OrthoDB v11: annotation of orthologs in the widest sampling of organismal diversity.

OrthoDB provides evolutionary and functional annotations of genes in a diverse sampling of eukaryotes, prokaryotes, and viruses. Genomics continues to accelerate our exploration of gene diversity and orthology is the most precise way of bridging gene functional knowledge with the rapidly expanding universe of genomic sequences. OrthoDB samples the most diverse organisms with the best quality genomics data to provide the leading coverage of species diversity. This update of the underlying data to over 18 000 prokaryotes and almost 2000 eukaryotes with over 100 million genes propels the coverage to another level. This achievement also demonstrates the scalability of the underlying OrthoLoger software for delineation of orthologs, freely available from https://orthologer.ezlab.org. In addition to the ab-initio computations of gene orthology used for the OrthoDB release, the OrthoLoger software allows mapping of novel gene sets to precomputed orthologs and thereby links to their annotations. The LEMMI-style benchmarking of OrthoLoger ensures its state-of-the-art performance and is available from https://lemortho.ezlab.org. The OrthoDB web interface has been further developed to include a pairwise orthology view from any gene to any other sampled species. OrthoDB-computed evolutionary annotations as well as extensively collated functional annotations can be accessed via REST API or SPARQL/RDF, downloaded or browsed online from https://www.orthodb.org.

Scaling-Up Performance-Based Financing in Burkina Faso: From PBF to User Fees Exemption Strategic Purchasing.

BACKGROUND: Numerous countries have undertaken performance-based financing (PBF) reforms to improve quality and quantity of healthcare services. However, only few reforms have successfully managed to achieve the different scale-up phases. In Burkina Faso, a pilot project was implemented, but was put on hold before being scaled. During the writing of this article, discussions to scale-up were still ongoing on a national strategic purchasing strategy within a government led user fee exemption policy. METHODS: This study's objective is to identify facilitators and barriers to scaling-up for that pilot, based on the World Health Organization's (WHO's) theoretical framework. Interviews were conducted in three health centres and in Ouagadougou to discuss the scale-up with different actors. The software QDA Miner© was used to help in the framework analysis. RESULTS: The low involvement of some key stakeholders (mainly decision-makers) and the unstable context hindered ownership of the project, thus its priority on the political agenda. PBF reform therefore lost its momentum to the benefit of a user fee exemption policy. This latter program was seen to be more beneficial since it addressed access to healthcare services, in comparison to service quality, which was the PBF's relative advantage. A scale-up of some PBF elements (eg, strategic purchasing tools) is however still in discussion in 2019, but would be integrated within the user fee exemption program. Increased costs during the PBF's implementation gave the impression that the project was too costly and not scalable. The involvement of an important funding agency (World Bank, WB) also fed the impression of high costs, which demotivated the actors, especially decision-makers. CONCLUSION: Contextual factors remain central to the implementation of PBF, while their evaluation and mitigation have remained unclear. The participation of key actors in scaling-up operations and the use of social science as tools to better understand the context is therefore primordial.

BUSCO: Assessing Genomic Data Quality and Beyond.

Evaluation of the quality of genomic "data products" such as genome assemblies or gene sets is of critical importance in order to recognize possible issues and correct them during the generation of new data. It is equally essential to guide subsequent or comparative analyses with existing data, as the correct interpretation of the results necessarily requires knowledge about the quality level and reliability of the inputs. Using datasets of near universal single-copy orthologs derived from OrthoDB, BUSCO can estimate the completeness and redundancy of genomic data by providing biologically meaningful metrics based on expected gene content. These can complement technical metrics such as contiguity measures (e.g., number of contigs/scaffolds, and N50 values). Here, we describe the use of the BUSCO tool suite to assess different data types that can range from genome assemblies of single isolates and assembled transcriptomes and annotated gene sets to metagenome-assembled genomes where the taxonomic origin of the species is unknown. BUSCO is the only tool capable of assessing all these types of sequences from both eukaryotic and prokaryotic species. The protocols detail the various BUSCO running modes and the novel workflows introduced in versions 4 and 5, including the batch analysis on multiple inputs, the auto-lineage workflow to run assessments without specifying a dataset, and a workflow for the evaluation of (large) eukaryotic genomes. The protocols further cover the BUSCO setup, guidelines to interpret the results, and BUSCO "plugin" workflows for performing common operations in genomics using BUSCO results, such as building phylogenomic trees and visualizing syntenies. © 2021 The Authors. Current Protocols published by Wiley Periodicals LLC. Basic Protocol 1: Assessing an input sequence with a BUSCO dataset specified manually Basic Protocol 2: Assessing an input sequence with a dataset automatically selected by BUSCO Basic Protocol 3: Assessing multiple inputs Alternate Protocol: Decreasing analysis runtime when assessing a large number of small genomes with BUSCO auto-lineage workflow and Snakemake Support Protocol 1: BUSCO setup Support Protocol 2: Visualizing BUSCO results Support Protocol 3: Building phylogenomic trees.

BUSCO Update: Novel and Streamlined Workflows along with Broader and Deeper Phylogenetic Coverage for Scoring of Eukaryotic, Prokaryotic, and Viral Genomes.

