Phylogenetic significance of the rpoA loss in the chloroplast genome of mosses

A recent survey of arthrodontous mosses revealed that their chloroplast genome lacks the gene encoding the alpha subunit of the RNA polymerase (i.e., rpoA), and that at least in Physcomitrella patens the gene has been transferred to the nuclear genome. Subsequently the gene was recorded from the cytoplasmic genome in Takakia and Sphagnum. Here we extend the survey to representatives of all major lineages of mosses to determine when in the evolutionary history of the Bryophyta the loss took place. Amplifications using primers annealing to the flanking regions of the rpoA gene yield a product that contains the gene in Takakia, Sphagnum, Andreaea, Oedipodium, Polytrichaceae, and Buxbaumia. The gene is lacking in all arthrodontous mosses, including Diphyscium but also in both species of Tetraphis. Reconstruction of the transfer on the phylogeny of mosses suggests (a) that the rpoA gene was lost twice and (b) that the gene was lost after the divergence of Buxbaumiidae and prior to the divergence of Diphyscium from the remaining Bryopsida

Deep sequencing of Ptilidium (Ptilidiaceae) suggests evolutionary stasis in liverwort plastid genome structure

Background and aims – Organellar genome sampling is patchy for non-vascular groups, with the earliest land plants poorly represented; currently only two liverworts, two mosses and one hornwort have sequenced, annotated plastid genomes. This is in part due to methodological difficulties that have hampered attempts to generate plastid genome data from liverworts. In this paper we present a method that overcomes some of the inherent difficulties by circumventing the need for plastid enrichment, but that also provides other valuable information from nuclear and mitochondrial regions including sequences from loci that may be phylogenetically useful, and potential population-level markers such as single nucleotide polymorphisms and microsatellites. Methods – A shotgun library developed from total genomic liverwort DNA was subjected to high-throughput pyrosequencing using the Roche 454 platform. Plastid reads were bioinformatically identified, assembled and annotated. To maximize usage of the vast number of reads generated using 454 sequencing technology, combined nuclear, mitochondrial and plastid contigs were also screened for microsatellite markers, and presumed nuclear contigs were scanned for protein domains. Key Results – This is the first plastid genome to be assembled for a leafy liverwort (i.e. Ptilidium) and also the first such genome to be sequenced using next generation technology for any bryophyte. The 119,007 base long plastid genome of Ptilidium pulcherrimum contains 88 protein-coding genes, four rRNAs and thirty tRNAs. The Inverted Repeat occurs between trn V-GAC and trn N-GUU. Functional copies of the two plastid-encoded sulphate import protein-coding genes (cysA and cysT) are absent, although pseudogenes are present in the same position that the functional genes occupy in Marchantia. Microsatellites: 197 novel potential primer pairs for P. pulcherrimum were found. Presumed nuclear Ptilidium contigs gave multiple hits to Class I transposable elements. Conclusions – The arrangement of genes is identical to the plastid of the complex thalloid liverwort Marchantia, suggesting that structural rearrangements are rare in hepatics. This dataset represents a valuable resource for novel phylogenetic and population level marker design in hepatics

Effect of Strain on the Growth of InAs/GaSb Superlattices: An X-Ray Study

We present a detailed x-ray diffraction study of the strain in InAs/GaSb superlattices grown by molecular beam epitaxy. The superlattices were grown with either InSb or GaAs interfaces. We show that the superlattice morphology, either planar or nanostructured, is dependent on the chemical bonds at the heterointerfaces. In both cases, the misfit strain has been determined for the superlattice layers and the interfaces. We also determined how the magnitude and sign of this strain is crucial in governing the morphology of the superlattice. Our analysis suggests that the growth of self-assembled nanostructures may be extended to many systems generally thought to have too small a lattice mismatch.Comment: 40 pages, 14 figures, 2 tables. Submitted to Journal of Applied Physics in November 200

