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bioRxiv2018

The Italian Autism Network (ITAN): A Resource for Molecular Genetics and Biomarker Investigations

BackgroundA substantial genetic component accounts for Autism Spectrum Disorders (ASD) aetiology, with some rare and common genetic risk factors recently identified. Large collections of DNAs from thoroughly characterized ASD families are an essential step to confirm genetic risk factors, identify new variants and investigate genotype-phenotype correlations. The Italian Autism Network aimed at constituting a clinical database and a biorepository of samples derived from ASD subjects and first-degree relatives extensively and consistently characterized by child psychiatry centers in Italy.\n\nMethodsThe study was approved by the ethical committee of the University of Verona, the coordinating site, and by the local ethical committees of each recruiting site. Certified staff was specifically trained at each site for the overall study conduct, for clinical protocol administration and handling of biological material. A centralized database was developed to collect clinical assessment and medical records from each recruiting site. Children were eligible for recruitment based on the following inclusion criteria: age 4-18 years, at least one parent or legal guardian giving voluntary written consent, meeting DSM-IV criteria for Autistic Disorder or Aspergers Disorder or Pervasive Developmental Disorder NOS. Affected individuals were assessed by full psychiatric, neurological and physical examination, evaluation with ADI-R and ADOS scales, cognitive assessment with Wechsler Intelligence Scale for Children or Preschool and Primary, Leiter International Performance Scale or Griffiths Mental Developmental Scale. Additional evaluations included language assessment, the Krug Aspergers Disorder Index, and instrumental examination such as EEG and structural MRI. DNA, RNA and plasma were collected from eligible individuals and relatives. A central laboratory was established to host the biorepository, perform DNA and RNA extraction and lymphocytes immortalisation.\n\nDiscussionThe study has led to an extensive collection of biological samples associated with standardised clinical assessments from a network of expert clinicians and psychologists. Eighteen sites have received ADI/ADOS training, thirteen of which have been actively recruiting. The clinical database currently includes information on 812 individuals from 249 families, and the biorepository has samples for 98% of the subjects. This effort has generated a highly valuable resource for conducting clinical and genetic research of ASD, amenable to further expansion.

neuroscience↗

bioRxiv2018

Optimizing the identification of causal variants across varying genetic architectures in crops

BackgroundAssociation studies use statistical links between genetic markers and variation in a phenotypes value across many individuals to identify genes controlling variation in the target phenotype. However, this approach, particularly conducted on a genome-wide scale (GWAS), has limited power to identify the genes responsible for variation in traits controlled by complex genetic architectures.\n\nResultsHere we employ simulation studies utilizing real-world genotype datasets from association populations in four species with distinct minor allele frequency distributions, population structures, and patterns linkage disequilibrium to evaluate the impact of variation in both heritability and trait complexity on both conventional mixed linear model based GWAS and two new approaches specifically developed for complex traits. Mixed linear model based GWAS rapidly losses power for more complex traits. FarmCPU, a method based on multi-locus mixed linear models, provides the greatest statistical power for moderately complex traits. A Bayesian approach adopted from genomic prediction provides the greatest statistical power to identify causal genetic loci for extremely complex traits.\n\nConclusionsUsing estimates of the complexity of the genetic architecture of target traits can guide the selection of appropriate statistical methods and improve the overall accuracy and power of GWAS.

genomics↗

bioRxiv2018

crisprQTL mapping as a genome-wide association framework for cellular genetic screens

