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Mimosoid legume plastome evolution: IR expansion, tandem repeat expansions and accelerated rate of evolution in clpP

https://doi.org/10.1038/srep16958
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What this work says

Outgoing claims: the papers this work cites, builds on, or argues with.

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Using the Velvet de novo Assembler for Short‐Read Sequencing Technologies
inferredcites →https://doi.org/10.1002/j.1460-2075.1991.tb07859.xopenalex-snapshot
Transfer of rpl22 to the nucleus greatly preceded its loss from the chloroplast and involved the gain of an intron.
inferredcites →https://doi.org/10.1002/tax.591002openalex-snapshot
Molecular phylogeny of Acacia Mill. (Mimosoideae: Leguminosae): Evidence for major clades and informal classification
inferredcites →https://doi.org/10.1006/mpev.1996.0038openalex-snapshot
The Distribution and Phylogenetic Significance of a 50-kb Chloroplast DNA Inversion in the Flowering Plant Family Leguminosae
inferredcites →https://doi.org/10.1007/978-94-007-2920-9_5openalex-snapshot
Plastid Genomes of Seed Plants
inferredcites →https://doi.org/10.1007/bf00355401openalex-snapshot
Chloroplast DNA evolution among legumes: Loss of a large inverted repeat occurred prior to other sequence rearrangements
inferredcites →https://doi.org/10.1007/bf00418529openalex-snapshot
Conservation of chloroplast genome structure among vascular plants
inferredcites →https://doi.org/10.1007/bf00985731openalex-snapshot
The chloroplast genome arrangement ofLobelia thuliniana (Lobeliaceae): Expansion of the inverted repeat in an ancestor of theCampanulales
inferredcites →https://doi.org/10.1007/bf02173220openalex-snapshot
Ebb and flow of the chloroplast inverted repeat
inferredcites →https://doi.org/10.1007/s00122-002-0967-4openalex-snapshot
Construction of a BAC library and its application to the identification of simple sequence repeats in peach [Prunus persica (L.) Batsch]
inferredcites →https://doi.org/10.1007/s00239-008-9086-4openalex-snapshot
Extensive Rearrangements in the Chloroplast Genome of Trachelium caeruleum Are Associated with Repeats and tRNA Genes
inferredcites →https://doi.org/10.1007/s00239-008-9180-7openalex-snapshot
Extensive Reorganization of the Plastid Genome of Trifolium subterraneum (Fabaceae) Is Associated with Numerous Repeated Sequences and Novel DNA Insertions
inferredcites →https://doi.org/10.1007/s00299-010-0929-2openalex-snapshot
Complete sequencing and comparative analyses of the pepper (Capsicum annuum L.) plastome revealed high frequency of tandem repeats and large insertion/deletions on pepper plastome
inferredcites →https://doi.org/10.1007/s11295-012-0573-9openalex-snapshot
Complete plastid genome sequence of Vaccinium macrocarpon: structure, gene content, and rearrangements revealed by next generation sequencing
inferredcites →https://doi.org/10.1016/b978-0-12-715007-9.50009-8openalex-snapshot
Plastid Chromosomes: Structure and Evolution
inferredcites →https://doi.org/10.1016/j.gene.2013.07.037openalex-snapshot
The complete chloroplast genome sequence of Mahonia bealei (Berberidaceae) reveals a significant expansion of the inverted repeat and phylogenetic relationship with other angiosperms
inferredcites →https://doi.org/10.1016/j.ympev.2008.06.013openalex-snapshot
Complete plastid genome sequence of the chickpea (Cicer arietinum) and the phylogenetic distribution of rps12 and clpP intron losses among legumes (Leguminosae)
inferredcites →https://doi.org/10.1016/j.ympev.2013.12.004openalex-snapshot
A recurring syndrome of accelerated plastid genome evolution in the angiosperm tribe Sileneae (Caryophyllaceae)
inferredcites →https://doi.org/10.1016/s0022-2836(05)80360-2openalex-snapshot
Basic Local Alignment Search Tool
inferredcites →https://doi.org/10.1038/nmeth.1923openalex-snapshot
Fast gapped-read alignment with Bowtie 2
inferredcites →https://doi.org/10.1073/pnas.0709121104openalex-snapshot
Analysis of 81 genes from 64 plastid genomes resolves relationships in angiosperms and identifies genome-scale evolutionary patterns
inferredcites →https://doi.org/10.1073/pnas.0806759105openalex-snapshot
Genome-wide analyses of Geraniaceae plastid DNA reveal unprecedented patterns of increased nucleotide substitutions
inferredcites →https://doi.org/10.1073/pnas.1403363111openalex-snapshot
The dynamic history of plastid genomes in the Campanulaceae sensu lato is unique among angiosperms
inferredcites →https://doi.org/10.1080/10635150590947131openalex-snapshot
Evolutionary Rates Analysis of Leguminosae Implicates a Rapid Diversification of Lineages during the Tertiary
inferredcites →https://doi.org/10.1080/10635150590950326openalex-snapshot
Integration of Morphological Data Sets for Phylogenetic Analysis of Amniota: The Importance of Integumentary Characters and Increased Taxonomic Sampling
inferredcites →https://doi.org/10.1080/10635150802429642openalex-snapshot
A Rapid Bootstrap Algorithm for the RAxML Web Servers
inferredcites →https://doi.org/10.1093/aob/mcu050openalex-snapshot
The first complete chloroplast genome of the Genistoid legume Lupinus luteus: evidence for a novel major lineage-specific rearrangement and new insights regarding plastome evolution in the legume family
inferredcites →https://doi.org/10.1093/bioinformatics/19.2.301openalex-snapshot
r8s: inferring absolute rates of molecular evolution and divergence times in the absence of a molecular clock
inferredcites →https://doi.org/10.1093/bioinformatics/bth352openalex-snapshot
Automatic annotation of organellar genomes with DOGMA
inferredcites →https://doi.org/10.1093/bioinformatics/btm619openalex-snapshot
Phyutility: a phyloinformatics tool for trees, alignments and molecular data
inferredcites →https://doi.org/10.1093/bioinformatics/btq033openalex-snapshot
BEDTools: a flexible suite of utilities for comparing genomic features
inferredcites →https://doi.org/10.1093/bioinformatics/btu170openalex-snapshot
Trimmomatic: a flexible trimmer for Illumina sequence data
inferredcites →https://doi.org/10.1093/gbe/evs006openalex-snapshot