Biogeophysical effects of CO2-fertilization on global climate

CO{sub 2}-fertilization affects plant growth, which modifies surface physical properties, altering the surface albedo, and fluxes of sensible and latent heat. We investigate how such CO{sub 2}-fertilization effects on vegetation and surface properties would affect the climate system. Using a global three-dimensional climate-carbon model that simulates vegetation dynamics, we compare two multi-century simulations: a ''Control'' simulation with no emissions, and a ''Physiol-noGHG'' simulation where physiological changes occur as a result of prescribed CO{sub 2} emissions, but where CO{sub 2}-induced greenhouse warming is not included. In our simulations, CO{sub 2}-fertilization produces warming; we obtain an annual- and global-mean warming of about 0.65 K (and land-only warming of 1.4 K) after 430 years. This century-scale warming is mostly due to a decreased surface albedo associated with the expansion of the Northern Hemisphere boreal forests. On decadal time scales, the CO{sub 2} uptake by afforestation should produce a cooling effect that exceeds this albedo-based warming; but if the forests remain in place, the CO{sub 2}-enhanced-greenhouse effect would diminish as the ocean equilibrates with the atmosphere, whereas the albedo effect would persist. Thus, on century time scales, there is the prospect for net warming from CO{sub 2}-fertilization of the land biosphere. Further study is needed to confirm and better quantify our results

Access to RNA-sequencing data from 1,173 plant species: The 1000 Plant transcriptomes initiative (1KP)

The 1000 Plant transcriptomes initiative (1KP) explored genetic diversity by sequencing RNA from 1,342 samples representing 1,173 species of green plants (Viridiplantae).This data release accompanies the initiative's final/capstone publication on a set of 3 analyses inferring species trees, whole genome duplications, and gene family expansions. These and previous analyses are based on de novo transcriptome assemblies and related gene predictions. Here, we assess their data and assembly qualities and explain how we detected potential contaminations.These data will be useful to plant and/or evolutionary scientists with interests in particular gene families, either across the green plant tree of life or in more focused lineages

Paralogs and off-target sequences improve phylogenetic resolution in a densely-sampled study of the breadfruit genus (Artocarpus, Moraceae)

We present a 517-gene phylogenetic framework for the breadfruit genus Artocarpus (ca. 70 spp., Moraceae), making use of silica-dried leaves from recent fieldwork and herbarium specimens (some up to 106 years old) to achieve 96% taxon sampling. We explore issues relating to assembly, paralogous loci, partitions, and analysis method to reconstruct a phylogeny that is robust to variation in data and available tools. Although codon partitioning did not result in any substantial topological differences, the inclusion of flanking noncoding sequence in analyses significantly increased the resolution of gene trees. We also found that increasing the size of data sets increased convergence between analysis methods but did not reduce gene-tree conflict. We optimized the HybPiper targeted-enrichment sequence assembly pipeline for short sequences derived from degraded DNA extracted from museum specimens. Although the subgenera of Artocarpus were monophyletic, revision is required at finer scales, particularly with respect to widespread species. We expect our results to provide a basis for further studies in Artocarpus and provide guidelines for future analyses of data sets based on target enrichment data, particularly those using sequences from both fresh and museum material, counseling careful attention to the potential of off-target sequences to improve resolution. [Artocarpus; Moraceae; noncoding sequences; phylogenomics; target enrichment.

Application of qRT-PCR and RNA-Seq analysis for the identification of housekeeping genes useful for normalization of gene expression values during Striga hermonthica development.

