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Conserved gene clusters in the scrambled plastomes of IRLC legumes (Fabaceae: Trifolieae and Fabeae)

https://doi.org/10.1101/040188
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What this work says

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

inferredcites →https://doi.org/10.1007/4735_2007_0223openalex-snapshot
Structure, function, and inheritance of plastid genomes
inferredcites →https://doi.org/10.1007/978-3-540-75376-6openalex-snapshot
Cell and Molecular Biology of Plastids
inferredcites →https://doi.org/10.1007/bf00039388openalex-snapshot
Regulation of gene expression in chloroplasts of higher plants
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/s00425-012-1782-zopenalex-snapshot
Complex RNA metabolism in the chloroplast: an update on the psbB operon
inferredcites →https://doi.org/10.1007/s11103-011-9762-4openalex-snapshot
The evolution of the plastid chromosome in land plants: gene content, gene order, gene function
inferredcites →https://doi.org/10.1016/0031-9422(80)85004-7openalex-snapshot
Deviations from michaelis-menten behaviour of plant glutamate dehydrogenase with ammonium as variable substrate
inferredcites →https://doi.org/10.1016/0092-8674(82)90170-2openalex-snapshot
Chloroplast DNA rearrangements are more frequent when a large inverted repeat sequence is lost
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.2012.08.023openalex-snapshot
MITOS: Improved de novo metazoan mitochondrial genome annotation
inferredcites →https://doi.org/10.1016/s0022-0000(02)00011-9openalex-snapshot
Efficient algorithms for multichromosomal genome rearrangements
inferredcites →https://doi.org/10.1038/nbt.1883openalex-snapshot
Full-length transcriptome assembly from RNA-Seq data without a reference genome
inferredcites →https://doi.org/10.1038/nmeth.2109openalex-snapshot
jModelTest 2: more models, new heuristics and parallel computing
inferredcites →https://doi.org/10.1073/pnas.84.24.9054openalex-snapshot
Rates of nucleotide substitution vary greatly among plant mitochondrial, chloroplast, and nuclear DNAs.
inferredcites →https://doi.org/10.1080/10635150390235520openalex-snapshot
A Simple, Fast, and Accurate Algorithm to Estimate Large Phylogenies by Maximum Likelihood
inferredcites →https://doi.org/10.1093/aob/mct306openalex-snapshot
Phylogenetic pinpointing of a paleopolyploidy event within the flax genus (Linum) using transcriptomics
inferredcites →https://doi.org/10.1093/bib/bbs012openalex-snapshot
Using Tablet for visual exploration of second-generation sequencing data
inferredcites →https://doi.org/10.1093/bioinformatics/bth352openalex-snapshot
Automatic annotation of organellar genomes with DOGMA
inferredcites →https://doi.org/10.1093/bioinformatics/btp324openalex-snapshot
Fast and accurate short read alignment with Burrows–Wheeler transform
inferredcites →https://doi.org/10.1093/bioinformatics/btp348openalex-snapshot
trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses
inferredcites →https://doi.org/10.1093/bioinformatics/btq062openalex-snapshot
Phybase: an R package for species tree analysis
inferredcites →https://doi.org/10.1093/bioinformatics/btq228openalex-snapshot
DendroPy: a Python library for phylogenetic computing
inferredcites →https://doi.org/10.1093/bioinformatics/btu033openalex-snapshot
RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies
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/mst010openalex-snapshot
MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability
inferredcites →https://doi.org/10.1093/molbev/mst197openalex-snapshot
MEGA6: Molecular Evolutionary Genetics Analysis Version 6.0
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/nar/25.17.3389openalex-snapshot
Gapped BLAST and PSI-BLAST: a new generation of protein database search programs
inferredcites →https://doi.org/10.1093/nar/gkr1185openalex-snapshot
Translation of partially overlapping psbD-psbC mRNAs in chloroplasts: the role of 5′-processing and translational coupling
inferredcites →https://doi.org/10.1093/nar/gks540openalex-snapshot
RobiNA: a user-friendly, integrated software solution for RNA-Seq-based transcriptomics
inferredcites →https://doi.org/10.1093/sysbio/22.3.240openalex-snapshot
Maximum Likelihood and Minimum-Steps Methods for Estimating Evolutionary Trees from Data on Discrete Characters
inferredcites →https://doi.org/10.1093/sysbio/syp031openalex-snapshot
Estimating Species Phylogenies Using Coalescence Times among Sequences
inferredcites →https://doi.org/10.1101/gr.092759.109openalex-snapshot
Circos: An information aesthetic for comparative genomics
inferredcites →https://doi.org/10.1101/gr.111955.110openalex-snapshot
Localized hypermutation and associated gene losses in legume chloroplast genomes
inferredcites →https://doi.org/10.1101/gr.1224503openalex-snapshot
OrthoMCL: Identification of Ortholog Groups for Eukaryotic Genomes
inferredcites →https://doi.org/10.1111/j.1469-8137.2010.03195.xopenalex-snapshot
Recombination and the maintenance of plant organelle genome stability
inferredcites →https://doi.org/10.1111/j.1558-5646.1971.tb01930.xopenalex-snapshot
ORIGIN OF EUKARYOTIC CELLS
inferredcites →https://doi.org/10.1111/nph.13743openalex-snapshot
Evolutionary dynamics of the plastid inverted repeat: the effects of expansion, contraction, and loss on substitution rates
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/10.1146/annurev-arplant-042809-112242openalex-snapshot
Chloroplast RNA Metabolism
inferredcites →https://doi.org/10.1146/annurev.genet.32.1.437openalex-snapshot
EVOLUTION AND MECHANISM OF TRANSLATION IN CHLOROPLASTS
inferredcites →https://doi.org/10.1186/1471-2105-5-187openalex-snapshot
prot4EST: Translating Expressed Sequence Tags from neglected genomes
inferredcites →https://doi.org/10.1186/1471-2148-4-2openalex-snapshot
A molecular timescale of eukaryote evolution and the rise of complex multicellular life
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/10.12705/622.8openalex-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.0011147openalex-snapshot
progressiveMauve: Multiple Genome Alignment with Gene Gain, Loss and Rearrangement
inferredcites →https://doi.org/10.1371/journal.pone.0078265openalex-snapshot
Complex Processing Patterns of mRNAs of the Large ATP Synthase Operon in Arabidopsis Chloroplasts
inferredcites →https://doi.org/10.32614/r.manualsopenalex-snapshot
R: A Language and Environment for Statistical Computing
inferredcites →https://doi.org/10.3732/ajb.1500299openalex-snapshot
Sources of inversion variation in the small single copy (SSC) region of chloroplast genomes

