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Comparative analysis of plastid genomes of non-photosynthetic Ericaceae and their photosynthetic relatives

https://doi.org/10.1038/srep30042
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What this work says

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

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T-coffee: a novel method for fast and accurate multiple sequence alignment 1 1Edited by J. Thornton
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Complete chloroplast genome sequences of Hordeum vulgare, Sorghum bicolor and Agrostis stolonifera, and comparative analyses with other grass genomes
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Parallel evolutionary paths to mycoheterotrophy in understorey Ericaceae and Orchidaceae: ecological evidence for mixotrophy in Pyroleae
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The evolution of the plastid chromosome in land plants: gene content, gene order, gene function
inferredcites →https://doi.org/10.1007/s11103-012-9884-3openalex-snapshot
Plastid genome evolution in mycoheterotrophic Ericaceae
inferredcites →https://doi.org/10.1007/s11105-014-0833-yopenalex-snapshot
The Largest Plastid Genome of Monocots: a Novel Genome Type Containing AT Residue Repeats in the Slipper Orchid Cypripedium japonicum
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Complete plastid genome sequence of Vaccinium macrocarpon: structure, gene content, and rearrangements revealed by next generation sequencing
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Deviations from michaelis-menten behaviour of plant glutamate dehydrogenase with ammonium as variable substrate
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Functional characterization of the thylakoid Ndh complex phosphorylation by site-directed mutations in the ndhF gene
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Structure and biogenesis of the chloroplast NAD(P)H dehydrogenase complex
inferredcites →https://doi.org/10.1016/j.bbabio.2010.12.003openalex-snapshot
The Clp protease system; a central component of the chloroplast protease network
inferredcites →https://doi.org/10.1016/j.bbabio.2015.02.004openalex-snapshot
Chloroplast RNA polymerases: Role in chloroplast biogenesis
inferredcites →https://doi.org/10.1016/j.plaphy.2010.04.009openalex-snapshot
Plastid ndh genes in plant evolution
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Why are plastid genomes retained in non-photosynthetic organisms?
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Streptophyte Terrestrialization in Light of Plastid Evolution
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)
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Basic Local Alignment Search Tool
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Regulation of rDNA transcription in plastids of higher plants
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Do nonasterid holoparasitic flowering plants have plastid genomes?
inferredcites →https://doi.org/10.1038/newbio244081a0openalex-snapshot
Effect of Mycorrhizal Infection on Nitrogen and Phosphorus Nutrition of Ericaceous Plants
inferredcites →https://doi.org/10.1038/srep16958openalex-snapshot
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SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing
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Automatic annotation of organellar genomes with DOGMA
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Clustal W and Clustal X version 2.0
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NextClip: an analysis and read preparation tool for Nextera Long Mate Pair libraries
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InterProScan 5: genome-scale protein function classification
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RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies
inferredcites →https://doi.org/10.1093/bioinformatics/btu170openalex-snapshot
Trimmomatic: a flexible trimmer for Illumina sequence data
inferredcites →https://doi.org/10.1093/emboj/17.4.868openalex-snapshot
Identification of a functional respiratory complex in chloroplasts through analysis of tobacco mutants containing disrupted plastid ndh genes
inferredcites →https://doi.org/10.1093/gbe/evu001openalex-snapshot