Recent Acceleration of Plastid Sequence and Structural Evolution Coincides with Extreme Mitochondrial Divergence in the Angiosperm Genus Silene
inferredcites →https://doi.org/10.1093/molbev/msl089openalex-snapshot
The Complete Chloroplast Genome Sequence of Pelargonium × hortorum: Organization and Evolution of the Largest and Most Highly Rearranged Chloroplast Genome of Land Plants
inferredcites →https://doi.org/10.1093/molbev/msm088openalex-snapshot
PAML 4: Phylogenetic Analysis by Maximum Likelihood
inferredcites →https://doi.org/10.1093/molbev/msq229openalex-snapshot
Extreme Reconfiguration of Plastid Genomes in the Angiosperm Family Geraniaceae: Rearrangements, Repeats, and Codon Usage
inferredcites →https://doi.org/10.1093/molbev/mst257openalex-snapshot
Reconstruction of the Ancestral Plastid Genome in Geraniaceae Reveals a Correlation between Genome Rearrangements, Repeats, and Nucleotide Substitution Rates
inferredcites →https://doi.org/10.1093/molbev/msu296openalex-snapshot
Multiple Polyploidy Events in the Early Radiation of Nodulating and Nonnodulating Legumes
inferredcites →https://doi.org/10.1093/nar/25.5.955openalex-snapshot
tRNAscan-SE: A Program for Improved Detection of Transfer RNA Genes in Genomic Sequence
inferredcites →https://doi.org/10.1093/nar/27.2.573openalex-snapshot
Tandem repeats finder: a program to analyze DNA sequences
inferredcites →https://doi.org/10.1093/oxfordjournals.molbev.a004033openalex-snapshot
Whole Chloroplast Genome Comparison of Rice, Maize, and Wheat: Implications for Chloroplast Gene Diversification and Phylogeny of Cereals
inferredcites →https://doi.org/10.1093/pcp/pcg003openalex-snapshot
The Plastid clpP Gene May Not be Essential for Plant Cell Viability
inferredcites →https://doi.org/10.1101/gr.089532.108openalex-snapshot
ABySS: A parallel assembler for short read sequence data
inferredcites →https://doi.org/10.1101/gr.097261.109openalex-snapshot
De novo assembly of human genomes with massively parallel short read sequencing
inferredcites →https://doi.org/10.1101/gr.111955.110openalex-snapshot
Localized hypermutation and associated gene losses in legume chloroplast genomes
inferredcites →https://doi.org/10.1104/pp.102.018150openalex-snapshot
The Rest of the Iceberg. Legume Diversity and Evolution in a Phylogenetic Context
inferredcites →https://doi.org/10.1104/pp.118.1.9openalex-snapshot
Gene Transfer from Organelles to the Nucleus: How Much, What Happens, and Why?1
inferredcites →https://doi.org/10.1111/j.1472-4642.2011.00782.xopenalex-snapshot
Trees and shrubs as invasive alien species – a global review
inferredcites →https://doi.org/10.1111/jse.12179openalex-snapshot
Plastid genome sequences of legumes reveal parallel inversions and multiple losses ofrps16in papilionoids
inferredcites →https://doi.org/10.1111/nph.12704openalex-snapshot
Mitochondrion‐to‐plastid DNA transfer: it happens
inferredcites →https://doi.org/10.1111/pbi.12179openalex-snapshot
Evolutionary and biotechnology implications of plastid genome variation in the inverted‐repeat‐lacking clade of legumes
inferredcites →https://doi.org/10.1186/1471-2105-4-6openalex-snapshot
GapCoder automates the use of indel characters in phylogenetic analysis
inferredcites →https://doi.org/10.1186/1471-2148-14-9openalex-snapshot
Caves as microrefugia: Pleistocene phylogeography of the troglophilic North American scorpion Pseudouroctonus reddelli
inferredcites →https://doi.org/10.1186/1471-2164-12-211openalex-snapshot
Building a model: developing genomic resources for common milkweed (Asclepias syriaca) with low coverage genome sequencing
inferredcites →https://doi.org/10.1186/s12862-014-0228-6openalex-snapshot
Evolutionary origin of highly repetitive plastid genomes within the clover genus (Trifolium)
inferredcites →https://doi.org/10.1186/s12862-014-0268-yopenalex-snapshot
Correlation between sequence divergence and polymorphism reveals similar evolutionary mechanisms acting across multiple timescales in a rapidly evolving plastid genome
inferredcites →https://doi.org/10.12705/622.8openalex-snapshot
Legume phylogeny and classification in the 21st century: Progress, prospects and lessons for other species–rich clades
inferredcites →https://doi.org/10.1371/journal.pone.0022594openalex-snapshot
MACSE: Multiple Alignment of Coding SEquences Accounting for Frameshifts and Stop Codons
inferredcites →https://doi.org/10.1371/journal.pone.0051687openalex-snapshot
Capturing the Biofuel Wellhead and Powerhouse: The Chloroplast and Mitochondrial Genomes of the Leguminous Feedstock Tree Pongamia pinnata
inferredcites →https://doi.org/10.1371/journal.pone.0060429openalex-snapshot
Complete Plastid Genome Sequencing of Trochodendraceae Reveals a Significant Expansion of the Inverted Repeat and Suggests a Paleogene Divergence between the Two Extant Species
inferredcites →https://doi.org/10.1371/journal.pone.0077965openalex-snapshot
Complete Chloroplast Genome of Sedum sarmentosum and Chloroplast Genome Evolution in Saxifragales
inferredcites →https://doi.org/10.1371/journal.pone.0079685openalex-snapshot
Balanced Gene Losses, Duplications and Intensive Rearrangements Led to an Unusual Regularly Sized Genome in Arbutus unedo Chloroplasts
inferredcites →https://doi.org/10.1371/journal.pone.0125768openalex-snapshot
The Complete Sequence of the Acacia ligulata Chloroplast Genome Reveals a Highly Divergent clpP1 Gene
inferredcites →https://doi.org/10.1600/036364415x686620openalex-snapshot
A Comparative Analysis of Whole Plastid Genomes from the Apiales: Expansion and Contraction of the Inverted Repeat, Mitochondrial to Plastid Transfer of DNA, and Identification of Highly Divergent Noncoding Regions
inferredcites →https://doi.org/10.2307/2419496openalex-snapshot
Multiple Independent Losses of Two Genes and One Intron from Legume Chloroplast Genomes
inferredcites →https://doi.org/10.3732/ajb.1000520openalex-snapshot
The evolutionary history of Mimosa (Leguminosae): Toward a phylogeny of the sensitive plants
inferredcites →https://doi.org/10.5860/choice.30-0290openalex-snapshot
Sensitivae censitae: a description of the genus Mimosa Linnaeus (Mimosaceae) in the New World

What points at this work

Incoming claims: where this work appears in other papers’ reference lists and arguments.

