ArticleBMC genomics2008
Gene rearrangement analysis and ancestral order inference from chloroplast genomes with inverted repeat.
Article in BMC genomics, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 27 papers.
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Who cites it
27 citing papers in PubMed.
- Characterisation of the chloroplast genome of Macrotyloma species: comparative analysis and phylogenomic insights.Scientific reports · 2026Article
- Revisiting Phryma leptostachya L.: phylogenetic relationships and biogeographical patterns from complete plastome.BMC plant biology · 2025Article
- Comparative and phylogenetic analysis of Potentilla and Dasiphora (Rosaceae) based on plastid genome.BMC plant biology · 2025Article
- Phylogeny, structural patterns, and polymorphisms inFrontiers in plant science · 2025Article
- Phylogenetic relationships, selective pressure and molecular markers development of six species in subfamily Polygonoideae based on complete chloroplast genomes.Scientific reports · 2024Article
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- Evolutionary differences in gene loss and pseudogenization among mycoheterotrophic orchids in the tribe Vanilleae (subfamily Vanilloideae).Frontiers in plant science · 2023Article
- Insights into taxonomy and phylogenetic relationships of elevenFrontiers in plant science · 2023Article
- Phylogenetic analysis based on single-copy orthologous proteins in highly variable chloroplast genomes of Corydalis.Scientific reports · 2022Article
- The Plastome Sequences ofInternational journal of molecular sciences · 2022Article
- Article
- Chloroplast genome sequence of Chongming lima bean (Phaseolus lunatus L.) and comparative analyses with other legume chloroplast genomes.BMC genomics · 2021Article
- Repeats in mitochondrial and chloroplast genomes characterize the ecotypes of theMolecular breeding : new strategies in plant improvement · 2021Article
- The plastome sequence of Bactris gasipaes and evolutionary analysis in tribe Cocoseae (Arecaceae).PloS one · 2021Article
- Comparative analysis of chloroplast genomes in Vasconcellea pubescens A.DC. and Carica papaya L.Scientific reports · 2020Article
- Evolution ofCommunications biology · 2019Article
- Article
- The Complete Chloroplast Genome Sequence of Tree of Heaven (Ailanthus altissima (Mill.) (Sapindales: Simaroubaceae), an Important Pantropical Tree.International journal of molecular sciences · 2018Article
- Complete Chloroplast Genome Sequence and Phylogenetic Analysis of Paeonia ostii.Molecules (Basel, Switzerland) · 2018Article
- Complete Chloroplast Genome of Medicinal Plant Lonicera japonica: Genome Rearrangement, Intron Gain and Loss, and Implications for Phylogenetic Studies.Molecules (Basel, Switzerland) · 2017Article
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5 authors.
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Abstract
backgroundGenome evolution is shaped not only by nucleotide substitutions, but also by structural changes including gene and genome duplications, insertions, deletions and gene order rearrangements. The most popular methods for reconstructing phylogeny from genome rearrangements include GRAPPA and MGR. However these methods are limited to cases where equal gene content or few deletions can be assumed. Since conserved duplicated regions are present in many chloroplast genomes, the inference of inverted repeats is needed in chloroplast phylogeny analysis and ancestral genome reconstruction.
resultsWe extend GRAPPA and develop a new method GRAPPA-IR to handle chloroplast genomes. A test of GRAPPA-IR using divergent chloroplast genomes from land plants and green algae recovers the phylogeny congruent with prior studies, while analysis that do not consider IR structure fail to obtain the accepted topology. Our extensive simulation study also confirms that GRAPPA has better accuracy then the existing methods.
conclusionsTests on a biological and simulated dataset show GRAPPA-IR can accurately recover the genome phylogeny as well as ancestral gene orders. Close analysis of the ancestral genome structure suggests that genome rearrangement in chloroplasts is probably limited by inverted repeats with a conserved core region. In addition, the boundaries of inverted repeats are hot spots for gene duplications or deletions. The new GRAPPA-IR is available from http://phylo.cse.sc.edu.
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