Anna Vlasova

Molecular signatures of plastic phenotypes in two eusocial insect species with simple societies

Significance In eusocial insect societies, such as ants and some bees and wasps, phenotypes are highly plastic, generating alternative phenotypes (queens and workers) from the same genome. The greatest plasticity is found in simple insect societies, in which individuals can switch between phenotypes as adults. The genomic, transcriptional, and epigenetic underpinnings of such plasticity are largely unknown. In contrast to the complex societies of the honeybee, we find that simple insect societies lack distinct transcriptional differentiation between phenotypes and coherently patterned DNA methylomes. Instead, alternative phenotypes are largely defined by subtle transcriptional network organization. These traits may facilitate genomic plasticity. These insights and resources will stimulate new approaches and hypotheses that will help to unravel the genomic processes that create phenotypic plasticity. Phenotypic plasticity is important in adaptation and shapes the evolution of organisms. However, we understand little about what aspects of the genome are important in facilitating plasticity. Eusocial insect societies produce plastic phenotypes from the same genome, as reproductives (queens) and nonreproductives (workers). The greatest plasticity is found in the simple eusocial insect societies in which individuals retain the ability to switch between reproductive and nonreproductive phenotypes as adults. We lack comprehensive data on the molecular basis of plastic phenotypes. Here, we sequenced genomes, microRNAs (miRNAs), and multiple transcriptomes and methylomes from individual brains in a wasp (Polistes canadensis) and an ant (Dinoponera quadriceps) that live in simple eusocial societies. In both species, we found few differences between phenotypes at the transcriptional level, with little functional specialization, and no evidence that phenotype-specific gene expression is driven by DNA methylation or miRNAs. Instead, phenotypic differentiation was defined more subtly by nonrandom transcriptional network organization, with roles in these networks for both conserved and taxon-restricted genes. The general lack of highly methylated regions or methylome patterning in both species may be an important mechanism for achieving plasticity among phenotypes during adulthood. These findings define previously unidentified hypotheses on the genomic processes that facilitate plasticity and suggest that the molecular hallmarks of social behavior are likely to differ with the level of social complexity.

PRGdb 2.0: towards a community-based database model for the analysis of R-genes in plants

The Plant Resistance Genes database (PRGdb; http://prgdb.org) is a comprehensive resource on resistance genes (R-genes), a major class of genes in plant genomes that convey disease resistance against pathogens. Initiated in 2009, the database has grown more than 6-fold to recently include annotation derived from recent plant genome sequencing projects. Release 2.0 currently hosts useful biological information on a set of 112 known and 104 310 putative R-genes present in 233 plant species and conferring resistance to 122 different pathogens. Moreover, the website has been completely redesigned with the implementation of Semantic MediaWiki technologies, which makes our repository freely accessed and easily edited by any scientists. To this purpose, we encourage plant biologist experts to join our annotation effort and share their knowledge on resistance-gene biology with the rest of the scientific community.

Genome and transcriptome analysis of the Mesoamerican common bean and the role of gene duplications in establishing tissue and temporal specialization of genes

BackgroundLegumes are the third largest family of angiosperms and the second most important crop class. Legume genomes have been shaped by extensive large-scale gene duplications, including an approximately 58 million year old whole genome duplication shared by most crop legumes.ResultsWe report the genome and the transcription atlas of coding and non-coding genes of a Mesoamerican genotype of common bean (Phaseolus vulgaris L., BAT93). Using a comprehensive phylogenomics analysis, we assessed the past and recent evolution of common bean, and traced the diversification of patterns of gene expression following duplication. We find that successive rounds of gene duplications in legumes have shaped tissue and developmental expression, leading to increased levels of specialization in larger gene families. We also find that many long non-coding RNAs are preferentially expressed in germ-line-related tissues (pods and seeds), suggesting that they play a significant role in fruit development. Our results also suggest that most bean-specific gene family expansions, including resistance gene clusters, predate the split of the Mesoamerican and Andean gene pools.ConclusionsThe genome and transcriptome data herein generated for a Mesoamerican genotype represent a counterpart to the genomic resources already available for the Andean gene pool. Altogether, this information will allow the genetic dissection of the characters involved in the domestication and adaptation of the crop, and their further implementation in breeding strategies for this important crop.