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Advances in Legume Systematics 14. Classification of Caesalpinioideae. Part 2: Higher-level classification
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Hybrid capture of 964 nuclear genes resolves evolutionary relationships in the mimosoid legumes and reveals the polytomous origins of a large pantropical radiation
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Phylotranscriptomics and genome size evolution in Leucaena (Fabaceae): Paleotetraploid genomic stability overshadows diploidization and environmental effects
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Carya luodianensis (Juglandaceae), a New Species From Guizhou Province, Southern China, Revealed by Morphological and Plastid Evidence
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Plastid Phylogenomics of Elatostemateae (Urticaceae): Insights Into Structural Variation and Phylogenetic Relationships
inferred← citeshttps://doi.org/10.1002/ece3.9821openalex-snapshot
Plastome evolution and phylogeny of the tribe Ruteae (Rutaceae)
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Plastome-Wide Nucleotide Substitution Rates Reveal Accelerated Rates in Papilionoideae and Correlations with Genome Features Across Legume Subfamilies
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Genetic, evolutionary and phylogenetic aspects of the plastome of annatto (Bixa orellana L.), the Amazonian commercial species of natural dyes
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Plastome evolution in the Caesalpinia group (Leguminosae) and its application in phylogenomics and populations genetics
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Molecular evolution and comparative genomics of highly threatened Malagasy rosewoods (Dalbergia, Fabaceae) unveil genome diversity and a fine-scale evolutionary framework
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Complete chloroplast genomes of three sand-fixing Salix shrubs from Northwest China: comparative and phylogenetic analysis and interspecific identification
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Complete plastomes of 17 species of maples (Sapindaceae: Acer): comparative analyses and phylogenomic implications
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Comparative plastid genomics of five Ormosia species (fabaceae): insights into structural variation and morphological homoplasy
inferred← citeshttps://doi.org/10.1007/s10265-025-01649-1openalex-snapshot
Enhancing Festuca chloroplast genome resources
inferred← citeshttps://doi.org/10.1007/s10528-024-10874-7openalex-snapshot
Repetitive Sequences, Codon Usage Bias and Phylogenetic Analysis of the Plastome of Miliusa glochidioides
inferred← citeshttps://doi.org/10.1007/s10709-025-00234-7openalex-snapshot
Comparative chloroplast genomic analysis of Pithecellobium dulce (Roxb.) Benth 1844 and related species within Caesalpinioideae
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Plastomes of Mimosoideae: structural and size variation, sequence divergence, and phylogenetic implication
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Diversity and evolution of plastomes in Saharan mimosoids: potential use for phylogenetic and population genetic studies
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Chloroplast genomes and nuclear sequences reveal the interspecific relationships of Crataegus bretschneideri C. K. Schneid. and related species in China
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Complete chloroplast genome sequence and variation analysis of Brassica oleracea L.
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Complete chloroplast genomes of four Syzygium species and comparative analysis with other Syzygium species
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The complete chloroplast genome sequence of Artemisia stechmanniana (Asteraceae): genome structure and phylogenetic analysis
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Complete plastid genome of Suriana maritima L. (Surianaceae) and its implications in phylogenetic reconstruction of Fabales
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Aberration or Analogy? The Atypical Plastomes of Geraniaceae
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Comprehensive analysis of the complete chloroplast genome of the cultivated soapberry and phylogenetic relationships of Sapindaceae
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Integrative chloroplast genomics unravels phylogenetic discordance in Glehnia (Apiaceae)
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Complete chloroplast genome of Albizia kalkora (Fabaceae) in Korea and its taxonomic position
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Complete chloroplast genome of Ixora finlaysoniana: comparative analysis and phylogenetic insights into Ixoroideae (Rubiaceae)
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Plastome characteristics of Cannabaceae
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Plastid phylogenomic insights into the evolution of subfamily Dialioideae (Leguminosae)
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Comparative analysis of plastomes in Oxalidaceae: Phylogenetic relationships and potential molecular markers
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Plastid phylogenomics resolves infrafamilial relationships of the Styracaceae and sheds light on the backbone relationships of the Ericales
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Plastome organization, genome-based phylogeny and evolution of plastid genes in Podophylloideae (Berberidaceae)
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Plastid phylogenomic insights into the evolution of the Caprifoliaceae s.l. (Dipsacales)