Expression quantitative trait locus (eQTL) and genome-wide association studies (GWAS) are powerful paradigms for mapping the determinants of gene expression and organismal phenotypes, respectively. However, eQTL mapping and GWAS are limited in scope (to naturally occurring, common genetic variants) and resolution (by linkage disequilibrium). Here, we present crisprQTL mapping, a framework in which large numbers of CRISPR/Cas9 perturbations are introduced to each cell on an isogenic background, followed by single-cell RNA-seq (scRNA-seq). crisprQTL mapping is analogous to conventional human eQTL studies, but with individual humans replaced by individual cells; genetic variants replaced by unique combinations of unlinked guide RNA (gRNA)-programmed perturbations per cell; and tissue-level RNA-seq of many individuals replaced by scRNA-seq of many cells. By randomly introducing gRNAs, a single population of cells can be leveraged to test for association between each perturbation and the expression of any potential target gene, analogous to how eQTL studies leverage populations of humans to test millions of genetic variants for associations with expression in a genome-wide manner. However, crisprQTL mapping is neither limited to naturally occurring, common genetic variants nor by linkage disequilibrium. As a proof-of-concept, we applied crisprQTL mapping to evaluate 1,119 candidate enhancers with no strong a priori hypothesis as to their target gene(s). Perturbations were made by a nuclease-dead Cas9 (dCas9) tethered to KRAB, and introduced at a mean allele frequency of 1.1% into a population of 47,650 profiled human K562 cells (median of 15 gRNAs identified per cell). We tested for differential expression of all genes within 1 megabase (Mb) of each candidate enhancer, effectively evaluating 17,584 potential enhancer-target gene relationships within a single experiment. At an empirical false discovery rate (FDR) of 10%, we identify 128 cis crisprQTLs (11%) whose targeting resulted in downregulation of 105 nearby genes. crisprQTLs were strongly enriched for proximity to their target genes (median 34.3 kilobases (Kb)) and the strength of H3K27ac, p300, and lineage-specific transcription factor (TF) ChIP-seq peaks. Our results establish the power of the eQTL mapping paradigm as applied to programmed variation in populations of cells, rather than natural variation in populations of individuals. We anticipate that crisprQTL mapping will facilitate the comprehensive elucidation of the cis-regulatory architecture of the human genome.

genomics↗

bioRxiv2018

Rapid sex-specific evolution of age at maturity is shaped by genetic architecture in Atlantic salmon

Understanding the mechanisms by which populations adapt to their environments is a fundamental aim in biology. However, it remains challenging to identify the genetic basis of traits, provide evidence of genetic changes and quantify phenotypic responses. Age at maturity in Atlantic salmon represents an ideal trait to study contemporary adaptive evolution as it has been associated with a single locus in the vgll3 region, and has also strongly changed in recent decades. Here, we provide an empirical example of contemporary adaptive evolution of a large effect locus driving contrasting sex-specific evolutionary responses at the phenotypic level. We identified an 18% decrease in the vgll3 allele associated with late maturity (L) in a large and diverse salmon population over 36 years, induced by sex-specific selection during the sea migration. Those genetic changes resulted in a significant evolutionary response in males only, due to sex-specific dominance patterns and vgll3 allelic effects. The vgll3 allelic and dominance effects differed greatly in a second population and were likely to generate different selection and evolutionary patterns. Our study highlights the importance of knowledge of genetic architecture to better understand fitness trait evolution and phenotypic diversity. It also emphasizes the potential role of adaptive evolution in the trend toward earlier maturation observed in numerous Atlantic salmon populations worldwide.

evolutionary biology↗

bioRxiv2018

The genetic architecture of target-site resistance to pyrethroid insecticides in the African malaria vectors Anopheles gambiae and Anopheles coluzzii

Resistance to pyrethroid insecticides is a major concern for malaria vector control, because these are the compounds used in almost all insecticide-treated bed-nets (ITNs), and are also widely used for indoor residual spraying (IRS). Pyrethroids target the voltage-gated sodium channel (VGSC), an essential component of the mosquito nervous system, but substitutions in the amino acid sequence can disrupt the activity of these insecticides, inducing a resistance phenotype. Here we use Illumina whole-genome sequence data from phase 1 of the Anopheles gambiae 1000 Genomes Project (Ag1000G) to provide a comprehensive account of genetic variation in the Vgsc gene in mosquito populations from eight African countries. In addition to the three known resistance alleles, we describe 20 non-synonymous nucleotide substitutions at appreciable frequency in one or more populations that are previously unknown in Anopheles mosquitoes. Thirteen of these novel alleles were found to occur almost exclusively on haplotypes carrying the known L995F resistance allele (L1014F in Musca domesticus codon numbering), and may enhance or compensate for the L995F resistance pheno-type. A novel mutation I1527T, which is adjacent to a predicted pyrethroid binding site, was found in tight linkage with either of two alleles causing a V402L substitution, similar to a combination of substitutions found to cause pyrethroid resistance in several other insect species. We analyse the genetic backgrounds on which non-synonymous alleles are found, to determine which alleles have experienced recent positive selection, and to refine our understanding of the spread of resistance between species and geographical locations. We describe twelve distinct haplotype groups with evidence of recent positive selection, five of which carry the known L995F resistance allele, five of which carry the known L995S resistance allele, one of which carries the novel I1527T allele, and one of which carries a novel M490I allele. Seven of these groups are localised to a single geographical location, and five comprise haplotypes from different countries, in one case separated by over 3000 km, providing new information about the geographical distribution and spread of resistance. We also find evidence for multiple introgression events transmitting resistance alleles between An. gambiae and An. coluzzii. We identify markers that could be used to design high-throughput, low-cost genetic assays for improved surveillance of pyrethroid resistance in the field. Our results demonstrate that the molecular basis of target-site pyrethroid resistance in malaria vectors is more complex than previously appreciated, and provide a foundation for the development of new genetic tools to track the spread insecticide resistance and improve the design of strategies for insecticide resistance management.

