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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.
GetOrganelle: a fast and versatile toolkit for accurate de novo assembly of organelle genomes
TLDR
GetOrganelle assemblies are more accurate than published and/or NOVOPlasty-reassembled plastomes as assessed by mapping and are able to reassemble the circular Plastomes from 47 datasets using GetOrganelle.
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.
Disintegration of the scrophulariaceae.
TLDR
A molecular systematic study of Scrophulariaceae sensu lato using DNA sequences of three plastid genes revealed at least five distinct monophyletic groups, which are newly erected herein to recognize the phylogenetic distinctiveness of tribe Calceolarieae.
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 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.
The evolution of the plastid chromosome in land plants: gene content, gene order, gene function
TLDR
This review bridges functional and evolutionary aspects of plastid chromosome architecture in land plants and their putative ancestors and suggests that the slow mode at which the plastome typically evolves is likely to be influenced by a combination of different molecular mechanisms.
The draft genome of the transgenic tropical fruit tree papaya (Carica papaya Linnaeus)
TLDR
Papaya offers numerous advantages as a system for fruit-tree functional genomics, and this draft genome sequence provides the foundation for revealing the basis of Carica’s distinguishing morpho-physiological, medicinal and nutritional properties.
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.
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