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inferredcites →https://doi.org/10.1093/gbe/evv019openalex-snapshot
Exploring the Limits for Reduction of Plastid Genomes: A Case Study of the Mycoheterotrophic Orchids Epipogium aphyllum and Epipogium roseum
inferredcites →https://doi.org/10.1093/gbe/evv134openalex-snapshot
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inferredcites →https://doi.org/10.1093/gbe/evv251openalex-snapshot
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inferredcites →https://doi.org/10.1093/gbe/evv256openalex-snapshot
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inferredcites →https://doi.org/10.1093/gbe/evw033openalex-snapshot
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inferredcites →https://doi.org/10.1093/molbev/msl089openalex-snapshot
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inferredcites →https://doi.org/10.1093/molbev/msm088openalex-snapshot
PAML 4: Phylogenetic Analysis by Maximum Likelihood
inferredcites →https://doi.org/10.1093/molbev/msm267openalex-snapshot
Functional Gene Losses Occur with Minimal Size Reduction in the Plastid Genome of the Parasitic Liverwort Aneura mirabilis
inferredcites →https://doi.org/10.1093/molbev/msn102openalex-snapshot
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inferredcites →https://doi.org/10.1093/molbev/msq115openalex-snapshot
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inferredcites →https://doi.org/10.1093/molbev/msq229openalex-snapshot
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inferredcites →https://doi.org/10.1093/molbev/msr028openalex-snapshot
Rampant Gene Loss in the Underground Orchid Rhizanthella gardneri Highlights Evolutionary Constraints on Plastid Genomes
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/msu051openalex-snapshot
Possible Loss of the Chloroplast Genome in the Parasitic Flowering Plant Rafflesia lagascae (Rafflesiaceae)
inferredcites →https://doi.org/10.1093/molbev/msu252openalex-snapshot
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inferredcites →https://doi.org/10.1093/molbev/msv134openalex-snapshot
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inferredcites →https://doi.org/10.1093/molbev/msv247openalex-snapshot
Proposal of a Twin Aarginine Translocator System-Mediated Constraint against Loss of ATP Synthase Genes from Nonphotosynthetic Plastid Genomes
inferredcites →https://doi.org/10.1093/mp/ssu022openalex-snapshot
The Translational Apparatus of Plastids and Its Role in Plant Development
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
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MUSCLE: multiple sequence alignment with high accuracy and high throughput
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VISTA: computational tools for comparative genomics
inferredcites →https://doi.org/10.1093/nar/gkq291openalex-snapshot
TranslatorX: multiple alignment of nucleotide sequences guided by amino acid translations
inferredcites →https://doi.org/10.1093/oxfordjournals.molbev.a026334openalex-snapshot
Selection of Conserved Blocks from Multiple Alignments for Their Use in Phylogenetic Analysis
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A codon-based model of nucleotide substitution for protein-coding DNA sequences.
inferredcites →https://doi.org/10.1101/gr.092759.109openalex-snapshot
Circos: An information aesthetic for comparative genomics
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inferredcites →https://doi.org/10.1104/pp.107.103846openalex-snapshot
Phage-Type RNA Polymerase RPOTmp Transcribes the rrn Operon from the PC Promoter at Early Developmental Stages in Arabidopsis
inferredcites →https://doi.org/10.1104/pp.113.214528openalex-snapshot
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inferredcites →https://doi.org/10.1104/pp.123.4.1337openalex-snapshot
Targeted Inactivation of the Plastid ndhB Gene in Tobacco Results in an Enhanced Sensitivity of Photosynthesis to Moderate Stomatal Closure
inferredcites →https://doi.org/10.1105/tpc.113.113373openalex-snapshot
Mechanisms of Functional and Physical Genome Reduction in Photosynthetic and Nonphotosynthetic Parasitic Plants of the Broomrape Family
inferredcites →https://doi.org/10.1105/tpc.114.135541openalex-snapshot
YCF1: A Green TIC?