genomics↗

bioRxiv2018

A robust ex vivo experimental platform for molecular-genetic dissection of adult human neocortical cell types and circuits

The powerful suite of available genetic tools is driving tremendous progress in understanding mouse brain cell types and circuits. However, the degree of conservation in human remains largely unknown in large part due to the lack of such tools and healthy tissue preparations. To close this gap, we describe a robust and stable adult human neurosurgically-derived ex vivo acute and cultured neocortical brain slice system optimized for rapid molecular-genetic manipulation. Surprisingly, acute human brain slices exhibited exceptional viability, and neuronal intrinsic membrane properties could be assayed for at least three days. Maintaining adult human slices in culture under sterile conditions further enabled the application of viral tools to drive rapid expression of exogenous transgenes. Widespread neuron-specific labeling was achieved as early as two days post infection with HSV-1 vectors, with virally-transduced neurons exhibiting membrane properties largely comparable to uninfected neurons over this short timeframe. Finally, we demonstrate the suitability of this culture paradigm for optical manipulation and monitoring of neuronal activity using genetically encoded probes, opening a path for applying modern molecular-genetic tools to study human brain circuit function.

neuroscience↗

bioRxiv2018

PCSK9 genetic variants, life-long lowering of LDL-cholesterol and cognition: a large-scale Mendelian randomization study

AimsPCSK9 inhibitors lower LDL cholesterol and are efficacious at reducing risk of vascular disease, however questions remain about potential adverse effects on cognitive function. We examined the association of LDL cholesterol-lowering genetic variants in PCSK9 with continuous measures of cognitive ability\n\nMethods and ResultsSix independent SNPs in PCSK9 were used in up to 337,348 individuals from the UK Biobank who underwent measures of cognitive ability (fluid reasoning, reaction time, trial making test and digit symbol coding. Scaled to a 50mg/dL lower LDL cholesterol, the PCSK9 allele score was associated with a lower risk of CHD (odds ratio 0.73; 95% CI: 0.60 to 0.90, P = 0.003). The scaled PCSK9 allele score nominally associated with worse log reaction time (0.04 standard deviations; 95%CI: 0.00, 0.08; P=0.038). Although no strong associations of the PCSK9 allele score were identified with any cognitive trait, the imprecision around the estimates meant that we could not exclude a similar magnitude of effect of genetic inhibition of PCSK9 to that seen with established risk factors, including APOEe4 or smoking status for any of the individual cognition traits. Point estimates for the PCSK9 allele score and cognition traits were all on the harmful side of unity.\n\nConclusionsUsing currently available data in UK Biobank, we are not able to rule out meaningful associations of PCSK9 genetic variants with cognition traits. These data highlight the need for further large-scale genetic analyses and, in parallel, continued pharmacovigilance for patients currently treated with PCSK9 inhibitors.

epidemiology↗

bioRxiv2018

Developing a network view of type 2 diabetes risk pathways through integration of genetic, genomic and functional data