Whole Genome Sequencing of Turbot (Scophthalmus maximus; Pleuronectiformes): A Fish Adapted to Demersal Life

The turbot is a flatfish (Pleuronectiformes) with increasing commercial value, which has prompted active genomic research aimed at more efficient selection. Here we present the sequence and annotation of the turbot genome, which represents a milestone for both boosting breeding programmes and ascertaining the origin and diversification of flatfish. We compare the turbot genome with model fish genomes to investigate teleost chromosome evolution. We observe a conserved macrosyntenic pattern within Percomorpha and identify large syntenic blocks within the turbot genome related to the teleost genome duplication. We identify gene family expansions and positive selection of genes associated with vision and metabolism of membrane lipids, which suggests adaptation to demersal lifestyle and to cold temperatures, respectively. Our data indicate a quick evolution and diversification of flatfish to adapt to benthic life and provide clues for understanding their controversial origin. Moreover, we investigate the genomic architecture of growth, sex determination and disease resistance, key traits for understanding local adaptation and boosting turbot production, by mapping candidate genes and previously reported quantitative trait loci. The genomic architecture of these productive traits has allowed the identification of candidate genes and enriched pathways that may represent useful information for future marker-assisted selection in turbot.

Extreme genomic erosion after recurrent demographic bottlenecks in the highly endangered Iberian lynx

BackgroundGenomic studies of endangered species provide insights into their evolution and demographic history, reveal patterns of genomic erosion that might limit their viability, and offer tools for their effective conservation. The Iberian lynx (Lynx pardinus) is the most endangered felid and a unique example of a species on the brink of extinction.ResultsWe generate the first annotated draft of the Iberian lynx genome and carry out genome-based analyses of lynx demography, evolution, and population genetics. We identify a series of severe population bottlenecks in the history of the Iberian lynx that predate its known demographic decline during the 20th century and have greatly impacted its genome evolution. We observe drastically reduced rates of weak-to-strong substitutions associated with GC-biased gene conversion and increased rates of fixation of transposable elements. We also find multiple signatures of genetic erosion in the two remnant Iberian lynx populations, including a high frequency of potentially deleterious variants and substitutions, as well as the lowest genome-wide genetic diversity reported so far in any species.ConclusionsThe genomic features observed in the Iberian lynx genome may hamper short- and long-term viability through reduced fitness and adaptive potential. The knowledge and resources developed in this study will boost the research on felid evolution and conservation genomics and will benefit the ongoing conservation and management of this emblematic species.

Genomic history of the origin and domestication of common bean unveils its closest sister species

BackgroundModern civilization depends on only a few plant species for its nourishment. These crops were derived via several thousands of years of human selection that transformed wild ancestors into high-yielding domesticated descendants. Among cultivated plants, common bean (Phaseolus vulgaris L.) is the most important grain legume. Yet, our understanding of the origins and concurrent shaping of the genome of this crop plant is limited.ResultsWe sequenced the genomes of 29 accessions representing 12 Phaseolus species. Single nucleotide polymorphism-based phylogenomic analyses, using both the nuclear and chloroplast genomes, allowed us to detect a speciation event, a finding further supported by metabolite profiling. In addition, we identified ~1200 protein coding genes (PCGs) and ~100 long non-coding RNAs with domestication-associated haplotypes. Finally, we describe asymmetric introgression events occurring among common bean subpopulations in Mesoamerica and across hemispheres.ConclusionsWe uncover an unpredicted speciation event in the tropical Andes that gave rise to a sibling species, formerly considered the “wild ancestor” of P. vulgaris, which diverged before the split of the Mesoamerican and Andean P. vulgaris gene pools. Further, we identify haplotypes strongly associated with genes underlying the emergence of domestication traits. Our findings also reveal the capacity of a predominantly autogamous plant to outcross and fix loci from different populations, even from distant species, which led to the acquisition by domesticated beans of adaptive traits from wild relatives. The occurrence of such adaptive introgressions should be exploited to accelerate breeding programs in the near future.