inferredcites →https://doi.org/10.1105/tpc.15.00363openalex-snapshot
YCF1: A Green TIC: Response to the de Vries et al. Commentary
inferredcites →https://doi.org/10.1126/science.1229262openalex-snapshot
Uncovering the Protein Translocon at the Chloroplast Inner Envelope Membrane
inferredcites →https://doi.org/10.1186/1471-2105-11-579openalex-snapshot
webPRANK: a phylogeny-aware multiple sequence aligner with interactive alignment browser
inferredcites →https://doi.org/10.1186/2047-217x-3-17openalex-snapshot
Data access for the 1,000 Plants (1KP) project
inferredcites →https://doi.org/10.1186/gb-2012-13-6-r56openalex-snapshot
Toward almost closed genomes with GapFiller
inferredcites →https://doi.org/10.1186/gb-2013-14-5-r47openalex-snapshot
REAPR: a universal tool for genome assembly evaluation
inferredcites →https://doi.org/10.1186/s12870-015-0484-7openalex-snapshot
NDH expression marks major transitions in plant evolution and reveals coordinate intracellular gene loss
inferredcites →https://doi.org/10.1371/journal.pone.0068591openalex-snapshot
The Plastid Genome of Najas flexilis: Adaptation to Submersed Environments Is Accompanied by the Complete Loss of the NDH Complex in an Aquatic Angiosperm
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.0129347openalex-snapshot
The First Complete Chloroplast Genome Sequences in Actinidiaceae: Genome Structure and Comparative Analysis
inferredcites →https://doi.org/10.1371/journal.pone.0150718openalex-snapshot
Complete Plastid Genome of the Recent Holoparasite Lathraea squamaria Reveals Earliest Stages of Plastome Reduction in Orobanchaceae
inferredcites →https://doi.org/10.14601/phytopathol_mediterr-14998u1.29openalex-snapshot
BIOEDIT: A USER-FRIENDLY BIOLOGICAL SEQUENCE ALIGNMENT EDITOR AND ANALYSIS PROGRAM FOR WINDOWS 95/98/ NT
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Phylogenetic Classification of Ericaceae: Molecular and Morphological Evidence
inferredcites →https://doi.org/10.3732/ajb.1200256openalex-snapshot
The plastid genome of the mycoheterotrophic Corallorhiza striata (Orchidaceae) is in the relatively early stages of degradation

What points at this work

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

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inferred← citeshttps://doi.org/10.1002/ajb2.1397openalex-snapshot
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Higher level constructive neutral evolution
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inferred← citeshttps://doi.org/10.1007/s12686-017-0933-8openalex-snapshot
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inferred← citeshttps://doi.org/10.1038/s41438-019-0191-xopenalex-snapshot
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inferred← citeshttps://doi.org/10.1038/s41598-022-25434-5openalex-snapshot
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inferred← citeshttps://doi.org/10.1073/pnas.2421485121openalex-snapshot
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inferred← citeshttps://doi.org/10.1080/23802359.2020.1806754openalex-snapshot
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inferred← citeshttps://doi.org/10.1080/23802359.2025.2487065openalex-snapshot
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inferred← citeshttps://doi.org/10.1080/23802359.2025.2590214openalex-snapshot
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inferred← citeshttps://doi.org/10.1086/719959openalex-snapshot
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inferred← citeshttps://doi.org/10.1093/aob/mcae084openalex-snapshot
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inferred← citeshttps://doi.org/10.1093/botlinnean/boaa056openalex-snapshot
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inferred← citeshttps://doi.org/10.1093/botlinnean/boag020openalex-snapshot
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inferred← citeshttps://doi.org/10.1093/gbe/evz187openalex-snapshot
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inferred← citeshttps://doi.org/10.1093/jxb/erz456openalex-snapshot
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inferred← citeshttps://doi.org/10.1093/plphys/kiab192openalex-snapshot
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inferred← citeshttps://doi.org/10.1101/2022.02.23.481500openalex-snapshot
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inferred← citeshttps://doi.org/10.1101/681718openalex-snapshot
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inferred← citeshttps://doi.org/10.1111/nph.14398openalex-snapshot
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inferred← citeshttps://doi.org/10.1111/nph.14681openalex-snapshot
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inferred← citeshttps://doi.org/10.1111/nph.15072openalex-snapshot
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inferred← citeshttps://doi.org/10.1134/s002689331705017xopenalex-snapshot
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inferred← citeshttps://doi.org/10.1155/2018/7203469openalex-snapshot
