The first complete chloroplast genome sequence of a lycophyte, Huperzia lucidula (Lycopodiaceae).

We used a unique combination of techniques to sequence the first complete chloroplast genome of a lycophyte, Huperzia lucidula. This plant belongs to a significant clade hypothesized to represent the sister group to all other vascular plants. We used fluorescence-activated cell sorting (FACS) to isolate the organelles, rolling circle amplification (RCA) to amplify the genome, and shotgun sequencing to 8x depth coverage to obtain the complete chloroplast genome sequence. The genome is 154,373 bp, containing inverted repeats of 15,314 bp each, a large single-copy region of 104,088 bp, and a small single-copy region of 19,657 bp. Gene order is more similar to those of mosses, liverworts, and hornworts than to gene order for other vascular plants. For example, the Huperzia chloroplast genome possesses the bryophyte gene order for a previously characterized 30 kb inversion, thus supporting the hypothesis that lycophytes are sister to all other extant vascular plants. The lycophyte chloroplast genome data also enable a better reconstruction of the basal tracheophyte genome, which is useful for inferring relationships among bryophyte lineages. Several unique characters are observed in Huperzia, such as movement of the gene ndhF from the small single copy region into the inverted repeat. We present several analyses of evolutionary relationships among land plants by using nucleotide data, inferred amino acid sequences, and by comparing gene arrangements from chloroplast genomes. The results, while still tentative pending the large number of chloroplast genomes from other key lineages that are soon to be sequenced, are intriguing in themselves, and contribute to a growing comparative database of genomic and morphological data across the green plants.

Phylogeny and ecological radiation of New World thistles (Cirsium, Cardueae - Compositae) based on ITS and ETS rDNA sequence data.

Sequence data from a portion of the external transcribed spacer (ETS) and internal transcribed spacers (ITS-1 and ITS-2) of 18S-26S nuclear ribosomal DNA were used to resolve historical biogeography and ecology of true thistles (Cirsium, Cardueae, Compositae) in the New World. The 650 base-pair, 3' portion of the ETS examined here showed a level of variation across taxa similar to that of the ITS sequences included. A maximum-likelihood tree based on combined ETS and ITS sequences leads us to suggest that the New World species of true thistles constitute a major lineage, which in turn comprises several smaller lineages. A western North American lineage shows weak quartet-puzzling support, but includes a well-supported lineage of species endemic to the California Floristic Province. Comparisons of this Californian lineage with other neoendemic angiosperm groups of the region show that the Californian Cirsium lineage exhibits unusually high ecological diversity for a group displaying such low levels of rDNA sequence divergence across taxa. Similarly low levels of sequence divergence were found throughout the New World Cirsium lineage. These results indicate either that Cirsium underwent a rapid ecological radiation in North America, or that rDNA evolution in North American Cirsium has been highly conservative.