ALBERT

Description: Target DNA enrichment combined with high-throughput sequencing technologies is a powerful approach to probing a large number of loci in genomes of interest. However, software algorithms that explicitly consider nucleotide sequence information of target loci in multiple reference species for optimizing design of target enrichment baits to be applicable across a wide range of species have not been developed. Here we present an algorithm that infers target DNA enrichment baits from multiple nucleotide sequence alignments. By applying clustering methods and the combinatorial 1-center sequence optimization to bait design, we are able to minimize the total number of baits required to efficiently probe target loci in multiple species. Consequently, more loci can be probed across species with a given number of baits. Using transcript sequences of 24 apoid wasps (Hymenoptera: Crabronidae, Sphecidae) from the 1KITE project and the gene models of Nasonia vitripennis , we inferred 57,650, 120-bp-long baits for capturing 378 coding sequence sections of 282 genes in apoid wasps. Illumina reduced-representation library sequencing confirmed successful enrichment of the target DNA when applying these baits to DNA of various apoid wasps. The designed baits furthermore enriched a major fraction of the target DNA in distantly related Hymenoptera, such as Formicidae and Chalcidoidea, highlighting the baits’ broad taxonomic applicability. The availability of baits with broad taxonomic applicability is of major interest in numerous disciplines, ranging from phylogenetics to biodiversity monitoring. We implemented our new approach in a software package, called BaitFisher, which is open source and freely available at https://github.com/cmayer/BaitFisher-package.git .

Description: Transfer RNAs (tRNAs) are present in all types of cells as well as in organelles. tRNAs of animal mitochondria show a low level of primary sequence conservation and exhibit ‘bizarre’ secondary structures, lacking complete domains of the common cloverleaf. Such sequences are hard to detect and hence frequently missed in computational analyses and mitochondrial genome annotation. Here, we introduce an automatic annotation procedure for mitochondrial tRNA genes in Metazoa based on sequence and structural information in manually curated covariance models. The method, applied to re-annotate 1876 available metazoan mitochondrial RefSeq genomes, allows to distinguish between remaining functional genes and degrading ‘pseudogenes’, even at early stages of divergence. The subsequent analysis of a comprehensive set of mitochondrial tRNA genes gives new insights into the evolution of structures of mitochondrial tRNA sequences as well as into the mechanisms of genome rearrangements. We find frequent losses of tRNA genes concentrated in basal Metazoa, frequent independent losses of individual parts of tRNA genes, particularly in Arthropoda, and wide-spread conserved overlaps of tRNAs in opposite reading direction. Direct evidence for several recent Tandem Duplication-Random Loss events is gained, demonstrating that this mechanism has an impact on the appearance of new mitochondrial gene orders.

Description: Two new natural compounds, (1 R ,2 E )-2-(6-hydroxyhexylidene)cyclopropyl- β - D -glucopyranoside ( 1 ) and (6 E )-6-[(2 R )-2-( β - D -glucopyranosyloxy)cyclopropylidene]hexanoic acid ( 2 ), glucosides of a very rare methylidenecyclopropane alcohol, as well as two known glycosides of phenolic acids, namely 4- O - β - D -glucopyranosylcaffeic acid ( 3 ) and ( E )-4- O - β - D -glucopyranosylcoumaric acid ( 4 ), and methyl α -fructofuranoside ( 5 ) were isolated for the first time from the rhizomes of the tree fern Metaxya rostrata C. Presl . The structures were elucidated on the basis of detailed spectroscopic data analysis, and the structure of 1 was additionally confirmed by X-ray crystal-structure analysis.

