Analysis of 81 genes from 64 plastid genomes resolves relationships in angiosperms and identifies genome-scale evolutionary patterns

By Robert K. Jansen, Zhengqiu Cai, Linda A. Raubeson, H. Daniell, Claude W. dePamphilis, J. Leebens-Mack, Kai F. Müller, Mary Guisinger-Bellian, R. Haberle, A. K. Hansen and 6 more. Proceedings of the National Academy of Sciences of the United States of America, 2007

1,071 citations recorded by the source corpus.

Subfields: Ecology, Evolution, Behavior and Systematics, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/f297de931889804f9aea74dd9668f355c9511c61

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Citations in the corpus

Polyploidy and angiosperm diversification. (2009, background): “Because phylogenetic analyses (e.g., P. Soltis et al., 1999 ; reviewed in D. Soltis et al., 2005 , Leebens-Mack et al., 2005 ; Jansen et al., 2007; Moore et al., 2007 ) identify Amborella trichopoda (Amborellaceae) as the probable single sister species to all other living fl owering plants,…”
Angiosperm phylogeny inferred from sequences of four mitochondrial genes (2010, methodology): “…Qiu et al., 1999, 2005, 2006a; Barkman et al., 2000; Graham & Olmstead, 2000; Soltis et al., 2000; Zanis et al., 2002; Borsch et al., 2003; Hilu et al., 2003; Stefanovic et al., 2004; LeebensMack et al., 2005; Jansen et al., 2007; Moore et al., 2007; Saarela et al., 2007; Goremykin et al., 2009).”
Phylogenetic analysis of 83 plastid genes further resolves the early diversification of eudicots (2010, background): “date the divergences of major lineages (12, 13, 15, 28), analyses of genome-scale phylogenetic matrices are still susceptible to error, which may be masked by high BS values.”
Integrating Early Cretaceous fossils into the phylogeny of living angiosperms: Magnoliidae and eudicots (2010, background): “The J/M tree incorporates relationships among mesangiosperms found in analyses of nearly complete chloroplast genomes (Jansen et al., 2007; Moore et al., 2007), with Chloranthaceae sister to Magnoliidae, Ceratophyllum sister to eudicots, and the two latter clades linked with monocots, but with the…”
The Linear Angiosperm Phylogeny Group (LAPG) III: A linear sequence of the families in APG III (2009, background): “Ceratophyllaceae have moved from within magnoliids and are now sister to the eudicots (Jansen et al., 2007; Moore et al., 2007).”
Angiosperm phylogeny: 17 genes, 640 taxa. (2011, neutral): “…the placement of Amborella as sister to all other extant angiosperms is well supported using complete plastid genome sequences (e.g., Leebens-Mack et al., 2005 ; Jansen et al., 2007 ; Moore et al., 2007 ), as well as in recent analyses of numerous nuclear gene trees ( Jiao et al., in press ).”
CpGAVAS, an integrated web server for the annotation, visualization, analysis, and GenBank submission of completely sequenced chloroplast genome sequences (2012, methodology): “Background Regions on chloroplast genomes have been widely used as phylogenetic [1,2] and DNA barcoding markers [3-5] to determine the phylogenetic relationships of organisms and the identity of particular DNA samples.”
The evolution of the plastid chromosome in land plants: gene content, gene order, gene function (2011, background): “Loss of rps and rpl genes from plastomes is rare, but has been detected in rosids (e.g. rpl22, rpl23, rps16; see Jansen et al. 2007; Jansen et al. 2010; Magee et al. 2010 for an overview) and a variety of non-photosynthetic or minimally photosynthetic angiosperms (Epifagus: dePamphilis and Palmer…”
Integrating Early Cretaceous Fossils into the Phylogeny of Living Angiosperms: ANITA Lines and Relatives of Chloranthaceae (2014, background): “…2008; Qiu et al. 2010; Moore et al. 2011; Zhang et al. 2012), although most indicate different relationships, such as analyses of whole chloroplast genomes (Jansen et al. 2007; Moore et al. 2007), in which Chloranthaceae are sister to the magnoliid clade and Ceratophyllum is sister to eudicots.”
Chloroplast genomes: diversity, evolution, and applications in genetic engineering (2016, background): “The majority of reported intron losses have been observed in specific plant groups or species, although some examples of intron loss (such as that in clpP) occur in diverse plant species, including monocots (Poaceae), eudicots (Onagraceae and Oleaceae) and gymnosperms (Pinus) [49].”
Genome Size Dynamics and Evolution in Monocots (2010, neutral): “[57] and Moore et al.”