SynthesisBMC biology2009
Increasing phylogenetic resolution at low taxonomic levels using massively parallel sequencing of chloroplast genomes.
Synthesis in BMC biology, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 288 papers.
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Who cites it
288 citing papers in PubMed.
- Plastome architecture and maternal relationships of cultivated almond (Prunus dulcis) and its wild relatives.Planta · 2026Article
- A global phylogenetic framework for Diospyros L. (Ebenaceae, Ericales): enhanced taxon and sample coverage through NGS, Sanger sequencing and herbariomics.Annals of botany · 2026Article
- Characterization ofEcology and evolution · 2026Article
- Characterisation of the chloroplast genome of Macrotyloma species: comparative analysis and phylogenomic insights.Scientific reports · 2026Article
- Unraveling the Chloroplast Genome of Stellaria media: Comprehensive Analysis, Taxonomic Implications, and Evolutionary Perspectives.Biochemical genetics · 2026Article
- Complex History of Organellar Introgression inEcology and evolution · 2026Article
- Plastome evolution and phylogenomics of Glycine (Leguminosae: Papilionoideae).BMC plant biology · 2026Article
- The complete chloroplast genome sequence of Typhonium flagelliforme, an anti-cancer medicinal plant: genome structure, comparative and phylogenetic relationship analysis within Araceae.Functional & integrative genomics · 2026Article
- Comprehensive analysis of chloroplast genome evolution in Poaceae: codon usage patterns, selection pressures, and phylogenomic relationships.BMC genomics · 2026Article
- The complete chloroplast genome ofMitochondrial DNA. Part B, Resources · 2026Article
- The complete chloroplast genome ofMitochondrial DNA. Part B, Resources · 2026Article
- The complete chloroplast genome sequence ofMitochondrial DNA. Part B, Resources · 2026Article
- Article
- Scaling Up Species Delimitation From DNA Barcodes to Whole Organelle Genomes: Strong Evidence for Discordance Among Genes and Methods for the Red Alga Dasyclonium.Molecular ecology resources · 2025Article
- Chloroplast genome analysis of Dendrocalamus × mutatus and its implications for bamboo classification.BMC plant biology · 2025Article
- Evolutionary genetics analysis for complete plastomes and diversification rate estimation of Deutzia and Philadelphus in tribe Philadelpheae (Hydrangeaceae).BMC plant biology · 2025Article
- Eight NewGenes · 2025Article
- Reporting complete chloroplast genome of endangered red mulberry, useful for understanding hybridization and phylogenetic relationships.Scientific reports · 2025Article
- Specimen Identification Through Multilocus Species Tree Constructed From Single-Copy Orthologs (SCOs): A Case Study inEcology and evolution · 2025Article
- Chloroplast genomic insights into adaptive evolution and rapid radiation in the genus Passiflora (Passifloraceae).BMC plant biology · 2025Article
228 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
3 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundMolecular evolutionary studies share the common goal of elucidating historical relationships, and the common challenge of adequately sampling taxa and characters. Particularly at low taxonomic levels, recent divergence, rapid radiations, and conservative genome evolution yield limited sequence variation, and dense taxon sampling is often desirable. Recent advances in massively parallel sequencing make it possible to rapidly obtain large amounts of sequence data, and multiplexing makes extensive sampling of megabase sequences feasible. Is it possible to efficiently apply massively parallel sequencing to increase phylogenetic resolution at low taxonomic levels?
resultsWe reconstruct the infrageneric phylogeny of Pinus from 37 nearly-complete chloroplast genomes (average 109 kilobases each of an approximately 120 kilobase genome) generated using multiplexed massively parallel sequencing. 30/33 ingroup nodes resolved with > or = 95% bootstrap support; this is a substantial improvement relative to prior studies, and shows massively parallel sequencing-based strategies can produce sufficient high quality sequence to reach support levels originally proposed for the phylogenetic bootstrap. Resampling simulations show that at least the entire plastome is necessary to fully resolve Pinus, particularly in rapidly radiating clades. Meta-analysis of 99 published infrageneric phylogenies shows that whole plastome analysis should provide similar gains across a range of plant genera. A disproportionate amount of phylogenetic information resides in two loci (ycf1, ycf2), highlighting their unusual evolutionary properties.
conclusionPlastome sequencing is now an efficient option for increasing phylogenetic resolution at lower taxonomic levels in plant phylogenetic and population genetic analyses. With continuing improvements in sequencing capacity, the strategies herein should revolutionize efforts requiring dense taxon and character sampling, such as phylogeographic analyses and species-level DNA barcoding.
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