Description: Background: Genetic information given to an individual newly diagnosed with a genetic condition is likely to have important health implications for other family members. The task of communicating with these relatives commonly falls to the newly diagnosed person. Talking to relatives about genetic information can be challenging and is influenced by many factors including family dynamics. Research shows that many relatives remain unaware of relevant genetic information and the possible impact on their own health. This study aims to evaluate whether a specific genetic counselling intervention for people newly diagnosed with a genetic condition, implemented over the telephone on a number of occasions, could increase the number of at-risk relatives who make contact with genetics services after a new genetic diagnosis within a family. Methods: This is a prospective, multi-centre randomised controlled trial being conducted at genetics clinics at five public hospitals in Victoria, Australia. A complex genetic counselling intervention has been developed specifically for this trial. Probands (the first person in a family to present with a diagnosis of a genetic condition) are being recruited and randomised into one of two arms - the telephone genetic counselling intervention arm and the control arm receiving usual care. The number of at-risk relatives for each proband will be estimated from a family pedigree collected at the time of diagnosis. The primary outcome will be measured by comparing the proportion of at-risk relatives in each arm of the trial who make subsequent contact with genetics services.DiscussionThis study, the first randomised controlled trial of a complex genetic counselling intervention to enhance family communication, will provide evidence about how best to assist probands to communicate important new genetic information to their at-risk relatives. This will inform genetic counselling practice in the context of future genomic testing.Trial registration: Australia and New Zealand Clinical Trials Register (ANZCTR):ANZCTRN12608000642381.

Description: Background: Despite considerable progress in systematics, a comprehensive scenario of the evolution of phenotypic characters in the mega-diverse Holometabola based on a solid phylogenetic hypothesis was still missing. We addressed this issue by de novo sequencing transcriptome libraries of representatives of all orders of holometabolan insects (13 species in total) and by using a previously published extensive morphological dataset. We tested competing phylogenetic hypotheses by analyzing various specifically designed sets of amino acid sequence data, using maximum likelihood (ML) based tree inference and Four-cluster Likelihood Mapping (FcLM). By maximum parsimony-based mapping of the morphological data on the phylogenetic relationships we traced evolutionary transformations at the phenotypic level and reconstructed the groundplan of Holometabola and of selected subgroups. Results: In our analysis of the amino acid sequence data of 1,343 single-copy orthologous genes, Hymenoptera are placed as sister group to all remaining holometabolan orders, i.e., to a clade Aparaglossata, comprising two monophyletic subunits Mecopterida (Amphiesmenoptera + Antliophora) and Neuropteroidea (Neuropterida + Coleopterida). The monophyly of Coleopterida (Coleoptera and Strepsiptera) remains ambiguous in the analyses of the transcriptome data, but appears likely based on the morphological data. Highly supported relationships within Neuropterida and Antliophora are Raphidioptera + (Neuroptera + monophyletic Megaloptera), and Diptera + (Siphonaptera + Mecoptera). ML tree inference and FcLM yielded largely congruent results. However, FcLM, which was applied here for the first time to large phylogenomic supermatrices, displayed additional signal in the datasets that was not identified in the ML trees. Conclusions: Our phylogenetic results imply that an orthognathous larva belongs to the groundplan of Holometabola, with compound eyes and well-developed thoracic legs, externally feeding on plants or fungi. Ancestral larvae of Aparaglossata were prognathous, equipped with single larval eyes (stemmata), and possibly agile and predacious. Ancestral holometabolan adults likely resembled in their morphology the groundplan of adult neopteran insects. Within Aparaglossata, the adult's flight apparatus and ovipositor underwent strong modifications. We show that the combination of well-resolved phylogenies obtained by phylogenomic analyses and well-documented extensive morphological datasets is an appropriate basis for reconstructing complex morphological transformations and for the inference of evolutionary histories.

