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The Genome of Black Cottonwood, Populus trichocarpa (Torr. & Gray)
TLDR
Analyzing the draft genome of the black cottonwood tree, Populus trichocarpa, revealed a whole-genome duplication event; about 8000 pairs of duplicated genes from that event survived in the Populus genome.
Ancestral polyploidy in seed plants and angiosperms
TLDR
Comprehensive phylogenomic analyses of sequenced plant genomes and more than 12.6 million new expressed-sequence-tag sequences from phylogenetically pivotal lineages are used to elucidate two groups of ancient gene duplications, implicating two WGDs in ancestral lineages shortly before the diversification of extant seed plants and extant angiosperms.
Analysis of 81 genes from 64 plastid genomes resolves relationships in angiosperms and identifies genome-scale evolutionary patterns
TLDR
Phylogenetic trees from multiple methods provide strong support for the position of Amborella as the earliest diverging lineage of flowering plants, followed by Nymphaeales and Austrobaileyales, and the plastid genome trees also provide strongSupport for a sister relationship between eudicots and monocots, and this group is sister to a clade that includes Chloranthales and magnoliids.
The banana (Musa acuminata) genome and the evolution of monocotyledonous plants
TLDR
This first monocotyledon high-continuity whole-genome sequence reported outside Poales represents an essential bridge for comparative genome analysis in plants and clarifies commelinid-monocotYledon phylogenetic relationships, reveals Poaceae-specific features and has led to the discovery of conserved non-coding sequences predating monocotinoid–eudicotylingon divergence.
The evolution of the SEPALLATA subfamily of MADS-box genes: a preangiosperm origin with multiple duplications throughout angiosperm history.
TLDR
Phylogenetic analyses of SEP sequences show that several gene duplications occurred during the evolution of this subfamily, providing potential opportunities for functional divergence.
Polyploidy and angiosperm diversification.
TLDR
Comparisons of diversification rates suggest that genome doubling may have led to a dramatic increase in species richness in several angiosperm lineages, including Poaceae, Solanaceae, Fabaceae, and Brassicaceae, but additional genomic studies are needed to pinpoint the exact phylogenetic placement of the ancient polyploidy events within these lineages.
Phylotranscriptomic analysis of the origin and early diversification of land plants
TLDR
Strong and robust support is found for a sister-group relationship between land plants and one group of streptophyte green algae, the Zygnematophyceae, and suggests that phylogenetic hypotheses used to understand the evolution of fundamental plant traits should be reevaluated.
Identification of shared single copy nuclear genes in Arabidopsis, Populus, Vitis and Oryza and their phylogenetic utility across various taxonomic levels
TLDR
Putatively orthologous, shared single copy nuclear genes provide a vast source of new evidence for plant phylogenetics, genome mapping, and other applications, as well as a substantial class of genes for which functional characterization is needed.
Orchid phylogenomics and multiple drivers of their extraordinary diversification
TLDR
A phylogeny based on 75 chloroplast genes for 39 species representing all orchid subfamilies and 16 of 17 tribes, time-calibrated against 17 angiosperm fossils shows that orchids appear to have undergone one significant acceleration of net species diversification in the orchidoids, and two accelerations and one deceleration in the upper epidendroids.
Positive selection and expression divergence following gene duplication in the sunflower CYCLOIDEA gene family.
TLDR
Results indicate that gene duplication and functional divergence have played a major role in diversification of the sunflower CYC gene family.
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