Genome wide association studies (GWAS) have identified several hundred susceptibility loci for Type 2 Diabetes (T2D). One critical, but unresolved, issue concerns the extent to which the mechanisms through which these diverse signals influencing T2D predisposition converge on a limited set of biological processes. However, the causal variants identified by GWAS mostly fall into non-coding sequence, complicating the task of defining the effector transcripts through which they operate. Here, we describe implementation of an analytical pipeline to address this question. First, we integrate multiple sources of genetic, genomic, and biological data to assign positional candidacy scores to the genes that map to T2D GWAS signals. Second, we introduce genes with high scores as seeds within a network optimization algorithm (the asymmetric prize-collecting Steiner Tree approach) which uses external, experimentally-confirmed protein-protein interaction (PPI) data to generate high confidence subnetworks. Third, we use GWAS data to test the T2D-association enrichment of the \"non-seed\" proteins introduced into the network, as a measure of the overall functional connectivity of the network. We find: (a) non-seed proteins in the T2D protein-interaction network so generated (comprising 705 nodes) are enriched for association to T2D (p=0.0014) but not control traits; (b) stronger T2D-enrichment for islets than other tissues when we use RNA expression data to generate tissue-specific PPI networks; and (c) enhanced enrichment (p=3.9xl0-5) when we combine analysis of the islet-specific PPI network with a focus on the subset of T2D GWAS loci which act through defective insulin secretion. These analyses reveal a pattern of non-random functional connectivity between causal candidate genes atT2D GWAS loci, and highlight the products of genes including YWHAG, SMAD4 or CDK2 as contributors to T2D-relevant islet dysfunction. The approach we describe can be applied to other complex genetic and genomic data sets, facilitating integration of diverse data types into disease-associated networks.\n\nAuthor summaryWe were interested in the following question: as we discover more and more genetic variants associated with a complex disease, such as type 2 diabetes, will the biological pathways implicated by those variants proliferate, or will the biology converge onto a more limited set of aetiological processes? To address this, we first took the 1895 genes that map to ~100 type 2 diabetes association signals, and pruned these to a set of 451 for which combined genetic, genomic and biological evidence assigned the strongest candidacy with respect to type 2 diabetes pathogenesis. We then sought to maximally connect these genes within a curated protein-protein interaction network. We found that proteins brought into the resulting diabetes interaction network were themselves enriched for diabetes association signals as compared to appropriate control proteins. Furthermore, when we used tissue-specific RNA abundance data to filter the generic protein-protein network, we found that the enrichment for type 2 diabetes association signals was enhanced within a network filtered for pancreatic islet expression, particularly when we selected the subset of diabetes association signals acting through reduced insulin secretion. Our data demonstrate convergence of the biological processes involved in type 2 diabetes pathogenesis and highlight novel contributors.

bioinformatics↗

bioRxiv2018

Integration of phased Hi-C and molecular phenotype data to study genetic and epigenetic effects on chromatin looping

While genetic variation at chromatin loops is relevant for human disease, the relationships between loop strength, genetics, gene expression, and epigenetics are unclear. Here, we quantitatively interrogate this relationship using Hi-C and molecular phenotype data across cell types and haplotypes. We find that chromatin loops consistently form across multiple cell types and quantitatively vary in strength, instead of exclusively forming within only one cell type. We show that large haplotype loop imbalance is primarily associated with imprinting and copy number variation, rather than genetically driven traits such as allele-specific expression. Finally, across cell types and haplotypes, we show that subtle changes in chromatin loop strength are associated with large differences in other molecular phenotypes, with a 2-fold change in looping corresponding to a 100-fold change in gene expression. Our study suggests that regulatory genetic variation could mediate its effects on gene expression through subtle modification of chromatin loop strength.

genomics↗

bioRxiv2018

Genetic mapping with allele dosage information in tetraploid Urochloa decumbens (Stapf) R.D. Webster reveals insights into spittlebug (Notozulia entreriana Berg) resistance