What points at this work

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

inferred← citeshttps://doi.org/10.1002/ece3.6839openalex-snapshot
Caught in the Act: Variation in plastid genome inverted repeat expansion within and between populations of Medicago minima
inferred← citeshttps://doi.org/10.1007/s00425-021-03753-7openalex-snapshot
Comparative plastid genomics of Mazaceae: focusing on a new recognized genus, Puchiumazus
inferred← citeshttps://doi.org/10.1007/s11738-023-03628-2openalex-snapshot
The complete sequence of Lens tomentosus chloroplast genome
inferred← citeshttps://doi.org/10.1016/j.scienta.2022.110912openalex-snapshot
The complete chloroplast genome sequence of Cicer echinospermum, genome organization and comparison with related species
inferred← citeshttps://doi.org/10.1016/j.ympev.2021.107235openalex-snapshot
Phylogenomic framework of the IRLC legumes (Leguminosae subfamily Papilionoideae) and intercontinental biogeography of tribe Wisterieae
inferred← citeshttps://doi.org/10.1038/s41598-022-17877-7openalex-snapshot
Complete chloroplast genome sequence of Lens ervoides and comparison to Lens culinaris
inferred← citeshttps://doi.org/10.1038/s41598-023-44599-1openalex-snapshot
The complete chloroplast genome of Cicer reticulatum and comparative analysis against relative Cicer species
inferred← citeshttps://doi.org/10.1093/gbe/evw278openalex-snapshot
Large-Scale Comparative Analysis Reveals the Mechanisms Driving Plastomic Compaction, Reduction, and Inversions in Conifers II (Cupressophytes)
inferred← citeshttps://doi.org/10.1186/s12870-023-04148-4openalex-snapshot
Plastome variations reveal the distinct evolutionary scenarios of plastomes in the subfamily Cereoideae (Cactaceae)
inferred← citeshttps://doi.org/10.1371/journal.pone.0229846openalex-snapshot
Extensive survey of the ycf4 plastid gene throughout the IRLC legumes: Robust evidence of its locus and lineage specific accelerated rate of evolution, pseudogenization and gene loss in the tribe Fabeae
inferred← citeshttps://doi.org/10.17816/ecogen33959openalex-snapshot
Characterization of variability of the intergenic spacers cpDNA trnH–psbA, trnY–trnT AND rpoB–trnC in representatives of Pisum L. (Tribe Fabeae)
inferred← citeshttps://doi.org/10.3389/fgene.2020.00073openalex-snapshot
Initial Characterization of the Chloroplast Genome of Vicia sepium, an Important Wild Resource Plant, and Related Inferences About Its Evolution
inferred← citeshttps://doi.org/10.3389/fpls.2021.608559openalex-snapshot
Identification of Vicia Species Native to South Korea Using Molecular and Morphological Characteristics
inferred← citeshttps://doi.org/10.3897/phytokeys.181.71259openalex-snapshot
Proposal to recognise the tribes Adinobotryeae and Glycyrrhizeae (Leguminosae subfamily Papilionoideae) based on chloroplast phylogenomic evidence
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