Mycoheterotrophic Epirixanthes (Polygalaceae) has a typical angiosperm mitogenome but unorthodox plastid genomes.

BACKGROUND AND AIMS: Fully mycoheterotrophic plants derive carbon and other nutrients from root-associated fungi and have lost the ability to photosynthesize. While mycoheterotroph plastomes are often degraded compared with green plants, the effect of this unusual symbiosis on mitochondrial genome evolution is unknown. By providing the first complete organelle genome data from Polygalaceae, one of only three eudicot families that developed mycoheterotrophy, we explore how both organellar genomes evolved after loss of photosynthesis. METHODS: We sequenced and assembled four complete plastid genomes and a mitochondrial genome from species of Polygalaceae, focusing on non-photosynthetic Epirixanthes. We compared these genomes with those of other mycoheterotroph and parasitic plant lineages, and assessed whether organelle genes in Epirixanthes experienced relaxed or intensified selection compared with autotrophic relatives. KEY RESULTS: Plastomes of two species of Epirixanthes have become substantially degraded compared with that of autotrophic Polygala. Although the lack of photosynthesis is presumably homologous in the genus, the surveyed Epirixanthes species have marked differences in terms of plastome size, structural rearrangements, gene content and substitution rates. Remarkably, both apparently replaced a canonical plastid inverted repeat with large directly repeated sequences. The mitogenome of E. elongata incorporated a considerable number of fossilized plastid genes, by intracellular transfer from an ancestor with a less degraded plastome. Both plastid and mitochondrial genes in E. elongata have increased substitution rates, but the plastid genes of E. pallida do not. Despite this, both species have similar selection patterns operating on plastid housekeeping genes. CONCLUSIONS: Plastome evolution largely fits with patterns of gene degradation seen in other heterotrophic plants, but includes highly unusual directly duplicated regions. The causes of rate elevation in the sequenced Epirixanthes mitogenome and of rate differences in plastomes of related mycoheterotrophic species are not currently understood.

The Evolution of HD2 Proteins in Green Plants.

In eukaryotes, protein deacetylation is carried out by two well-conserved histone deacetylase (HDAC) families: RPD3/HDA1 and SIR2. Intriguingly, model plants such as Arabidopsis express an additional plant-specific HDAC family, termed type-2 HDACs (HD2s). Transcriptomic analyses from more than 1300 green plants generated by the 1000 plants (1KP) consortium showed that HD2s appeared early in green plant evolution, the first members being detected in several streptophyte green alga. The HD2 family has expanded via several rounds of successive duplication; members are expressed in all major green plant clades. Interestingly, angiosperm species express new HD2 genes devoid of a zinc-finger domain, one of the main structural features of HD2s. These variants may have been associated with the origin and/or the biology of the ovule/seed.

Characterization of the adenosine deaminase-related growth factor (ADGF) gene family in Drosophila.

A novel family of growth factors, with sequence similarity to adenosine deaminase, has been identified in various organisms including flesh fly, tsetse fly, sand fly, mollusk and human. The human homologue, CECR1, is a candidate gene for the genetic disorder cat eye syndrome. Here, we describe six members of this growth factor family in Drosophila and two in vertebrates. The six Drosophila genes, named adenosine deaminase-related growth factors (ADGF), are found at three different chromosomal locations, with one singleton, two in an inverted orientation, and three in a tandem arrangement. These genes show distinct patterns of expression as measured by RT-PCR and Northern blots, indicating gene-specific function. The presence of six ADGF genes in the Drosophila genome suggests that gene duplication and divergence has been important for these growth factors in insect development. Phylogenetic analysis of the 14 extant ADGF-like gene products shows there are at least three major groups, two of which are found in Drosophila. The third appears specific to the vertebrate line. Seven gene duplications are inferred among the ADGF-like genes, most of which occurred long before the origin of Drosophila. Our analysis predicts the existence of several other unsampled ADGF-like genes, both within the species examined here, and in other related invertebrates.

Utility of 17 chloroplast genes for inferring the phylogeny of the basal angiosperms.

Sequences from 14 slowly evolving chloroplast genes (including three highly conserved introns) were obtained for representative basal angiosperm and seed-plant taxa, using novel primers described here. These data were combined with published sequences from atpB, rbcL, and newly obtained sequences from ndhF. Combined data from these 17 genes permit sturdy, well-resolved inference of major aspects of basal angiosperm relationships, demonstrating that the new primers are valuable tools for sorting out the deepest events in flowering plant phylogeny. Sequences from the inverted repeat (IR) proved to be particularly reliable (low homoplasy, high retention index). Representatives of Cabomba and Illicium were the first two successive branches of the angiosperms in an initial sampling of 19 exemplar taxa. This result was strongly supported by bootstrap analysis and by two small insertion/deletion events in the slowly evolving introns. Several paleoherb groups (representatives of Piperales) formed a strongly supported clade with taxa representing core woody magnoliids (Laurales, Magnoliales, and Winteraceae). The monophyly of the sampled eudicots and monocots was also well supported. Analyses of three major partitions of the data showed many of the same clades and supported the rooting seen with all the data combined. While Amborella trichopoda was supported as the sister group of the remaining angiosperms when we added Amborella and Nymphaea odorata to the analysis, a strongly conflicting rooting was observed when Amborella alone was added.