Urochloa decumbens (Stapf) R.D. Webster is one of the most important African forage grasses in Brazilian beef production. Currently available genetic-genomic resources for this species are restricted mainly due to polyploidy and apomixis. Therefore, crucial genomic-molecular studies such as the construction of genetic maps and the mapping of quantitative trait loci (QTLs) are very challenging and consequently affect the advancement of molecular breeding. The objectives of this work were to (i) construct an integrated U. decumbens genetic map for a full-sibling progeny using GBS-based markers with allele dosage information, (ii) detect QTLs for spittlebug (Notozulia entreriana) resistance, and (iii) seek putative candidate genes involved in resistance/defense against pathogens. We used the Setaria viridis genome as reference to align GBS reads and selected 4,240 high-quality SNPs markers with allele dosage information. Of these markers, 1,000 were distributed throughout nine homologous groups with a cumulative map length of 1,335.09 cM and an average marker density of 1.33 cM. We detected QTLs for resistance to spittlebug, an important pasture insect pest, that explained between 4.66% and 6.24% of the phenotypic variation. These QTLs are in regions containing putative candidate genes related to resistance/defense against pathogens. Because this is the first genetic map with SNP autotetraploid dosage data and QTL detection in U. decumbens, it will be useful for future evolutionary studies, genome assembly, and other QTL analyses in Urochloa spp. Moreover, the results might facilitate the isolation of spittlebug-related candidate genes and help clarify the mechanism of spittlebug resistance. These approaches will improve selection efficiency and accuracy in U. decumbens molecular breeding and shorten the breeding cycle.

plant biology↗

bioRxiv2018

Heliaphen, an outdoor high-throughput phenotyping platform designed to integrate genetics and crop modeling

Heliaphen is an outdoor pot platform designed for high-throughput phenotyping. It allows automated management of drought scenarios and plant monitoring during the whole plant cycle. A robot moving between plants growing in 15L pots monitors plant water status and phenotypes plant or leaf morphology, from which we can compute more complex traits such as the response of leaf expansion (LE) or plant transpiration (TR) to water deficit. Here, we illustrate the platform capabilities for sunflower on two practical cases: a genetic and genomics study for the response to drought of yield-related traits and a simulation study, where we use measured parameters as inputs for a crop simulation model. For the genetic study, classical measurements of thousand-kernel weight (TKW) were done on a sunflower bi-parental population under water stress and control conditions managed automatically. The association study using the TKW drought-response highlighted five genetic markers. A complementary transcriptomic experiment identified closeby candidate genes differentially expressed in the parental backgrounds in drought conditions. For the simulation study, we used the SUNFLO crop simulation model to assess the impact of two traits measured on the platform (LE and TR) on crop yield in a large population of environments. We conducted simulations in 42 contrasted locations across Europe and 21 years of climate data. We defined the pattern of abiotic stresses occurring at this continental scale and identified ideotypes (i.e. genotypes with specific traits values) that are more adapted to specific environment types. This study exemplifies how phenotyping platforms can help with the identification of the genetic architecture of complex response traits and the estimation of eco-physiological model parameters in order to define ideotypes adapted to different environmental conditions.

plant biology↗

bioRxiv2018

Learning from Longitudinal Data in Electronic Health Record and Genetic Data to Improve Cardiovascular Event Prediction

BackgroundCurrent approaches to predicting Cardiovascular disease rely on conventional risk factors and cross-sectional data. In this study, we asked whether: i) machine learning and deep learning models with longitudinal EHR information can improve the prediction of 10-year CVD risk, and ii) incorporating genetic data can add values to predictability.\n\nMethodsWe conducted two experiments. In the first experiment, we modeled longitudinal EHR data with aggregated features and temporal features. We applied logistic regression (LR), random forests (RF) and gradient boosting trees (GBT) and Convolutional Neural Networks (CNN) and Recurrent Neural Networks, using Long Short-Term Memory (LSTM) units. In the second experiment, we proposed a late-fusion framework to incorporate genetic features.\n\nResultsOur study cohort included 109, 490 individuals (9,824 were cases and 99, 666 were controls) from Vanderbilt University Medical Centers (VUMC) de-identified EHRs. American College of Cardiology and the American Heart Association (ACC/AHA) Pooled Cohort Risk Equations had areas under receiver operating characteristic curves (AUROC) of 0.732 and areas under receiver under precision and recall curves (AUPRC) of 0.187. LSTM, CNN and GBT with temporal features achieved best results, which had AUROC of 0.789, 0.790, and 0.791, and AUPRC of 0.282, 0.280 and 0.285, respectively. The late fusion approach achieved a significant improvement for the prediction performance.\n\nConclusionsMachine learning and deep learning with longitudinal features improved the 10-year CVD risk prediction. Incorporating genetic features further enhanced 10-year CVD prediction performance, underscoring the importance of integrating relevant genetic data whenever available in the context of routine care.

