Exceptionally high rates of positive selection on the rbcL gene in the genus Ilex (Aquifoliaceae).

Background: The genus Ilex (Aquifoliaceae) has a near-cosmopolitan distribution in mesic habitats from tropical to temperate lowlands and in alpine forests. It has a high rate of hybridization and plastid capture, and comprises four geographically structured plastid groups. A previous study showed that the plastid rbcL gene, coding for the large subunit of Rubisco, has a particularly high rate of non-synonymous substitutions in Ilex, when compared with other plant lineages.

Correction: Phylogeny, character evolution and spatiotemporal diversification of the species-rich and world-wide distributed tribe Rubieae (Rubiaceae).

[This corrects the article DOI: 10.1371/journal.pone.

Phylogeny, character evolution and spatiotemporal diversification of the species-rich and world-wide distributed tribe Rubieae (Rubiaceae).

The Rubiaceae tribe Rubieae has a world-wide distribution with up to 1,000 species. These collectively exhibit an enormous ecological and morphological diversity, making Rubieae an excellent group for macro- and microevolutionary studies. Previous molecular phylogenetic analyses used only a limited sampling within the tribe or missed lineages crucial for understanding character evolution in this group.

Potential DNA transfer from the chloroplast to the nucleus in Eryngium alpinum.

Very divergent psbA-trnH chloroplast sequences were, for some Eryngiun alpinum individuals, repeatedly obtained and could not be attributed to contaminations nor to casual intraspecific variation. The design of external primers allowed the amplification of two different sequences for the same individuals. The divergent sequences were found to be more variable than their counterparts, to have a low GC content and to display a nonsynonymous substitution in psbA C-terminal region, all reasons that led us to hypothesize that they are paraloguous fragments transferred into the nucleus (NuPt).

The history of extant Ilex species (Aquifoliaceae): evidence of hybridization within a Miocene radiation.

The history and diversification of the genus Ilex (Aquifoliaceae), based on 108 different species (116 specimens), are inferred from the analysis of two nuclear (ITS and nepGS) and three plastid (rbcL, trnL-F and atpB-rbcL) sequences. Nuclear and plastid trees are highly incongruent and the nuclear tree is more compatible with current taxonomic classifications than the plastid one. The most recent common ancestor (MRCA) of extant species is dated from the Miocene, although the Ilex stem lineage can be traced back to the late Cretaceous, according to fossil records.

A plastid gene phylogeny of the non-photosynthetic parasitic Orobanche (Orobanchaceae) and related genera.

The phylogenetic relationships of the non-photosynthetic Orobanche sensu lato (Orobanchaceae), which includes some of the economically most important parasitic weeds, remain insufficiently understood and controversial. This concerns both the phylogenetic relationships within the genus, in particular its monophyly or lack thereof, and the relationships to other holoparasitic genera such as Cistanche or Conopholis. Here we present the first comprehensive phylogenetic study of this group based on a region from the plastid genome (rps2 gene).

Horizontal gene transfer of a plastid gene in the non-photosynthetic flowering plants Orobanche and Phelipanche (Orobanchaceae).

Plastid sequences are among the most widely used in phylogenetic and phylogeographic studies in flowering plants, where they are usually assumed to evolve like non-recombining, uniparentally transmitted, single-copy genes. Among others, this assumption can be violated by intracellular gene transfer (IGT) within cells or by the exchange of genes across mating barriers (horizontal gene transfer, HGT). We report on HGT of a plastid region including rps2, trnL-F, and rbcL in a group of non-photosynthetic flowering plants.

A fully automatable enzymatic method for DNA extraction from plant tissues.

Background: DNA extraction from plant tissues, unlike DNA isolation from mammalian tissues, remains difficult due to the presence of a rigid cell wall around the plant cells. Currently used methods inevitably require a laborious mechanical grinding step, necessary to disrupt the cell wall for the release of DNA.

Results: Using a cocktail of different carbohydrases, a method was developed that enables a complete digestion of the plant cell walls and subsequent DNA release.

Are both sympatric species Ilex perado and Ilex canariensis secretly hybridizing? Indication from nuclear markers collected in Tenerife.

Background: Intra-specific and intra-individual polymorphism is frequently observed in nuclear markers of Ilex (Aquifoliaceae) and discrepancy between plastid and nuclear phylogenies is the rule in this genus. These observations suggest that inter-specific plastid or/and nuclear introgression played an important role in the process of evolution of Ilex. With the aim of a precise understanding of the evolution of this genus, two distantly related sympatric species collected in Tenerife (Canary Islands), I.

Phylogeny and intraspecific variability of holoparasitic Orobanche (Orobanchaceae) inferred from plastid rbcL sequences.

The rbcL sequences of 106 specimens representing 28 species of the four recognized sections of Orobanche were analyzed and compared. Most sequences represent pseudogenes with premature stop codons. This study confirms that the American lineage (sects.

The cpcB-cpcA locus as a tool for the genetic characterization of the genus Arthrospira (Cyanobacteria): evidence for horizontal transfer.

To investigate the genetic diversity of the genus Arthrospira and to compare it with other cyanobacteria, sequences of 670 nt from the phycocyanin operon were determined for 23 natural, cultivated or commercial strains of Arthrospira and compared with sequences from 20 other non-Arthrospira cyanobacterial strains. The sequenced DNA fragment comprises the last 255 nt of cpcB, the cpcB-cpcA spacer and the first 304 nt of cpcA. The resulting phylogenetic tree confirms that the genus Arthrospira is not related to Spirulina.