inferred← citeshttps://doi.org/10.1038/s41598-018-31938-wopenalex-snapshot
Reconfiguration of the plastid genome in Lamprocapnos spectabilis: IR boundary shifting, inversion, and intraspecific variation
inferred← citeshttps://doi.org/10.1038/s41598-019-50620-3openalex-snapshot
The complete chloroplast genome of Stryphnodendron adstringens (Leguminosae - Caesalpinioideae): comparative analysis with related Mimosoid species
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The complete chloroplast genome of Gleditsia sinensis and Gleditsia japonica: genome organization, comparative analysis, and development of taxon specific DNA mini-barcodes
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Calophyllaceae plastomes, their structure and insights in relationships within the clusioids
inferred← citeshttps://doi.org/10.1038/s41598-023-41287-yopenalex-snapshot
Complete chloroplast genome of Lens lamottei reveals intraspecies variation among with Lens culinaris
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Structure, gene composition, divergence time and phylogeny analysis of the woody desert species Neltuma alba, Neltuma chilensis and Strombocarpa strombulifera
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Comparative analysis of plastid genomes of non-photosynthetic Ericaceae and their photosynthetic relatives
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Analysis of the complete plastomes of Albizia kalkora (Roxb.) Prain 1897 (Fabaceae)
inferred← citeshttps://doi.org/10.1080/23802359.2024.2345794openalex-snapshot
Characterization of the complete chloroplast genome of Helicteres hirsuta Lour. 1790 (Helicteriodeae: Malvaceae)
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Complete chloroplast genome of Lamiophlomis rotata : comparative genome analysis and phylogenetic analysis
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New insights into the evolutionary characteristic between the New World and Old World Lupinus species using complete chloroplast genomes
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More than a spiny morphology: plastome variation in the prickly pear cacti (Opuntieae)
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Novel perspectives on plastome evolution in Onagraceae
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Evolutionary dynamics and adaptive mechanisms of Impatiens species in response to climate change: insights from chloroplast genomics and ecological niche modelling in Southwest China
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The evolutionary fate of the chloroplast and nuclear rps16 genes as revealed through the sequencing and comparative analyses of four novel legume chloroplast genomes from Lupinus
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Unprecedented Intraindividual Structural Heteroplasmy in Eleocharis (Cyperaceae, Poales) Plastomes
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PacBio-Based Mitochondrial Genome Assembly of Leucaena trichandra (Leguminosae) and an Intrageneric Assessment of Mitochondrial RNA Editing
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Lost and Found: Return of the Inverted Repeat in the Legume Clade Defined by Its Absence
inferred← citeshttps://doi.org/10.1093/jxb/erw500openalex-snapshot
A novel inversion in the chloroplast genome of marama (Tylosema esculentum)
inferred← citeshttps://doi.org/10.1093/plcell/koab021openalex-snapshot
Genome-wide signatures of plastid-nuclear coevolution point to repeated perturbations of plastid proteostasis systems across angiosperms
inferred← citeshttps://doi.org/10.1093/sysbio/syaa041openalex-snapshot
The Origin of the Legumes is a Complex Paleopolyploid Phylogenomic Tangle Closely Associated with the Cretaceous–Paleogene (K–Pg) Mass Extinction Event
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The pattern of interaction political actors on situations of tenurial conflict in watershed
inferred← citeshttps://doi.org/10.1111/jpy.12515openalex-snapshot
Comparative DNA sequence analyses of Pyramimonas parkeae (Prasinophyceae) chloroplast genomes
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Plastome evolution in the Caesalpinia group (Caesalpinioideae, Fabaceae): Comparative genomics reveals genome dynamics, phylogenetic insights and adaptive evolution
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Large‐scale genomic sequence data resolve the deepest divergences in the legume phylogeny and support a near‐simultaneous evolutionary origin of all six subfamilies
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Precipitation is the main axis of tropical plant phylogenetic turnover across space and time
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Comparative Complete Chloroplast Genome Analyses and Contribution to the Understanding of Chloroplast Phylogeny and Adaptive Evolution in Subgenus Anguinum
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Legumes of Kerala, India: a checklist
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Comparative genomics revealed new insights into the plastome evolution of Ludwigia (Onagraceae, Myrtales)
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PACVr: plastome assembly coverage visualization in R
inferred← citeshttps://doi.org/10.1186/s12862-021-01800-1openalex-snapshot
Exploring the evolutionary characteristics between cultivated tea and its wild relatives using complete chloroplast genomes
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Comparative analysis of dioecious Amaranthus plastomes and phylogenomic implications within Amaranthaceae s.s.
inferred← citeshttps://doi.org/10.1186/s12864-023-09847-8openalex-snapshot
Comparative and phylogenetic analysis of Chiloschista (Orchidaceae) species and DNA barcoding investigation based on plastid genomes
