The genomic basis of evolutionary differentiation among honey bees.

In contrast to the western honey bee, Apis mellifera, other honey bee species have been largely neglected despite their importance and diversity. The genetic basis of the evolutionary diversification of honey bees remains largely unknown. Here, we provide a genome-wide comparison of three honey bee species, each representing one of the three subgenera of honey bees, namely the dwarf (Apis florea), giant (A. dorsata), and cavity-nesting (A. mellifera) honey bees with bumblebees as an outgroup. Our analyses resolve the phylogeny of honey bees with the dwarf honey bees diverging first. We find that evolution of increased eusocial complexity in Apis proceeds via increases in the complexity of gene regulation, which is in agreement with previous studies. However, this process seems to be related to pathways other than transcriptional control. Positive selection patterns across Apis reveal a trade-off between maintaining genome stability and generating genetic diversity, with a rapidly evolving piRNA pathway leading to genomes depleted of transposable elements, and a rapidly evolving DNA repair pathway associated with high recombination rates in all Apis species. Diversification within Apis is accompanied by positive selection in several genes whose putative functions present candidate mechanisms for lineage-specific adaptations, such as migration, immunity, and nesting behavior.

Phylogenomics Identifies an Ancestral Burst of Gene Duplications Predating the Diversification of Aphidomorpha.

Aphids (Aphidoidea) are a diverse group of hemipteran insects that feed on plant phloem sap. A common finding in studies of aphid genomes is the presence of a large number of duplicated genes. However, when these duplications occurred remains unclear, partly due to the high relatedness of sequenced species. To better understand the origin of aphid duplications we sequenced and assembled the genome of Cinara cedri, an early branching lineage (Lachninae) of the Aphididae family. We performed a phylogenomic comparison of this genome with 20 other sequenced genomes, including the available genomes of five other aphids, along with the transcriptomes of two species belonging to Adelgidae (a closely related clade to the aphids) and Coccoidea. We found that gene duplication has been pervasive throughout the evolution of aphids, including many parallel waves of recent, species-specific duplications. Most notably, we identified a consistent set of very ancestral duplications, originating from a large-scale gene duplication predating the diversification of Aphidomorpha (comprising aphids, phylloxerids, and adelgids). Genes duplicated in this ancestral wave are enriched in functions related to traits shared by Aphidomorpha, such as association with endosymbionts, and adaptation to plant defenses and phloem-sap-based diet. The ancestral nature of this duplication wave (106-227 Ma) and the lack of sufficiently conserved synteny make it difficult to conclude whether it originated from a whole-genome duplication event or, alternatively, from a burst of large-scale segmental duplications. Genome sequencing of other aphid species belonging to different Aphidomorpha and related lineages may clarify these findings.

Gene duplications, divergence and recombination shape adaptive evolution of the fish ectoparasite Gyrodactylus bullatarudis.

Determining the molecular basis of parasite adaptation to its host is an important component in understanding host-parasite coevolution and the epidemiology of parasitic infections. Here, we investigate short- and long-term adaptive evolution in the eukaryotic parasite Gyrodactylus bullatarudis infecting Caribbean guppies (Poecilia reticulata), by comparing the reference genome of Tobagonian G. bullatarudis with other Platyhelminthes, and by analysing resequenced samples from local Trinidadian populations. At the macroevolutionary timescale, we observed duplication of G-protein and serine proteases genes, which are probably important in host-parasite arms races. Serine protease also showed strong evidence of ongoing, diversifying selection at the microevolutionary timescale. Furthermore, our analyses revealed that a hybridization event, involving two divergent genomes, followed by recombination has dramatically affected the genetic composition of Trinidadian populations. The recombinant genotypes invaded Trinidad and replaced local parasites in all populations. We localized more than 300 genes in regions fixed in local populations for variants of different origin, possibly due to diversifying selection pressure from local host populations. In addition, around 70 genes were localized in regions identified as heterozygous in some, but not all, individuals. This pattern is consistent with a very recent spread of recombinant parasites. Overall, our results are consistent with the idea that recombination between divergent genomes can result in particularly successful parasites.

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

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.

Genomic analysis of a migratory divide reveals candidate genes for migration and implicates selective sweeps in generating islands of differentiation.

