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Ceratophyllaceae is a group of cosmopolitan aquatic plants with unusual morphologies, including inconspicuous flowers and greatly reduced roots, with an ancient origin supported by related fossils since the early Cretaceous.
Resolving the relationships among these five groups will inform the order of their divergence and identify the sister groups of eudicots and monocots, the two largest angiosperm groups.
Here transcriptome data sets are obtained from 26 species lacking sequenced genomes, representing each of the five groups: eudicots, monocots, magnoliids, Chloranthaceae and Ceratophyllaceae.
Moreover, single-copy genes and genes from inverted repeated region (IR) of 86 plastid genomes were reanalysed extensively to identify possible causes of different topologies when using different datasets.
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Sequenced genomes of 30 angiosperm species are available (Supplementary Table 1), but they have uneven phylogenetic distribution, being concentrated in a few eudicot and monocot groups.
Here, to provide a better representation of the five mesangiosperm lineages, 25 new angiosperm transcriptome data sets were generated (Table 1), including those of representatives for the three smaller groups (magnoliids, Chloranthaceae and Ceratophyllaceae), which lack sequenced genomes.
Angiosperm phylogeny is the foundation of studies of gene function and phenotypic evolution, divergence time estimation and biogeography.