inferred← citeshttps://doi.org/10.1186/s12864-024-10046-2openalex-snapshot
Characterization of Firmiana danxiaensis plastomes and comparative analysis of Firmiana: insight into its phylogeny and evolution
inferred← citeshttps://doi.org/10.1186/s12864-024-10458-0openalex-snapshot
Complete chloroplast genome structural characterization of two Aerides (Orchidaceae) species with a focus on phylogenetic position of Aerides flabellata
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Complete chloroplast genome of two Brachycorythis (Orchidaceae) species from China: comparative analysis and phylogenetic implications
inferred← citeshttps://doi.org/10.1186/s12870-018-1249-xopenalex-snapshot
Gene loss and genome rearrangement in the plastids of five Hemiparasites in the family Orobanchaceae
inferred← citeshttps://doi.org/10.1186/s12870-020-02518-wopenalex-snapshot
Plastome phylogenomic study of Gentianeae (Gentianaceae): widespread gene tree discordance and its association with evolutionary rate heterogeneity of plastid genes
inferred← citeshttps://doi.org/10.1186/s12870-021-03053-yopenalex-snapshot
The chloroplast genome evolution of Venus slipper (Paphiopedilum): IR expansion, SSC contraction, and highly rearranged SSC regions
inferred← citeshttps://doi.org/10.1186/s12870-021-03202-3openalex-snapshot
Extensive genomic rearrangements mediated by repetitive sequences in plastomes of Medicago and its relatives
inferred← citeshttps://doi.org/10.1186/s12870-022-03480-5openalex-snapshot
Phylogenomic and comparative analyses of Coffeeae alliance (Rubiaceae): deep insights into phylogenetic relationships and plastome evolution
inferred← citeshttps://doi.org/10.1186/s12870-022-03515-xopenalex-snapshot
Gene loss, genome rearrangement, and accelerated substitution rates in plastid genome of Hypericum ascyron (Hypericaceae)
inferred← citeshttps://doi.org/10.1186/s12870-023-04088-zopenalex-snapshot
Comparison of plastid genomes and ITS of two sister species in Gentiana and a discussion on potential threats for the endangered species from hybridization
inferred← citeshttps://doi.org/10.1186/s12870-024-05665-6openalex-snapshot
Phylogenomics and plastome evolution of Lithospermeae (Boraginaceae)
inferred← citeshttps://doi.org/10.1186/s12870-024-05974-wopenalex-snapshot
Comparative genomics and phylogenetic analysis of six Malvaceae species based on chloroplast genomes
inferred← citeshttps://doi.org/10.1186/s12870-024-06040-1openalex-snapshot
Complete chloroplast genome of eight Phaius (Orchidaceae) species from China: comparative analysis and phylogenetic relationship
inferred← citeshttps://doi.org/10.1186/s12870-025-06586-8openalex-snapshot
Plastome phylogenomics unravels the evolutionary relationships and biogeographic history of Chloranthaceae
inferred← citeshttps://doi.org/10.1186/s12870-025-07191-5openalex-snapshot
Comparative chloroplast genome of six species in Hypoxidaceae from China: insights into phylogenetic relationships and molecular marker development
inferred← citeshttps://doi.org/10.1186/s12870-025-07408-7openalex-snapshot
Reconstructing the evolutionary trajectory of Chamaelirium (Melanthiaceae) through phylogenomics: insights from plastome dynamics and historical biogeography
inferred← citeshttps://doi.org/10.1186/s12870-026-09337-5openalex-snapshot
Comparative analysis of complete chloroplast genomes provides insights into phylogenetic relationships and screening of polymorphic markers in Dimocarpus and related species
inferred← citeshttps://doi.org/10.12705/661.3openalex-snapshot
A new subfamily classification of the Leguminosae based on a taxonomically comprehensive phylogeny: The Legume Phylogeny Working Group (LPWG)
inferred← citeshttps://doi.org/10.1371/journal.pone.0162324openalex-snapshot
Chloroplast Genome Evolution in Actinidiaceae: clpP Loss, Heterogenous Divergence and Phylogenomic Practice
inferred← citeshttps://doi.org/10.1371/journal.pone.0173766openalex-snapshot
The distinct plastid genome structure of Maackia fauriei (Fabaceae: Papilionoideae) and its systematic implications for genistoids and tribe Sophoreae
inferred← citeshttps://doi.org/10.1371/journal.pone.0190321openalex-snapshot
Comparative genomic analysis of Genlisea (corkscrew plants—Lentibulariaceae) chloroplast genomes reveals an increasing loss of the ndh genes
inferred← citeshttps://doi.org/10.1371/journal.pone.0218743openalex-snapshot
Plastid genome evolution in tribe Desmodieae (Fabaceae: Papilionoideae)
inferred← citeshttps://doi.org/10.1371/journal.pone.0225469openalex-snapshot
Complete Chloroplast Genomes of Vachellia nilotica and Senegalia senegal: Comparative Genomics and Phylogenomic Placement in a New Generic System
inferred← citeshttps://doi.org/10.1371/journal.pone.0233167openalex-snapshot
Comparative analysis of plastid genomes within the Campanulaceae and phylogenetic implications
inferred← citeshttps://doi.org/10.1371/journal.pone.0263253openalex-snapshot
The complete chloroplast genome sequencing analysis revealed an unusual IRs reduction in three species of subfamily Zygophylloideae
inferred← citeshttps://doi.org/10.1371/journal.pone.0286083openalex-snapshot
Characterization and comparative analysis of the complete plastid genomes of four Astragalus species
inferred← citeshttps://doi.org/10.15287/afr.2019.1413openalex-snapshot
Structural, evolutionary and phylogenomic features of the plastid genome of Carya illinoinensis cv. Imperial
inferred← citeshttps://doi.org/10.1534/genetics.116.188268openalex-snapshot
Positive Selection in Rapidly Evolving Plastid–Nuclear Enzyme Complexes
inferred← citeshttps://doi.org/10.17138/tgft(7)56-213openalex-snapshot
Tropical Grasslands-Forrajes Tropicales Vol.7 No.2 [May 2019]
inferred← citeshttps://doi.org/10.17138/tgft(7)65-73openalex-snapshot