epidemiology↗

bioRxiv2018

Varicose veins of lower extremities: insights from the first large-scale genetic study

Varicose veins of lower extremities (VVs) are a common multifactorial vascular disease. Genetic factors underlying VVs development remain largely unknown. Here we report the first large-scale study of VVs performed on a freely available genetic data of 408,455 European-ancestry individuals. We identified 7 reliably associated loci that explain 10% of the SNP-based heritability, and prioritized the most likely causal genes CASZ1, PPP3R1, EBF1, STIM2, and HFE. Genetic correlation analysis confirmed known epidemiological associations and found genetic overlap with various traits including fluid intelligence score, educational attainment, smoking, and pain. Finally, we observed causal effects of height, weight, both fat and fat-free mass, and plasma levels of MICB and CD209 proteins.

genomics↗

bioRxiv2018

The genetic prehistory of the Andean highlands 7,000 Years BP though European contact

The peopling of the Andean highlands above 2500m in elevation was a complex process that included cultural, biological and genetic adaptations. Here we present a time series of ancient whole genomes from the Andes of Peru, dating back to 7,000 calendar years before present (BP), and compare them to 64 new genome-wide genetic variation datasets from both high and lowland populations. We infer three significant features: a split between low and high elevation populations that occurred between 9200-8200 BP; a population collapse after European contact that is significantly more severe in South American lowlanders than in highland populations; and evidence for positive selection at genetic loci related to starch digestion and plausibly pathogen resistance after European contact. Importantly, we do not find selective sweep signals related to known components of the human hypoxia response, which may suggest more complex modes of genetic adaptation to high altitude.\n\nOne Sentence SummaryAncient DNA from the Andes reveals a complex picture of human adaptation from early settlement to the colonial period.

genomics↗

bioRxiv2018

Disentangling the contribution of childhood and adulthood circumstances and genetics to phenotypic aging: prospective cohort study

ObjectivesTo evaluate the extent to which childhood and adulthood circumstances and genetics contribute to phenotypic aging, using a multi-system-based signature of aging that has been shown to capture mortality and morbidity risk.\n\nDesignProspective population-based cohort study.\n\nSettingUnited States (U.S.).\n\nParticipants2,339 adults (aged 51+ years) from U.S. Health and Retirement Study, who participated in the Core Survey, the 2016 Venous Blood Study, the 2015 Life History Mail Survey, the Enhanced Face-To-Face interview (2006-2016), and were part of the genetic sample.\n\nMain outcomes measurePhenotypic Age, a validated aging measure based on a linear combination of chronological age and nine multi-system biomarkers. For most analyses, we examined \"PhenoAgeAccel\", which represents phenotypic aging after accounting for chronological age (i.e. whether a person appears older [positive value] or younger [negative value] than expected, physiologically).\n\nResultsThe Shapley Value Decomposition approach revealed that together all 11 domains (four childhood and adulthood circumstances domains, five polygenic scores [PGSs] domains, demographics, and behaviors domains) accounted for about 30% of variance in PhenoAgeAccel. Among the four circumstances domains, adulthood adversity was the largest contributor (9%), while adulthood socioeconomic status (SES), childhood adversity, and childhood SES accounted for 2.8%, 2.1%, 0.7%, respectively. Collectively, all PGSs contributed 3.8% of variance in PhenoAgeAccel. Further, six subpopulations/clusters--identified using a hierarchical cluster analysis based on childhood and adulthood SES and adversity--showed differences in average levels of phenotypic aging. Finally, there was a significant gene-by-environment interaction between a previously validated PGS for coronary artery disease and the most apparently disadvantaged subpopulation/cluster--suggesting a multiplicative effect of adverse environment coupled with genetic risk on phenotypic aging.\n\nConclusionsSocioenvironmental circumstances during both childhood and adulthood account for a sizable proportion of the difference in phenotypic aging among U.S. older adults. The detrimental effects may further be exacerbated among persons with a genetic predisposition to coronary artery disease.