Differential gene flow, reductions in diversity following linked selection and/or features of the genome can structure patterns of genomic differentiation during the process of speciation. Possible sources of reproductive isolation are well studied between coastal and inland subspecies groups of Swainson's thrushes, with differences in seasonal migratory behaviour likely playing a key role in reducing hybrid fitness. We assembled and annotated a draft reference genome for this species and generated whole-genome shotgun sequence data for populations adjacent to the hybrid zone between these groups. We documented substantial genomewide heterogeneity in relative estimates of genetic differentiation between the groups. Within population diversity was lower in areas of high relative differentiation, supporting a role for selective sweeps in generating this pattern. Absolute genetic differentiation was reduced in these areas, further suggesting that recurrent selective sweeps in the ancestral population and/or between divergent populations following secondary contact likely occurred. Relative genetic differentiation was also higher near centromeres and on the Z chromosome, suggesting that features of the genome also contribute to genomewide heterogeneity. Genes linked to migratory traits were concentrated in islands of differentiation, supporting previous suggestions that seasonal migration is under divergent selection between Swainson's thrushes. Differences in migratory behaviour likely play a central role in the speciation of many taxa; we developed the infrastructure here to permit future investigations into the role several candidate genes play in reducing gene flow between not only Swainson's thrushes but other species as well.

The genome of melon (Cucumis melo L.).

We report the genome sequence of melon, an important horticultural crop worldwide. We assembled 375 Mb of the double-haploid line DHL92, representing 83.3% of the estimated melon genome. We predicted 27,427 protein-coding genes, which we analyzed by reconstructing 22,218 phylogenetic trees, allowing mapping of the orthology and paralogy relationships of sequenced plant genomes. We observed the absence of recent whole-genome duplications in the melon lineage since the ancient eudicot triplication, and our data suggest that transposon amplification may in part explain the increased size of the melon genome compared with the close relative cucumber. A low number of nucleotide-binding site-leucine-rich repeat disease resistance genes were annotated, suggesting the existence of specific defense mechanisms in this species. The DHL92 genome was compared with that of its parental lines allowing the quantification of sequence variability in the species. The use of the genome sequence in future investigations will facilitate the understanding of evolution of cucurbits and the improvement of breeding strategies.

Finding the missing honey bee genes: lessons learned from a genome upgrade.

BACKGROUND: The first generation of genome sequence assemblies and annotations have had a significant impact upon our understanding of the biology of the sequenced species, the phylogenetic relationships among species, the study of populations within and across species, and have informed the biology of humans. As only a few Metazoan genomes are approaching finished quality (human, mouse, fly and worm), there is room for improvement of most genome assemblies. The honey bee (Apis mellifera) genome, published in 2006, was noted for its bimodal GC content distribution that affected the quality of the assembly in some regions and for fewer genes in the initial gene set (OGSv1.0) compared to what would be expected based on other sequenced insect genomes. RESULTS: Here, we report an improved honey bee genome assembly (Amel_4.5) with a new gene annotation set (OGSv3.2), and show that the honey bee genome contains a number of genes similar to that of other insect genomes, contrary to what was suggested in OGSv1.0. The new genome assembly is more contiguous and complete and the new gene set includes ~5000 more protein-coding genes, 50% more than previously reported. About 1/6 of the additional genes were due to improvements to the assembly, and the remaining were inferred based on new RNAseq and protein data. CONCLUSIONS: Lessons learned from this genome upgrade have important implications for future genome sequencing projects. Furthermore, the improvements significantly enhance genomic resources for the honey bee, a key model for social behavior and essential to global ecology through pollination.

Characterization of add-on testing before and after automation at a core laboratory.