The evolutionary history of Leucaena: Recent research, new genomic resources and future directions
inferred← citeshttps://doi.org/10.18174/390196openalex-snapshot
Utilization of complete chloroplast genomes for phylogenetic studies
inferred← citeshttps://doi.org/10.20944/preprints201804.0106.v1openalex-snapshot
Complete Chloroplast Genome Sequences of Clematis: IR Expansion and Relative Rates of Synonymous Substitutions
inferred← citeshttps://doi.org/10.20944/preprints202312.2150.v1openalex-snapshot
Chloroplast Genome Comparison and Evolution Analysis of Dendrobium (Orchidaceae) among Multiple Photosynthetic Pathways
inferred← citeshttps://doi.org/10.21203/rs.3.rs-2303224/v1openalex-snapshot
Comparative chloroplast genomes of Annonaceae species: Enlargement of plastomes in size, IR region, and gene content
inferred← citeshttps://doi.org/10.21203/rs.3.rs-257472/v1openalex-snapshot
The Chloroplast Genome Evolution of Venus Slipper (Paphiopedilum): IR Expansion, SSC Contraction, and Highly Rearranged SSC Regions
inferred← citeshttps://doi.org/10.21203/rs.3.rs-3422232/v1openalex-snapshot
Comparative analysis of the complete plastid genomes of desert trees Neltuma and Strombocarpa genera
inferred← citeshttps://doi.org/10.21203/rs.3.rs-719966/v1openalex-snapshot
The Complete Chloroplast Genome of Chinese Hickory (Carya Cathayensis) and Genetic Comparison to Its Closely Related Species
inferred← citeshttps://doi.org/10.2139/ssrn.5033369openalex-snapshot
Comparative Analysis of Chloroplast Genomes in Six Chimonobambusa Bamboo Species
inferred← citeshttps://doi.org/10.22541/au.170668337.73168692/v1openalex-snapshot
Comparative Analysis of Complete Chloroplast Genomes and Multiple DNA Sequences Reveals Interspecific Relationships of C. bretschneideri and Related Species in China
inferred← citeshttps://doi.org/10.24275/uami.td96k2542openalex-snapshot
Análisis filogenético del género Mimosa sect. Batocaulon: series Acanthocarpae, Boreales y Distachyae (Leguminosae), basado en datos moleculares
inferred← citeshttps://doi.org/10.3389/fgene.2021.772415openalex-snapshot
Comparative Analysis of the Complete Chloroplast Genomes of Nine Paphiopedilum Species
inferred← citeshttps://doi.org/10.3389/fgene.2022.849182openalex-snapshot
Structural Characterization of the Acer ukurunduense Chloroplast Genome Relative to Related Species in the Acer Genus
inferred← citeshttps://doi.org/10.3389/fphar.2024.1371390openalex-snapshot
Comparative genomics and phylogenomics of the genus Glycyrrhiza (Fabaceae) based on chloroplast genomes
inferred← citeshttps://doi.org/10.3389/fpls.2017.01875openalex-snapshot
Plastome Rearrangements in the “Adenocalymma-Neojobertia” Clade (Bignonieae, Bignoniaceae) and Its Phylogenetic Implications
inferred← citeshttps://doi.org/10.3389/fpls.2018.00138openalex-snapshot
Plastid Genome Evolution in the Early-Diverging Legume Subfamily Cercidoideae (Fabaceae)
inferred← citeshttps://doi.org/10.3389/fpls.2018.00324openalex-snapshot
Sequencing and Analysis of Strobilanthes cusia (Nees) Kuntze Chloroplast Genome Revealed the Rare Simultaneous Contraction and Expansion of the Inverted Repeat Region in Angiosperm
inferred← citeshttps://doi.org/10.3389/fpls.2019.00796openalex-snapshot
Comparative Chloroplast Genomics at Low Taxonomic Levels: A Case Study Using Amphilophium (Bignonieae, Bignoniaceae)
inferred← citeshttps://doi.org/10.3389/fpls.2020.00151openalex-snapshot
New Insights Into the Plastome Evolution of the Millettioid/Phaseoloid Clade (Papilionoideae, Leguminosae)
inferred← citeshttps://doi.org/10.3389/fpls.2021.609729openalex-snapshot
Chloroplast Genomes of Two Species of Cypripedium: Expanded Genome Size and Proliferation of AT-Biased Repeat Sequences
inferred← citeshttps://doi.org/10.3389/fpls.2021.778933openalex-snapshot
Comparative Chloroplast Genomics of Sophora Species: Evolution and Phylogenetic Relationships in the Early-Diverging Legume Subfamily Papilionoideae (Fabaceae)
inferred← citeshttps://doi.org/10.3389/fpls.2022.1043740openalex-snapshot
Extensive reorganization of the chloroplast genome of Corydalis platycarpa: A comparative analysis of their organization and evolution with other Corydalis plastomes
inferred← citeshttps://doi.org/10.3389/fpls.2022.1075098openalex-snapshot
The ecological adaptation of the unparalleled plastome character evolution in slipper orchids
inferred← citeshttps://doi.org/10.3389/fpls.2022.870949openalex-snapshot
Deep Insights Into the Plastome Evolution and Phylogenetic Relationships of the Tribe Urticeae (Family Urticaceae)
inferred← citeshttps://doi.org/10.3389/fpls.2022.965335openalex-snapshot
Comparative chloroplast genome analysis of Ficus (Moraceae): Insight into adaptive evolution and mutational hotspot regions
inferred← citeshttps://doi.org/10.3389/fpls.2022.987443openalex-snapshot
The chloroplast genome of Salix floderusii and characterization of chloroplast regulatory elements
inferred← citeshttps://doi.org/10.3389/fpls.2022.990064openalex-snapshot
Comparative plastomes of Carya species provide new insights into the plastomes evolution and maternal phylogeny of the genus
inferred← citeshttps://doi.org/10.3389/fpls.2023.1100876openalex-snapshot
Chloroplast genomes of four Carex species: Long repetitive sequences trigger dramatic changes in chloroplast genome structure
inferred← citeshttps://doi.org/10.3389/fpls.2023.1111968openalex-snapshot
The complete chloroplast genome of Hibiscus syriacus using long-read sequencing: Comparative analysis to examine the evolution of the tribe Hibisceae
inferred← citeshttps://doi.org/10.3389/fpls.2023.1144406openalex-snapshot
Plastome evolution in the East Asian lobelias (Lobelioideae) using phylogenomic and comparative analyses
inferred← citeshttps://doi.org/10.3389/fpls.2023.1258794openalex-snapshot