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inferred← citeshttps://doi.org/10.1186/s12870-016-0929-7openalex-snapshot
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inferred← citeshttps://doi.org/10.1186/s12870-018-1249-xopenalex-snapshot
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inferred← citeshttps://doi.org/10.1186/s12870-023-04682-1openalex-snapshot
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inferred← citeshttps://doi.org/10.1186/s13059-020-02154-5openalex-snapshot
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inferred← citeshttps://doi.org/10.1371/journal.pone.0265449openalex-snapshot
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inferred← citeshttps://doi.org/10.1515/chem-2025-0245openalex-snapshot
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inferred← citeshttps://doi.org/10.18699/icg-plantgen2019-55openalex-snapshot
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inferred← citeshttps://doi.org/10.18699/icg-plantgen2019-82openalex-snapshot
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inferred← citeshttps://doi.org/10.32604/phyton.2025.061424openalex-snapshot
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inferred← citeshttps://doi.org/10.3389/fpls.2021.602598openalex-snapshot
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inferred← citeshttps://doi.org/10.3389/fpls.2024.1393225openalex-snapshot
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inferred← citeshttps://doi.org/10.3390/horticulturae9030302openalex-snapshot
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inferred← citeshttps://doi.org/10.3390/ijms19010319openalex-snapshot
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inferred← citeshttps://doi.org/10.3390/microorganisms10010122openalex-snapshot
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inferred← citeshttps://doi.org/10.6084/m9.figshare.24883523openalex-snapshot
Additional file 1 of Distinctive plastome evolution in carnivorous angiosperms
inferred← citeshttps://doi.org/10.6084/m9.figshare.24883800openalex-snapshot
Additional file 2 of Distinctive plastome evolution in carnivorous angiosperms
inferred← citeshttps://doi.org/10.7287/peerj.12106v0.1/reviews/1openalex-snapshot
Peer Review #1 of "Genomic comparison of non-photosynthetic plants from the family Balanophoraceae with their photosynthetic relatives (v0.1)"
inferred← citeshttps://doi.org/10.7287/peerj.12106v0.1/reviews/2openalex-snapshot
Peer Review #2 of "Genomic comparison of non-photosynthetic plants from the family Balanophoraceae with their photosynthetic relatives (v0.1)"
inferred← citeshttps://doi.org/10.7287/peerj.12106v0.2/reviews/3openalex-snapshot
Peer Review #3 of "Genomic comparison of non-photosynthetic plants from the family Balanophoraceae with their photosynthetic relatives (v0.2)"
inferred← citeshttps://doi.org/10.7287/peerj.9309v0.1/reviews/1openalex-snapshot
Peer Review #1 of "Mitochondrial genome of the nonphotosynthetic mycoheterotrophic plant Hypopitys monotropa, its structure, gene expression and RNA editing (v0.1)"
inferred← citeshttps://doi.org/10.7287/peerj.9309v0.1/reviews/2openalex-snapshot
Peer Review #2 of "Mitochondrial genome of the nonphotosynthetic mycoheterotrophic plant Hypopitys monotropa, its structure, gene expression and RNA editing (v0.1)"
inferred← citeshttps://doi.org/10.7287/peerj.9309v0.1/reviews/3openalex-snapshot
Peer Review #3 of "Mitochondrial genome of the nonphotosynthetic mycoheterotrophic plant Hypopitys monotropa, its structure, gene expression and RNA editing (v0.1)"
inferred← citeshttps://doi.org/10.7287/peerj.9309v0.2/reviews/3openalex-snapshot
Peer Review #3 of "Mitochondrial genome of the nonphotosynthetic mycoheterotrophic plant Hypopitys monotropa, its structure, gene expression and RNA editing (v0.2)"
inferred← citeshttps://doi.org/10.7717/peerj.12106openalex-snapshot
Genomic comparison of non-photosynthetic plants from the family Balanophoraceae with their photosynthetic relatives
inferred← citeshttps://doi.org/10.7717/peerj.9048openalex-snapshot
Long-reads reveal that Rhododendron delavayi plastid genome contains extensive repeat sequences, and recombination exists among plastid genomes of photosynthetic Ericaceae
inferred← citeshttps://doi.org/10.7717/peerj.9309openalex-snapshot
Mitochondrial genome of the nonphotosynthetic mycoheterotrophic plant Hypopitys monotropa , its structure, gene expression and RNA editing
inferred← citeshttps://doi.org/10.7868/s0026898417050044openalex-snapshot
ИДЕНТИФИКАЦИЯ И?ЭКСПРЕССИЯ ГЕНА РЕЦЕПТОРНОЙ КИНАЗЫ ERECTA У?МИКОГЕТЕРОТРОФНОГО РАСТЕНИЯ MONOTROPA HYPOPITYS, "Молекулярная биология"
Editorial review for independent work. ICSAC — the Institute for Complexity Science and Advanced Computing — runs a structured editorial panel for researchers publishing outside journals, and publishes on CiteStamp rails. Submission is free and goes through ORCID: icsacinstitute.org/submit.