Brain Transcriptome Sequencing of a Natural Model of Alzheimer's Disease

Alzheimers disease (AD) is a slowly progressive disease characterized by impairment of memory and eventually by disturbances in reasoning, planning, language, and perception. Ageing is the greatest risk factor for its development but mutations in amyloid precursor protein (APP), apolipoprotein E (APOE), microtubule-associated protein tau (MAPT) among others, are also a major factor (Blasko et al., 2004). The symptoms of AD result from neurofibrillary tangles that are composed of aggregates of hyper-phosphorylated tau protein and an increase in the production of amyloid-beta (Aβ) protein in the brain that leads to deposits of senile plaques. As such, there is a worldwide effort to find an effective disease-modifying treatment that can reverse symptoms and/or delay onset of the disease. Transgenic mouse models exist that mimic a range of AD–related pathologies, although none of the models fully replicate all pathological features of the human disease (Birch et al., 2014). Drugs developed using these mouse models have failed in phase III clinical trials (Mangialasche et al., 2010; Braidy et al., 2012; Saraceno et al., 2013). These failures question not only our accurate understanding of the disease (Castellani and Perry, 2012) but also the validity of the animal models upon which the drug discovery efforts are rooted (Windisch, 2014; Nazem et al., 2015). Animal models have contributed significantly to our understanding of the underlying mechanisms of AD. To date, however, these findings have not resulted in target validation in humans and successful translation to disease-modifying therapies. The Octodon degus (O. degus) is a model that naturally integrates multiple AD pathological hallmarks like tau fibrilary tangles and β-amyloid deposits (Inestrosa et al., 2005, 2015; Deacon et al., 2015). The Aβ peptide sequence in O. degus is 97.5% homologous to the human Aβ peptide sequence (Inestrosa et al., 2005). The species presents acetylcholine (AChE)-rich pyramidal neurons in their forebrain, which decline in numbers during the progression to an AD-like behavioral state, similar to that seen in AD patients (Ardiles et al., 2012). Affected O. degus also present the characteristic medical signs and symptoms surrounding AD like macular degeneration, diabetes and circadian rhythm dysfunction (Laurijssens et al., 2013). Behavioral experiments have shown that the O. degus can also present behavioral deficits and neural alterations in the frontal cortex and aggression similar to those seen in patients with AD (Tarragon et al., 2013). Most importantly, the O. degus shows a correlation of expression with human AD- related genes making this model a powerful tool to characterize the effects of novel treatments for AD and identify new therapeutic targets. Our findings advance the use of the O. degus as an effective tool for AD research.

Ten steps to get started in Genome Assembly and Annotation

As a part of the ELIXIR-EXCELERATE efforts in capacity building, we present here 10 steps to facilitate researchers getting started in genome assembly and genome annotation. The guidelines given are broadly applicable, intended to be stable over time, and cover all aspects from start to finish of a general assembly and annotation project. Intrinsic properties of genomes are discussed, as is the importance of using high quality DNA. Different sequencing technologies and generally applicable workflows for genome assembly are also detailed. We cover structural and functional annotation and encourage readers to also annotate transposable elements, something that is often omitted from annotation workflows. The importance of data management is stressed, and we give advice on where to submit data and how to make your results Findable, Accessible, Interoperable, and Reusable (FAIR).

Expression of the transcribed ultraconserved region 70 and the related long non-coding RNA AC092652.2-202 has prognostic value in Chronic Lymphocytic Leukaemia

Sajida Kazi Fergus Mckiddie Julia Anderson Catherine Bagot Caroline Duncan Mark Drummond Ron Kerr Mohammed Khan Mark McColl Huw Roddie Nicole Priddee Roger Staff Ranjit Thomas Henry G. Watson Department of Haematology, Aberdeen Royal Infirmary, Department of Nuclear Medicine, Aberdeen Royal Infirmary, Aberdeen, Department of Haematology, Royal Infirmary Edinburgh, Edinburgh, Department of Haematology, Glasgow Royal Infirmary, Glasgow, Department of Haematology, Raigmore Hospital, Inverness, Department of Haematology, Beatson Cancer Centre, Glasgow, Department of Haematology, Ninewells Hospital, Dundee, Department of Haematology, University Hospital Crosshouse, Ayrshire, Department of Haematology, Western General Hospital, Edinburgh, and NHS Dumfries and Galloway, Dumfries, UK. E-mail: henrywatson@nhs.net

Phylogenomics: The Evolution of Common Bean as Seen from the Perspective of All of Its Genes

Phaseolus vulgaris is the most important legume species for human nourishment. However, until very recently genomics resources for this plant have been scarce, which preventing fully understanding the parallel domestications occurred at two geographical regions: Mesoamerica and Andes. The first reference genome for P. vulgaris, the Andean landrace G19833, was published in 2014, followed in 2016 by the Mesoamerican reference genome, the breeding line BAT93. These resources have allowed elucidating the evolutionary trajectory of P. vulgaris as species, and of both gene pools. First, it has been possible to confirm that the common bean has not undergone a specific whole genome duplication event similarly to the one of Glycine max around ~12 million years ago. Second, there is a high degree of concordance between both gene pools in terms of gene content and evolutionary profiles. This includes also the pattern of specialization of gene expression profiles across different relative evolutionary ages. We confirmed the trend observed for the Mesoamerican genome: retained duplicated genes tend to specialize their expression profiles overtime. New analyses using available transcriptomic data gene co-expression networks for both gene pools have been generated and compared for this review in order to look for commonalities and differences. Genes associated to photosynthesis and to response to different stresses account for the largest modules of these networks, although some differences were detected which may have roles in the domestication syndrome of both gene pools. However, more sequencing data are needed to a better understanding of common bean genome function and to deepen on the domestication processes of both gene pools. It is expected that third generation sequencing technologies will play an important role in those efforts, leading to better genome assemblies and gene-sets. This will focus further efforts on improving breeding lines while keeping genetic diversity of landraces and wild accessions of P. vulgaris.