Chloroplast genome assembly of Serjania erecta Raldk: comparative analysis reveals gene number variation and selection in protein-coding plastid genes of Sapindaceae
inferred← citeshttps://doi.org/10.3389/fpls.2024.1297499openalex-snapshot
Polyphyly of Boehmeria (Urticaceae) congruent with plastome structural variation
inferred← citeshttps://doi.org/10.3389/fpls.2024.1351388openalex-snapshot
Comparative analysis of plastid genomes reveals rearrangements, repetitive sequence features, and phylogeny in the Annonaceae
inferred← citeshttps://doi.org/10.3389/fpls.2025.1673127openalex-snapshot
Dispersed repeats and inverted repeat expansion drive major plastomic rearrangements in Calliandra haematocephala (Leguminosae: Mimoseae)
inferred← citeshttps://doi.org/10.3389/fpls.2026.1766257openalex-snapshot
Comparative and phylogenetic analysis of chloroplast genomes in the subtribe Leptoboeinae (Gesneriaceae)
inferred← citeshttps://doi.org/10.3390/f12040441openalex-snapshot
Complete Chloroplast Genome of Clethra fargesii Franch., an Original Sympetalous Plant from Central China: Comparative Analysis, Adaptive Evolution, and Phylogenetic Relationships
inferred← citeshttps://doi.org/10.3390/f15101785openalex-snapshot
Comparative Genomics of Eight Complete Chloroplast Genomes of Phyllostachys Species
inferred← citeshttps://doi.org/10.3390/genes11080863openalex-snapshot
Extensive Genetic Connectivity and Historical Persistence Are Features of Two Widespread Tree Species in the Ancient Pilbara Region of Western Australia
inferred← citeshttps://doi.org/10.3390/genes13020369openalex-snapshot
The Complete Chloroplast Genome of Carya cathayensis and Phylogenetic Analysis
inferred← citeshttps://doi.org/10.3390/genes13122402openalex-snapshot
The Complete Chloroplast Genome Sequence of Machilus chuanchienensis (Lauraceae): Genome Structure and Phylogenetic Analysis
inferred← citeshttps://doi.org/10.3390/horticulturae10040383openalex-snapshot
Characteristics and Comparative Analysis of the Complete Plastomes of Apostasia fujianica and Neuwiedia malipoensis (Apostasioideae)
inferred← citeshttps://doi.org/10.3390/horticulturae10070744openalex-snapshot
Chloroplast Genome Profiling and Phylogenetic Insights of the “Qixiadaxiangshui” Pear (Pyrus bretschneideri Rehd.1)
inferred← citeshttps://doi.org/10.3390/horticulturae10121375openalex-snapshot
Characterization of the Complete Chloroplast Genomes and Phylogenetic Analysis of Sapotaceae
inferred← citeshttps://doi.org/10.3390/horticulturae11060641openalex-snapshot
Complete Chloroplast Genome of Two Papilionanthe (Aeridinae, Epidendroideae, Orchidaceae) Species: Comparative Analysis and Phylogenetic Insights
inferred← citeshttps://doi.org/10.3390/horticulturae8050391openalex-snapshot
Comparative Analyses of Chloroplast Genomes Provide Comprehensive Insights into the Adaptive Evolution of Paphiopedilum (Orchidaceae)
inferred← citeshttps://doi.org/10.3390/ijms19041037openalex-snapshot
Whole-Genome Comparison Reveals Heterogeneous Divergence and Mutation Hotspots in Chloroplast Genome of Eucommia ulmoides Oliver
inferred← citeshttps://doi.org/10.3390/ijms19051419openalex-snapshot
Sequencing, Characterization, and Comparative Analyses of the Plastome of Caragana rosea var. rosea
inferred← citeshttps://doi.org/10.3390/ijms20092196openalex-snapshot
Dynamic Chloroplast Genome Rearrangement and DNA Barcoding for Three Apiaceae Species Known as the Medicinal Herb “Bang-Poong”
inferred← citeshttps://doi.org/10.3390/ijms20153788openalex-snapshot
Intergeneric Relationships within the Family Salicaceae s.l. Based on Plastid Phylogenomics
inferred← citeshttps://doi.org/10.3390/ijms232415616openalex-snapshot
A Large Intergenic Spacer Leads to the Increase in Genome Size and Sequential Gene Movement around IR/SC Boundaries in the Chloroplast Genome of Adiantum malesianum (Pteridaceae)
inferred← citeshttps://doi.org/10.3390/ijms241210287openalex-snapshot
Sequencing and Analysis of Complete Chloroplast Genomes Provide Insight into the Evolution and Phylogeny of Chinese Kale (Brassica oleracea var. alboglabra)
inferred← citeshttps://doi.org/10.3390/ijms241512473openalex-snapshot
Comparative Phylogenetic Analysis for Aerides (Aeridinae, Orchidaceae) Based on Six Complete Plastid Genomes
inferred← citeshttps://doi.org/10.3390/ijms241914735openalex-snapshot
A Comprehensive Analysis of Chloroplast Genome Provides New Insights into the Evolution of the Genus Chrysosplenium
inferred← citeshttps://doi.org/10.3390/ijms25010184openalex-snapshot
Characterization of Angraecum (Angraecinae, Orchidaceae) Plastomes and Utility of Sequence Variability Hotspots
inferred← citeshttps://doi.org/10.3390/ijms25179538openalex-snapshot
Plastome Evolution and Comparative Analyses of a Recently Radiated Genus Vanda (Aeridinae, Orchidaceae)
inferred← citeshttps://doi.org/10.3390/ijms26094387openalex-snapshot
Comparative Chloroplast Genomics of Actinidia deliciosa Cultivars: Insights into Positive Selection and Population Evolution
inferred← citeshttps://doi.org/10.3390/molecules23071537openalex-snapshot
Whole-Genome Comparison Reveals Divergent IR Borders and Mutation Hotspots in Chloroplast Genomes of Herbaceous Bamboos (Bambusoideae: Olyreae)
inferred← citeshttps://doi.org/10.3390/molecules24020261openalex-snapshot
The Complete Plastid Genome of Magnolia zenii and Genetic Comparison to Magnoliaceae species
inferred← citeshttps://doi.org/10.3390/plants10020283openalex-snapshot
Chloroplast Genome of Rambutan and Comparative Analyses in Sapindaceae
inferred← citeshttps://doi.org/10.3390/plants10020397openalex-snapshot
Two Korean Endemic Clematis Chloroplast Genomes: Inversion, Reposition, Expansion of the Inverted Repeat Region, Phylogenetic Analysis, and Nucleotide Substitution Rates
inferred← citeshttps://doi.org/10.3390/plants9040456openalex-snapshot