Evolutionary significance of an unusual chloroplast DNA inversion found in two basal angiosperm lineages.

Two basal lineages of flowering plants possess an intergenic inversion in the chloroplast inverted repeat (IR), a region of the genome from which there have been few previous reports of this class of structural mutation. The size of the inversion (approximately 200 bp) places it in a class not previously seen in the plastid genome. The two lineages with the rearrangement, representatives of the orders Laurales and Nymphaeales, are not closely related and the inversion therefore probably arose independently in each group. The inversion is bordered by short, but highly conserved, inverted repeat motifs that were most likely associated with the inversion process. A stem-loop structure that involves these motifs may play a functional role in mRNA stability. It is seen in all optimal or nearly optimal predicted RNA foldings of the intergenic region.

Phylogenetic congruence and discordance among one morphological and three molecular data sets from Pontederiaceae.

A morphological data set and three sources of data from the chloroplast genome (two genes and a restriction site survey) were used to reconstruct the phylogenetic history of the pickerelweed family Pontederiaceae. The chloroplast data converged towards a single tree, presumably the true chloroplast phylogeny of the family. Unrooted trees estimated from each of the three chloroplast data sets were identical or extremely similar in shape to each other and mostly robustly supported. There was no evidence of significant heterogeneity among the data sets, and the few topological differences seen among unrooted trees from each chloroplast data set are probably artifacts of sampling error on short branches. Despite well-documented differences in rates of evolution for different characters in individual data sets, equally weighted parsimony permits accurate reconstructions of chloroplast relationships in Pontederiaceae. A separate morphology-based data set yielded trees that were very different from the chloroplast trees. Although there was substantial support from the morphological evidence for several major clades supported by chloroplast trees, most of the conflicting phylogenetic structure on the morphology trees was not robust. Nonetheless, several statistical tests of incongruence indicate significant heterogeneity between molecules and morphology. The source of this apparent incongruence appears to be a low ratio of phylogenetic signal to noise in the morphological data.

Surface spectroscopic studies of Biomer.

The objective of this work was to determine whether there is a significant difference in composition between the air facing and mold facing sides of Biomer and to see if the mold itself affects the polymer surface. A detailed analysis of Biomer was undertaken using x-ray photoelectron spectroscopy (ESCA), secondary ion mass spectroscopy (SIMS), and low energy ion scattering spectroscopy (ISS). Previous workers have used FTIR and ESCA to study Biomer and comparisons with their results will be discussed. Because of the increase in surface sensitivity SIMS and ISS can be valuable tools for studying polymeric materials. SIMS has been used to identify the structure of the Biomer air and mold facing surfaces from both glass and nickel molds. ESCA and ISS have indicated the presence of a silicon contaminant on the air and mold facing surfaces and SIMS has shown that the form of the silicon contaminant is probably a polysiloxane.

Surface spectroscopic studies of Avcothane.

Avcothane is a commercially available copolymer of polyether, polyurethane, and polydimethylsiloxane; it is used primarily in aortic balloon pumps. The pumps consist of three segments which are cemented or fused together to form the balloon. The objective of this work is to characterize the surfaces, inside and outside, of the three balloon pump sections. By using x-ray photoelectron spectroscopy (ESCA), ion scattering spectroscopy (ISS), and secondary ion mass spectrometry (SIMS) a detailed analysis of the Avcothane surfaces can be performed and comparisons between various surfaces made. Previous workers have reported ESCA and Auger electron spectroscopy (AES) measurements of Avcothane and comparisons with their results will be presented. SIMS and ISS are useful analytical tools for studying polymeric biomaterials because these techniques are usually more surface sensitive than either ESCA or AES. SIMS and ISS data indicate that a thin fluorine-rich film (probably a fluorocarbon polymer) is present on the Avcothane surface. Signals from the fluorine-rich layer are more intense from the inside of the balloon pump and the intensity generally decreases from top to bottom. The outside sections of the aortic balloon pump also show the presence of fluorine, but the signals are far less intense than from the inside. One possible explanation for the fluorine-rich layer is that a fluorine-containing compound is deposited on the balloon pump during molding and preparation. Another possibility is that the layer is deposited during preparation of the Avcothane itself, but is essentially removed from the outside during sterilization.