Objectives: Add-on testing refers to the process that occurs in clinical laboratories when clinicians request that additional tests be performed on a previously analysed specimen. This is a common but inefficient procedure, highly time-consuming, especially at core laboratories and could be optimised by automating these procedures. The aims of this study are: 1) To describe patterns of add-on testing at a core laboratory at a tertiary hospital, 2) To evaluate turnaround time (TAT) before and after automation of the pre-, post- and analytical phases. Methods: Retrospective, observational study conducted at the biochemistry area of a core laboratory of all add-on orders received in two different months (pre-automation and post-automation). Results: A total of 2464 add-on orders were analysed, representing around 5 % of total requests. Most orders were for either one (>50 %) or two (≈20 %) tests. Most orders were received during the week (from Monday to Friday), particularly during the morning shift (>50 %). More than 50 % of requests were made by the Emergency Department. The two most common add-on parameters were C-reactive protein and N-terminal pro-brain natriuretic peptide. After automation, the median TAT decreased by 42.3 % (from 52 to 22 min). The largest decreases in TAT were observed for routine samples (58.89 %) and fully automated analyses (56.86 %). Conclusions: Automation of our core laboratory substantially reduced turnaround time for add-on testing, indicating an increase in efficiency. Automation eliminated several manual steps in the process, leading to a mean reduction of 15 work hours per day (more than 2 full-time equivalents).

Global trends of whole-genome duplications revealed by the ciliate Paramecium tetraurelia.

The duplication of entire genomes has long been recognized as having great potential for evolutionary novelties, but the mechanisms underlying their resolution through gene loss are poorly understood. Here we show that in the unicellular eukaryote Paramecium tetraurelia, a ciliate, most of the nearly 40,000 genes arose through at least three successive whole-genome duplications. Phylogenetic analysis indicates that the most recent duplication coincides with an explosion of speciation events that gave rise to the P. aurelia complex of 15 sibling species. We observed that gene loss occurs over a long timescale, not as an initial massive event. Genes from the same metabolic pathway or protein complex have common patterns of gene loss, and highly expressed genes are over-retained after all duplications. The conclusion of this analysis is that many genes are maintained after whole-genome duplication not because of functional innovation but because of gene dosage constraints.

Volatile Composition of Sparkling Wines of cv. Chardonnay Cultivated under Different Training Systems in Serra da Mantiqueira (Brazil).

The grapevine is a climbing plant and allows for the manipulation of vegetative canopies to change the microclimate and exposure of leaves and clusters to solar radiation, affecting the primary and secondary metabolisms of plants. Thus, this work aimed to evaluate how the lyre and Geneva double-curtain (GDC) training systems could contribute to the volatile composition of sparkling wines in replicates of vinifications carried out in the Serra da Mantiqueira (Brazil) in two consecutive summer harvests (2017 and 2018). Fifty-four free volatile compounds were identified by HS-SPME/GC-MS in the wines in both systems and vintages. Multivariate analysis differentiated the vintages in component 1 (22.7%) and the training systems in component 2 (7.1%). The crops were differentiated by aldehydes in 2017 and in 2018 by isoamyl acetate ester, probably derived from the amino acid leucine, the season having been more humid, with lower temperatures and less radiation. For the training systems, besides the alcohol compounds, the GDC was differentiated by the terpenoid compounds geranylacetone and ß-damascenone, which may contribute more pleasant aromas to sparkling wines. This work promotes additional research and enables winegrowers, through the management of their vineyards, to achieve sparkling wines with different volatile compositions.

Co-evolution of the branch site and SR proteins in eukaryotes.

Serine-arginine-rich (SR) proteins are essential for splicing in metazoans but are absent in yeast. By contrast, many fungi have SR protein homologs with variable arginine-rich regions analogous to the arginine-serine-rich (RS) domain in metazoans. The density of RS repeats in these regions correlates with the conservation of the branch site signal, providing evidence for an ancestral origin of SR proteins and indicating that the SR proteins and the branch site co-evolved.

FA-nf: A Functional Annotation Pipeline for Proteins from Non-Model Organisms Implemented in Nextflow.

Functional annotation allows adding biologically relevant information to predicted features in genomic sequences, and it is, therefore, an important procedure of any de novo genome sequencing project. It is also useful for proofreading and improving gene structural annotation. Here, we introduce FA-nf, a pipeline implemented in Nextflow, a versatile computational workflow management engine. The pipeline integrates different annotation approaches, such as NCBI BLAST+, DIAMOND, InterProScan, and KEGG. It starts from a protein sequence FASTA file and, optionally, a structural annotation file in GFF format, and produces several files, such as GO assignments, output summaries of the abovementioned programs and final annotation reports. The pipeline can be broken easily into smaller processes for the purpose of parallelization and easily deployed in a Linux computational environment, thanks to software containerization, thus helping to ensure full reproducibility.

Therapeutic Exercise and Pain Neurophysiology Education in Female Patients with Fibromyalgia Syndrome: A Feasibility Study.