Abstract Striga is a root parasitic weed that attacks many of the staple crops in Africa, India and Southeast Asia, inflicting tremendous losses in yield and for which there are few effective control measures. Studies of parasitic plant virulence and host resistance will be greatly facilitated by the recent emergence of genomic resources that include extensive transcriptome sequence datasets spanning all life stages of S. hermonthica. Functional characterization of Striga genes will require detailed analyses of gene expression patterns. Quantitative real-time PCR is a powerful tool for quantifying gene expression, but correct normalization of expression levels requires identification of control genes that have stable expression across tissues and life stages. Since no S. hermonthica housekeeping genes have been established for this purpose, we evaluated the suitability of six candidate housekeeping genes across key life stages of S. hermonthica from seed conditioning to flower initiation using qRT-PCR and high-throughput cDNA sequencing. Based on gene expression analysis by qRT-PCR and RNA-Seq across heterogeneous Striga life stages, we determined that using the combination of three genes, UBQ1, PP2A and TUB1 provides the best normalization for gene expression throughout the parasitic life cycle. The housekeeping genes characterized here provide robust standards that will facilitate powerful descriptions of parasite gene expression patterns

Genetic analysis of peripheral nerve conduction velocity in twins

We studied variation in peripheral nerve conduction velocity (PNCV) and intelligence in a group of 16-year-old Dutch twins. It has been suggested that both brain nerve conduction velocity and PNCV are positively correlated with intelligence (Reed, 1984) and that heritable differences in NCV may explain part of the well established heritability of intelligence. The Standard Progressive Matrices test was administered to 210 twin pairs to obtain IQ scores. Median nerve PNCV was determined in a subgroup of 156 pairs. Genetic analyses showed a heritability of 0.65 for Raven IQ score and 0.77 for PNCV. However, there was no significant phenotypic correlation between IQ score and PNCV. © 1995 Plenum Publishing Corporation

Complete chloroplast genome sequence of Holoparasite Cistanche Deserticola (Orobanchaceae) reveals gene loss and horizontal gene transfer from Its host Haloxylon Ammodendron (Chenopodiaceae)

The central function of chloroplasts is to carry out photosynthesis, and its gene content and structure are highly conserved across land plants. Parasitic plants, which have reduced photosynthetic ability, suffer gene losses from the chloroplast (cp) genome accompanied by the relaxation of selective constraints. Compared with the rapid rise in the number of cp genome sequences of photosynthetic organisms, there are limited data sets from parasitic plants. The authors report the complete sequence of the cp genome of Cistanche deserticola, a holoparasitic desert species belonging to the family Orobanchaceae

Parasitic Plants Striga and Phelipanche Dependent upon Exogenous Strigolactones for Germination Have Retained Genes for Strigolactone Biosynthesis

Abstract Strigolactones are plant hormones with multiple functions, including regulating various aspects of plant architecture such as shoot branching, facilitating the colonization of plant roots by arbuscular mycorrhizal fungi, and acting as seed germination stimulants for certain parasitic plants of the family Orobanchaceae. The obligate parasitic species Phelipanche aegyptiaca and Striga hermonthica require strigolactones for germination, while the facultative parasite Triphysaria versicolor does not. It has been hypothesized that P. aegyptiaca and S. hermonthica would have undergone evolutionary loss of strigolactone biosynthesis as a part of their mechanism to enable specific detection of exogenous strigolactones. We analyzed the transcriptomes of P. aegyptiaca, S. hermonthica and T. versicolor and identified genes known to act in strigolactone synthesis (D27, CCD7, CCD8, and MAX1), perception (MAX2 and D14) and transport (PDR12). These genes were then analyzed to assess likelihood of function. Transcripts of all strigolactone-related genes were found M. Das et al. 1152 in P. aegyptiaca and S. hermonthica, and evidence points to their encoding functional proteins. Gene open reading frames were consistent with homologs from Arabidopsis and other strigolactone-producing plants, and all genes were expressed in parasite tissues. In general, the genes related to strigolactone synthesis and perception appeared to be evolving under codon-based selective constraints in strigolactone-dependent species. Bioassays of S. hermonthica root extracts indicated the presence of strigolactone class stimulants on germination of P. aegyptiaca seeds. Taken together, these results indicate that Phelipanche aegyptiaca and S. hermonthica have retained functional genes involved in strigolactone biosynthesis, suggesting that the parasites use both endogenous and exogenous strigolactones and have mechanisms to differentiate the two