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Automatic annotation of organellar genomes with DOGMA
TLDR
The Dual Organellar GenoMe Annotator (DOGMA) automates the annotation of organellar genomes and allows the use of BLAST searches against a custom database, and conservation of basepairing in the secondary structure of animal mitochondrial tRNAs to identify and annotate genes.
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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.
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Hybridization and the Extinction of Rare Plant Species
TLDR
It is suggested that hybridization is an increasing threat to rare species because ecological barriers are being disrupted by human activities and the negative consequences of hybridization are unlikely to be compensated for by immigration from conspecific populations.
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Everywhere but Antarctica: using a supertree to understand the diversity and distribution of the Compositae.
TLDR
The results of molecular phylogenetic studies of members of tribes Helenieae, Heliantheae, and Eupatorieae (Asteraceae) and General systematics and proposed taxonomic changes in current classification are presented.
Extreme reconfiguration of plastid genomes in the angiosperm family Geraniaceae: rearrangements, repeats, and codon usage.
TLDR
Geraniaceae plastid genomes were sequenced and compared with other rosids and the previously published Pelargonium hortorum plastome to propose that increases in genomic rearrangements, repetitive DNA, nucleotide substitutions, and GC content may be caused by relaxed selection resulting from improper DNA repair.
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Two chloroplast DNA inversions originated simultaneously during the early evolution of the sunflower family (Asteraceae).
TLDR
The phylogenetic distribution of two inversions is identical among the members of Asteraceae, suggesting that the inversion events likely occurred simultaneously or within a short time period shortly after the origin of the family.
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Extensive Rearrangements in the Chloroplast Genome of Trachelium caeruleum Are Associated with Repeats and tRNA Genes
TLDR
The Trachelium chloroplast genome shares with Pelargonium and Jasminum both a higher number of repeats and larger repeated sequences in comparison to eight other angiosperm chloropleft genomes, and these are concentrated near rearrangement endpoints.
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Bridging the Rubicon: phylogenetic analysis reveals repeated colonizations of marine and fresh waters by thalassiosiroid diatoms.
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Identifying the basal angiosperm node in chloroplast genome phylogenies: sampling one's way out of the Felsenstein zone.
TLDR
Whereas long sequences reduce variance in branch lengths and molecular dating estimates, the impact of improved taxon sampling on the rooting of the angiosperm phylogeny together with the results of parametric bootstrap analyses demonstrate how long-branch attraction might mislead genome-scale phylogenetic analyses.
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Comparative chloroplast genomics: analyses including new sequences from the angiosperms Nuphar advena and Ranunculus macranthus
TLDR
Although plastome nucleotide composition shows "A+T richness", an A+T bias is not apparent upon more in-depth analysis, at least in these aspects.
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