BACKGROUND: We compared the effects of therapeutic exercise (TE) combined with pain neurophysiology education (PNE) to those of TE in isolation on pain intensity, general fibromyalgia impact, mechanical pain sensitivity, pain catastrophizing, psychological distress and quality of life in women with fibromyalgia syndrome (FMS). METHODS: A feasibility study with a 3 month follow-up was designed. Thirty-two patients with FMS were randomly assigned to PNE + TE group (n = 16) or to TE group (n = 16). Both groups received 30 sessions of TE (3 per week), and the PNE + TE group received eight face-to-face educational sessions. The measuring instruments used were the visual analogue scale, a standard pressure algometer, the Revised Fibromyalgia Impact Questionnaire, the Pain Catastrophizing Scale, the Hospital Anxiety and Depression Scale and the Health Assessment Questionnaire. RESULTS: The PNE + TE group showed a statistically significant decrease on pain intensity compared to TE group at short term (p = 0.015). No between-groups differences were found for mechanical pain sensitivity, general fibromyalgia impact, pain catastrophizing, psychological distress or quality of life (p > 0.05). CONCLUSIONS: The combination of PNE and TE was more effective than TE for reducing pain intensity in the short-term. No differences were found for psychological distress, pain catastrophizing and quality of life after the intervention or at 3 months of follow-up.

Optical and physical mapping with local finishing enables megabase-scale resolution of agronomically important regions in the wheat genome.

BACKGROUND: Numerous scaffold-level sequences for wheat are now being released and, in this context, we report on a strategy for improving the overall assembly to a level comparable to that of the human genome. RESULTS: Using chromosome 7A of wheat as a model, sequence-finished megabase-scale sections of this chromosome were established by combining a new independent assembly using a bacterial artificial chromosome (BAC)-based physical map, BAC pool paired-end sequencing, chromosome-arm-specific mate-pair sequencing and Bionano optical mapping with the International Wheat Genome Sequencing Consortium RefSeq v1.0 sequence and its underlying raw data. The combined assembly results in 18 super-scaffolds across the chromosome. The value of finished genome regions is demonstrated for two approximately 2.5 Mb regions associated with yield and the grain quality phenotype of fructan carbohydrate grain levels. In addition, the 50 Mb centromere region analysis incorporates cytological data highlighting the importance of non-sequence data in the assembly of this complex genome region. CONCLUSIONS: Sufficient genome sequence information is shown to now be available for the wheat community to produce sequence-finished releases of each chromosome of the reference genome. The high-level completion identified that an array of seven fructosyl transferase genes underpins grain quality and that yield attributes are affected by five F-box-only-protein-ubiquitin ligase domain and four root-specific lipid transfer domain genes. The completed sequence also includes the centromere.

Comparative gene finding in chicken indicates that we are closing in on the set of multi-exonic widely expressed human genes.

The recent availability of the chicken genome sequence poses the question of whether there are human protein-coding genes conserved in chicken that are currently not included in the human gene catalog. Here, we show, using comparative gene finding followed by experimental verification of exon pairs by RT-PCR, that the addition to the multi-exonic subset of this catalog could be as little as 0.2%, suggesting that we may be closing in on the human gene set. Our protocol, however, has two shortcomings: (i) the bioinformatic screening of the predicted genes, applied to filter out false positives, cannot handle intronless genes; and (ii) the experimental verification could fail to identify expression at a specific developmental time. This highlights the importance of developing methods that could provide a reliable estimate of the number of these two types of genes.

MECP2 Duplications in Symptomatic Females: Report on 3 Patients Showing the Broad Phenotypic Spectrum.

Xq28 microduplications including the MECP2 gene constitute a 100% penetrant X-linked syndrome in males caused by overexpression of normal MeCP2 protein. A small number of cases of affected females have been reported. This can be due to the location of the duplicated material into an autosome, but it can also be due to the location of the duplicated material into one of the X chromosomes and random or unfavorable skewed X chromosome inactivation, which is much more likely to occur but may be underdiagnosed because of the resulting broad phenotypic spectrum. In order to contribute to the phenotypic delineation of Xq28 microduplications including MECP2 in symptomatic females, the authors present clinical and molecular data on 3 patients illustrating the broad phenotypic spectrum. Our finding underlines the importance of quantitative analysis of MECP2 in females with intellectual disability and raises the question of the indication in females with borderline intellectual performances or learning difficulties.

