ArticleAnnals of botany2016
Variable presence of the inverted repeat and plastome stability in Erodium.
Article in Annals of botany, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 64 papers.
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64 citing papers in PubMed, 105 citations in OpenAlex.
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- Comparative Analysis of Complete Chloroplast Genomes and Phylogenetic Relationships in Medicinally Important Pantropical GenusInternational journal of molecular sciences · 2025Article
- Dispersed repeats and inverted repeat expansion drive major plastomic rearrangements inFrontiers in plant science · 2025Article
- Removal of the large inverted repeat from the plastid genome reveals gene dosage effects and leads to increased genome copy number.Nature plants · 2024Article
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- Comparative Analysis of Chloroplast Pan-Genomes and Transcriptomics Reveals Cold Adaptation inInternational journal of molecular sciences · 2024Article
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- Comparative chloroplast genomics and insights into the molecular evolution of Tanaecium (Bignonieae, Bignoniaceae).Scientific reports · 2023Article
- Ancient Horizontal Gene Transfers from Plastome to Mitogenome of a Nonphotosynthetic Orchid,International journal of molecular sciences · 2023Article
- Complete chloroplast genomes provide insights into evolution and phylogeny of Zingiber (Zingiberaceae).BMC genomics · 2023Article
- Intraspecific phylogeny and genomic resources development for an important medical plantFrontiers in plant science · 2023Article
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- Chloroplast genomes of fourFrontiers in plant science · 2023Article
- Structural Plastome Evolution in Holoparasitic Hydnoraceae with Special Focus on Inverted and Direct Repeats.Genome biology and evolution · 2022Article
4 more citing papers are in PubMed but not listed here.
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Authors and funding
7 authors at 2 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
BACKGROUND AND
aimsSeveral unrelated lineages such as plastids, viruses and plasmids, have converged on quadripartite genomes of similar size with large and small single copy regions and a large inverted repeat (IR). Except for Erodium (Geraniaceae), saguaro cactus and some legumes, the plastomes of all photosynthetic angiosperms display this structure. The functional significance of the IR is not understood and Erodium provides a system to examine the role of the IR in the long-term stability of these genomes. We compared the degree of genomic rearrangement in plastomes of Erodium that differ in the presence and absence of the IR.
methodsWe sequenced 17 new Erodium plastomes. Using 454, Illumina, PacBio and Sanger sequences, 16 genomes were assembled and categorized along with one incomplete and two previously published Erodium plastomes. We conducted phylogenetic analyses among these species using a dataset of 19 protein-coding genes and determined if significantly higher evolutionary rates had caused the long branch seen previously in phylogenetic reconstructions within the genus. Bioinformatic comparisons were also performed to evaluate plastome evolution across the genus. KEY
resultsErodium plastomes fell into four types (Type 1-4) that differ in their substitution rates, short dispersed repeat content and degree of genomic rearrangement, gene and intron content and GC content. Type 4 plastomes had significantly higher rates of synonymous substitutions (dS) for all genes and for 14 of the 19 genes non-synonymous substitutions (dN) were significantly accelerated. We evaluated the evidence for a single IR loss in Erodium and in doing so discovered that Type 4 plastomes contain a novel IR.
conclusionsThe presence or absence of the IR does not affect plastome stability in Erodium. Rather, the overall repeat content shows a negative correlation with genome stability, a pattern in agreement with other angiosperm groups and recent findings on genome stability in bacterial endosymbionts.
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