montane Zingiberaceae Taxa in China.Frontiers in plant science · 2021Article
- Chloroplast Genomes of Two Species ofFrontiers in plant science · 2021Article
- Insights into Comparative Genomics, Codon Usage Bias, and Phylogenetic Relationship of Species from Biebersteiniaceae and Nitrariaceae Based on Complete Chloroplast Genomes.Plants (Basel, Switzerland) · 2020Article
- A Repertory of Rearrangements and the Loss of an Inverted Repeat Region in Passiflora Chloroplast Genomes.Genome biology and evolution · 2020Article
- Rampant Nuclear Transfer and Substitutions of Plastid Genes in Passiflora.Genome biology and evolution · 2020Article
- Plastome phylogenomic study of Gentianeae (Gentianaceae): widespread gene tree discordance and its association with evolutionary rate heterogeneity of plastid genes.BMC plant biology · 2020Article
- Evolutionary dynamics of the chloroplast genome sequences of six Colobanthus species.Scientific reports · 2020Article
- Unprecedented Intraindividual Structural Heteroplasmy in Eleocharis (Cyperaceae, Poales) Plastomes.Genome biology and evolution · 2020Article
- Interspecific Hybrids BetweenFrontiers in plant science · 2020Article
Corrections and comments
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Authors and funding
6 authors at 2 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
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.
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