The First Glimpse of Streptocarpus ionanthus (Gesneriaceae) Phylogenomics: Analysis of Five Subspecies’ Chloroplast Genomes
inferred← citeshttps://doi.org/10.36103/mf941m18openalex-snapshot
COMPARATIVE ANALYSIS OF THE COMPLETE CHLOROPLAST GENOME OF THREE PROSOPIS SPECIES IN JORDAN
inferred← citeshttps://doi.org/10.48130/frures-0024-0006openalex-snapshot
Chloroplast genome sequencing of Carya Illinoinensis cv. Xinxuan-4, a new pecan pollinated cultivar
inferred← citeshttps://doi.org/10.5772/intechopen.75673openalex-snapshot
The Intertwined Chloroplast and Nuclear Genome Coevolution in Plants
inferred← citeshttps://doi.org/10.6084/m9.figshare.14708200openalex-snapshot
Additional file 1 of The chloroplast genome evolution of Venus slipper (Paphiopedilum): IR expansion, SSC contraction, and highly rearranged SSC regions
inferred← citeshttps://doi.org/10.6084/m9.figshare.14708203openalex-snapshot
Additional file 2 of The chloroplast genome evolution of Venus slipper (Paphiopedilum): IR expansion, SSC contraction, and highly rearranged SSC regions
inferred← citeshttps://doi.org/10.6084/m9.figshare.22611559openalex-snapshot
Additional file 1 of Comparison of plastid genomes and ITS of two sister species in Gentiana and a discussion on potential threats for the endangered species from hybridization
inferred← citeshttps://doi.org/10.6084/m9.figshare.22611562openalex-snapshot
Additional file 2 of Comparison of plastid genomes and ITS of two sister species in Gentiana and a discussion on potential threats for the endangered species from hybridization
inferred← citeshttps://doi.org/10.6084/m9.figshare.22611565openalex-snapshot
Additional file 3 of Comparison of plastid genomes and ITS of two sister species in Gentiana and a discussion on potential threats for the endangered species from hybridization
inferred← citeshttps://doi.org/10.6084/m9.figshare.22611568openalex-snapshot
Additional file 4 of Comparison of plastid genomes and ITS of two sister species in Gentiana and a discussion on potential threats for the endangered species from hybridization
inferred← citeshttps://doi.org/10.6084/m9.figshare.22611571openalex-snapshot
Additional file 5 of Comparison of plastid genomes and ITS of two sister species in Gentiana and a discussion on potential threats for the endangered species from hybridization
inferred← citeshttps://doi.org/10.6084/m9.figshare.24761421openalex-snapshot
Additional file 1 of Comparative and phylogenetic analysis of Chiloschista (Orchidaceae) species and DNA barcoding investigation based on plastid genomes
inferred← citeshttps://doi.org/10.6084/m9.figshare.24761971openalex-snapshot
Additional file 2 of Comparative and phylogenetic analysis of Chiloschista (Orchidaceae) species and DNA barcoding investigation based on plastid genomes
inferred← citeshttps://doi.org/10.6084/m9.figshare.25954946openalex-snapshot
Additional file 1 of Complete chloroplast genome structural characterization of two Aerides (Orchidaceae) species with a focus on phylogenetic position of Aerides flabellata
inferred← citeshttps://doi.org/10.6084/m9.figshare.25955007openalex-snapshot
Additional file 2 of Complete chloroplast genome structural characterization of two Aerides (Orchidaceae) species with a focus on phylogenetic position of Aerides flabellata
inferred← citeshttps://doi.org/10.6084/m9.figshare.26587638openalex-snapshot
Additional file 1 of Comparative analysis of dioecious Amaranthus plastomes and phylogenomic implications within Amaranthaceae s.s.
inferred← citeshttps://doi.org/10.6084/m9.figshare.26587641openalex-snapshot
Additional file 2 of Comparative analysis of dioecious Amaranthus plastomes and phylogenomic implications within Amaranthaceae s.s.
inferred← citeshttps://doi.org/10.6084/m9.figshare.26587644openalex-snapshot
Additional file 3 of Comparative analysis of dioecious Amaranthus plastomes and phylogenomic implications within Amaranthaceae s.s.
inferred← citeshttps://doi.org/10.6084/m9.figshare.26587647openalex-snapshot
Additional file 4 of Comparative analysis of dioecious Amaranthus plastomes and phylogenomic implications within Amaranthaceae s.s.
inferred← citeshttps://doi.org/10.6084/m9.figshare.26587650openalex-snapshot
Additional file 5 of Comparative analysis of dioecious Amaranthus plastomes and phylogenomic implications within Amaranthaceae s.s.
inferred← citeshttps://doi.org/10.6084/m9.figshare.26587653openalex-snapshot
Additional file 6 of Comparative analysis of dioecious Amaranthus plastomes and phylogenomic implications within Amaranthaceae s.s.
inferred← citeshttps://doi.org/10.6084/m9.figshare.26728840openalex-snapshot
Additional file 3 of Complete chloroplast genome structural characterization of two Aerides (Orchidaceae) species with a focus on phylogenetic position of Aerides flabellata
inferred← citeshttps://doi.org/10.6084/m9.figshare.26728843openalex-snapshot
Additional file 4 of Complete chloroplast genome structural characterization of two Aerides (Orchidaceae) species with a focus on phylogenetic position of Aerides flabellata
inferred← citeshttps://doi.org/10.70675/700e3b61zcba8z432cz9ecaz075c11e403aaopenalex-snapshot
Structural diversity and contrasted evolution of cytoplasmic genomes in flowering plants : a phylogenomic approach in Oleaceae
inferred← citeshttps://doi.org/10.70675/b4e71136zb4f3z4374z8439zb87677585bbfopenalex-snapshot
La symbiose fixatrice d'azote au sein du genre Lupinus : histoire évolutive, aspects fonctionnels et gènes symbiotiques dans un contexte de spécificité hôte-symbiote
inferred← citeshttps://doi.org/10.7717/peerj.12400openalex-snapshot
Comparative plastomics of Amaryllidaceae: inverted repeat expansion and the degradation of the ndh genes in Strumaria truncata Jacq.
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