epidemiology↗

bioRxiv2018

The comparative and genetic methods for East European Unionidae taxonomy

Taxonomy of freshwater mussels from family Unionidae has been ambiguous for a long time. A number of methods used for their identification, including the so-called comparative method, are based on shell morphology. However, this morphology turned out to have a high level of within-species variation, and the shape of the shell of a specimen depends strongly on its environment and conditions of growth. For these reasons, the number of species recognized by the comparative method kept increasing. We applied both the comparative morphological method and methods of molecular genetics to address the taxonomy of Unionidae. We performed the comprehensive study of 70 specimens of Unionidae mussels collected from the River Ivitza, Volga basin. The specimens represented 14 comparative species, belonging to 4 comparative genera of Unionidae: Colletopterum, Pseudanodonta, Unio and Crassiana. Sequencing of the nuclear (ITS1) and mitochondrial (COI, 16S rDNA) genetic regions revealed 5 groups with high within-group genetic homogeneity separated from each other by long genetic distances. According to the comparison with the available sequences, these groups correspond to 3 Eastern European genera and 5 species: Anodonta anatina, Pseudanodonta complanata, Unio pictorum, Unio tumidus and Unio crassus. The results obtained indicate that the comparative method is inappropriate for the taxonomic analysis of East European Unionidae.

zoology↗

bioRxiv2018

Dual RNA-seq reveals large-scale non-conserved genotype x genotype specific genetic reprograming and molecular crosstalk in the mycorrhizal symbiosis

Arbuscular mycorrhizal fungi (AMF) impact plant growth and are a major driver of plant diversity and productivity. We quantified the contribution of intra-specific genetic variability in cassava (Manihot esculenta) and Rhizophagus irregularis to gene reprogramming in symbioses using dual RNA-sequencing. A large number of cassava genes exhibited altered transcriptional responses to the fungus but transcription of most of these plant genes (72%) responded in a different direction or magnitude depending on the plant genotype. Two AMF isolates displayed large differences in their transcription, but the direction and magnitude of the transcriptional responses for a large number of these genes was also strongly influenced by the genotype of the plant host. This indicates that unlike the highly conserved plant genes necessary for the symbiosis establishment, plant and fungal gene transcriptional responses are not conserved and are greatly influenced by plant and fungal genetic differences, even at the within-species level. The transcriptional variability detected allowed us to identify an extensive gene network showing the interplay in plant-fungal reprogramming in the symbiosis. Key genes illustrated that the two organisms jointly program their cytoskeleton organisation during growth of the fungus inside roots. Our study reveals that plant and fungal genetic variation plays a strong role in shaping the genetic reprograming in response to symbiosis, indicating considerable genotype x genotype interactions in the mycorrhizal symbiosis. Such variation needs to be considered in order to understand the molecular mechanisms between AMF and their plant hosts in natural communities.

plant biology↗

bioRxiv2018

Psidium guajava in the Galapagos Islands: population genetics and history of an invasive species

The threat of invasive plant species in island populations prompts the need to better understand their population genetics and dynamics. In the Galapagos islands, this is exemplified by the introduced guava (Psidium guajava), considered one of the greatest threats to the local biodiversity due to its effective spread in the archipelago and its ability to outcompete endemic species. To better understand its history and genetics, we analyzed individuals from three inhabited islands in the Galapagos archipelago with 11 SSR markers. Our results reveal similar genetic diversity between islands, suggestive of gene flow between them. Populations appear to be distinct between the islands of San Cristobal and Isabela, with the population of Santa Cruz being composed as a mixture from both. Additional evidence for genetic bottlenecks and the inference of introduction events suggests an original introduction of the species in San Cristobal, from where it was later introduced to Isabela, and finally into Santa Cruz. Alternatively, an independent introduction event for Isabela is also possible. These results are contrasted with the historical record, providing a first overview of the history of P. guajava in the Galapagos islands and its current population dynamics.

evolutionary biology↗