Description: Our study highlights that eCO2 affects species and functional trait composition of a soil seed bank in a permanent grassland. The observed patterns indicate that species that rely on generative reproduction and produce long‐term‐persistent seeds have a competitive advantage under eCO2 over species that rely on vegetative reproduction and short‐term‐persistent seeds. Abstract Questions Soil seed banks buffer plant populations against environmental variability. But environmental changes can have profound impact on them. Several studies addressed the effect of climate change on aboveground vegetation, but studies on changes in the seed bank are rare. Thus, we studied the seed bank of a temperate grassland at a long‐term FACE (Free‐Air Carbon dioxide Enrichment) site, with the following questions: (a) Are there general differences in the species composition between aboveground vegetation and seed bank; (b) what are the impacts of elevated CO2 (eCO2) on seed density and species composition of the seed bank; and (c) are there differences in the functional traits of the seed bank species under eCO2 versus ambient CO2 (aCO2)? Location Temperate grassland, Gießen, Germany. Method Thirty soil cores were taken in six FACE rings. Emerging seedlings were identified to species level after germination and aboveground vegetation was sampled. From the seed bank data, we derived diversity measures and weighted means of species traits, e.g., seed longevity and regeneration type, and compared eCO2 (+20% CO2 above ambient conditions) with aCO2 treatment. Results Nonmetric multidimensional scaling ordination revealed a clear separation between seed bank and aboveground vegetation but no clear CO2 effect. Analyses revealed higher seed densities under eCO2. Species diversity and Shannon diversity were not significantly affected. Evenness decreased significantly under eCO2. There are shifts in functional traits of seed bank species. Seed density of long‐term‐persistent species increased, while short‐term‐persistent species decreased. Seed densities of species with generative reproduction increased under eCO2, while numbers of species with vegetative reproduction decreased. Conclusion The observed trait compositions of the seed bank under eCO2 indicate that species relying on generative reproduction and production of long‐term‐persistent seeds have a competitive advantage under eCO2. The changes in the plant communities described above may lead to profound changes in the supply of grassland ecosystem services.

Description: Orthology characterizes genes of different organisms that arose from a single ancestral gene via speciation, in contrast to paralogy, which is assigned to genes that arose via gene duplication. An accurate ort...

Description: Body plan development in multi-cellular organisms is largely determined by homeotic genes. Expression of homeotic genes, in turn, is partially regulated by insulator binding proteins (IBPs). While only a few e...

Description: Aims After abandonment of grasslands, secondary succession leads to the invasion by woody species. This process begins with the accumulation of tree litter in the forest–grassland ecotone. Our objectives were to determine the relationships between litter amounts and vegetation composition and cover along natural forest–grassland ecotones and to experimentally study the initial effects of tree litter accumulation on grassland vegetation and on microsite conditions. Methods We established 11 transects varying from 12 to 15 m in length in different forest–grassland ecotones in the Lahn-Dill highlands, Germany, and measured the mass and cover of tree litter and the cover and composition of vegetation at five sequential positions along each transect by using 1 m 2 plots with five replications. In a field experiment, we established plots subjected to different litter amounts (0, 200 and 600g m –2 ) and evaluated changes in grassland vegetation, soil temperature and soil nutrient availability below the litter layer. Important Findings Tree litter amounts decrease from 650 to 65g m –2 across the forest–grassland ecotone. Vegetation changed from shrubs and annual species (adapted to more stressful conditions) in the forests edge to grasses, rosettes and hemirosette species (with higher competitive abilities) in the grassland. These anthropogenic forest–grassland ecotones showed abrupt edges, and the two adjacent ecosystems were characterized by different species pools and functional groups. In the field experiment, the presence of a litter layer reduced vegetation biomass and cover; the species richness was only reduced in the treatment with high litter (600g m –2 ). Additionally, adding litter on top of vegetation also reduced thermal amplitude and the number of frost days, while increasing the availability of some nutrients, such as nitrogen and aluminium, the latter being an indicator of soil acidification. Adding a tree litter layer of 600g m –2 in grassland areas had strong effects on the composition and diversity of grassland vegetation by reducing the cover of several key grassland species. In, or near, forest edges, litter accumulation rapidly changes established vegetation, microsite conditions and soil nutrients.