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

BACKGROUND: Legumes 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. RESULTS: We 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. CONCLUSIONS: The 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.

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

BACKGROUND: Genomic 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. RESULTS: We 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. CONCLUSIONS: The 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.

Gene finding in the chicken genome.

BACKGROUND: Despite the continuous production of genome sequence for a number of organisms, reliable, comprehensive, and cost effective gene prediction remains problematic. This is particularly true for genomes for which there is not a large collection of known gene sequences, such as the recently published chicken genome. We used the chicken sequence to test comparative and homology-based gene-finding methods followed by experimental validation as an effective genome annotation method. RESULTS: We performed experimental evaluation by RT-PCR of three different computational gene finders, Ensembl, SGP2 and TWINSCAN, applied to the chicken genome. A Venn diagram was computed and each component of it was evaluated. The results showed that de novo comparative methods can identify up to about 700 chicken genes with no previous evidence of expression, and can correctly extend about 40% of homology-based predictions at the 5' end. CONCLUSIONS: De novo comparative gene prediction followed by experimental verification is effective at enhancing the annotation of the newly sequenced genomes provided by standard homology-based methods.

[Diet quality in college students with different academic profile]. / CALIDAD DE LA DIETA EN ESTUDIANTES UNIVERSITARIOS CON DISTINTO PERFIL ACADÉMICO.

INTRODUCTION: We can find in Spain several university studies concerning diet and lifestyle, showing them as an effective strategy to prevent chronic diseases. OBJECTIVES: To evaluate the energy and nutrient intake and adherence to the Mediterranean Diet (DM) in a group of college students with different academic profile and to compare the quality of the diet among students attending degrees in Health Science (HS) and those attending other degree courses (not HS). METHODS: 77 students (80.3% female) from the Campus of Soria, 37 HS students and 40 not HS (mean age 21.2 ± 2.1 years), completed a questionnaire on socio-biographical data, the test KIDMED of adhesion to Mediterranean diet and recorded food intake for seven days. The amount of energy and nutrients was estimated using the software Nutriber (version 1.1.1.3r). Student t test or U Mann-Whitney were used to compare means of independent samples and the criterion of significance was set at p <0,05. RESULTS AND DISCUSSION: The respondent students, regardless of their academic profile, follow a low calorie diet with more protein and fat consumption than the recommended amount, and less carbohydrate and fiber, which is reflected in the insufficient intake of some vitamins and minerals. However, we observed a higher percentage of respondents with high adhesion to the parameters of the DM in the HS group (51.4%) than in the No HS group (30.8%).

Introducción: En España son varios los estudios universitarios que abordan los temas de alimentación y estilo de vida, y demuestran que éstos son una estrategia eficaz para la prevención de enfermedades crónicas. Objetivos: Evaluar la ingesta de energía y nutrientes y la adhesión a la Dieta Mediterránea (DM) en un grupo de estudiantes universitarios con distinto perfil académico y comparar la calidad de la dieta entre estudiantes que cursan grados en Ciencias de la Salud (CS) y los de otras carreras (No CS). Métodos: 77 estudiantes (80,3% mujeres) del Campus de Soria, 37 de grados en CS y 40 de No CS de edad media 21,2 ± 2,1 años, cumplimentaron un cuestionario sobre datos socio-biográficos, el test KIDMED y registraron la ingesta de alimentos durante siete días. La estimación de la cantidad de energía y nutrientes se realizó mediante el programa informático NUTRIBER (versión 1.1.1.3r) y para la comparación de medias de muestras independientes se utilizaron las pruebas t de Student o U de Mann-Whitney y el criterio de significación se estableció en p < 0,05. Resultados y Discusión: Los estudiantes encuestados, con independencia de su perfil académico, siguen una dieta hipocalórica con mayor consumo de proteínas y de grasas de las recomendadas y menor de hidratos de carbono y fibra, lo que se refleja en el aporte insuficiente de algunas vitaminas y minerales. A pesar de ello, observamos un mayor porcentaje de encuestados con adhesión alta a los parámetros de la DM en el grupo CS (51,4%) que en el grupo no CS (30,8 %).