Methods for evaluating the quality of genomic and metagenomic data are essential to aid genome assembly procedures and to correctly interpret the results of subsequent analyses. BUSCO estimates the completeness and redundancy of processed genomic data based on universal single-copy orthologs. Here, we present new functionalities and major improvements of the BUSCO software, as well as the renewal and expansion of the underlying data sets in sync with the OrthoDB v10 release. Among the major novelties, BUSCO now enables phylogenetic placement of the input sequence to automatically select the most appropriate BUSCO data set for the assessment, allowing the analysis of metagenome-assembled genomes of unknown origin. A newly introduced genome workflow increases the efficiency and runtimes especially on large eukaryotic genomes. BUSCO is the only tool capable of assessing both eukaryotic and prokaryotic species, and can be applied to various data types, from genome assemblies and metagenomic bins, to transcriptomes and gene sets.

Sustainability determinants of the Burkinabe performance-based financing project.

PURPOSE: A performance-based financing (PBF) pilot project was implemented in 2011 in Burkina Faso. After more than five years of implementation (data collection in 2016), the project's sustainability was not guaranteed. This study's objective is to assess this project's sustainability in 2016 by identifying the presence/absence of different determinants of sustainability according to the conceptual framework of Seppey et al. (2017). DESIGN/METHODOLOGY/APPROACH: It uses a case study approach using in-depth interviews with various actors at the local, district/regional and national levels. Participants (n = 37) included health practitioners, management team members, implementers and senior members of health directions. A thematic analysis based on the conceptual framework was conducted, as well as an inductive analysis. FINDINGS: Results show the project's sustainability level was weak according to an unequal presence of sustainability's determinants; some activities are being maintained but not fully routinised. Discrepancies between the project and the context's values appeared to be important barriers towards sustainability. Project's ownership by key stakeholders also seemed superficial despite the implementers' leadership towards its success. The project's objective towards greater autonomy for health centres was also directly confronting the Burkinabe's hierarchical health system. ORIGINALITY/VALUE: This study reveals many fits and misfits between a PBF project and its context affecting its ability to sustain activities through time. It also underlines the importance of using a conceptual framework in implementing and evaluating interventions. These results could be interesting for decision-makers and implementers in further assessing PBF projects elsewhere.

The Bgee suite: integrated curated expression atlas and comparative transcriptomics in animals.

Bgee is a database to retrieve and compare gene expression patterns in multiple animal species, produced by integrating multiple data types (RNA-Seq, Affymetrix, in situ hybridization, and EST data). It is based exclusively on curated healthy wild-type expression data (e.g., no gene knock-out, no treatment, no disease), to provide a comparable reference of normal gene expression. Curation includes very large datasets such as GTEx (re-annotation of samples as 'healthy' or not) as well as many small ones. Data are integrated and made comparable between species thanks to consistent data annotation and processing, and to calls of presence/absence of expression, along with expression scores. As a result, Bgee is capable of detecting the conditions of expression of any single gene, accommodating any data type and species. Bgee provides several tools for analyses, allowing, e.g., automated comparisons of gene expression patterns within and between species, retrieval of the prefered conditions of expression of any gene, or enrichment analyses of conditions with expression of sets of genes. Bgee release 14.1 includes 29 animal species, and is available at https://bgee.org/ and through its Bioconductor R package BgeeDB.

LEMMI: a continuous benchmarking platform for metagenomics classifiers.

Studies of microbiomes are booming, along with the diversity of computational approaches to make sense out of the sequencing data and the volumes of accumulated microbial genotypes. A swift evaluation of newly published methods and their improvements against established tools is necessary to reduce the time between the methods' release and their adoption in microbiome analyses. The LEMMI platform offers a novel approach for benchmarking software dedicated to metagenome composition assessments based on read classification. It enables the integration of newly published methods in an independent and centralized benchmark designed to be continuously open to new submissions. This allows developers to be proactive regarding comparative evaluations and guarantees that any promising methods can be assessed side by side with established tools quickly after their release. Moreover, LEMMI enforces an effective distribution through software containers to ensure long-term availability of all methods. Here, we detail the LEMMI workflow and discuss the performances of some previously unevaluated tools. We see this platform eventually as a community-driven effort in which method developers can showcase novel approaches and get unbiased benchmarks for publications, and users can make informed choices and obtain standardized and easy-to-use tools.

Re-thinking global and public health projects during the COVID-19 pandemic context: Considerations and recommendations for early- and not-so-early-career researchers.

This commentary aims to provide a glimpse into some of the early and continuing impacts of the COVID-19 pandemic on our global and public health projects: research in low-resourced settings; research with vulnerable populations, such as asylum seekers, Indigenous communities, children, and mental health service users; and research with healthcare professionals, frontline workers, and health planners. In the early context of restrictions caused by COVID-19, this commentary highlights our research setbacks and challenges, and the ways in which we are adapting research methodologies, while considering ethical implications related to the pandemic and their impacts on conducting global and public health research. As we learn to become increasingly aware of some of our limitations in the face of the pandemic, some positives are also worth highlighting: we are mobilizing our training and research skills to participate in COVID-19 projects and to disseminate knowledge on COVID-19, including through papers such as this one. However, we do acknowledge that these opportunities have not been equitable. Each thematic section of this commentary concludes with key recommendations related to research in the early and continuing context of the COVID-19 pandemic that we believe to be applicable to early- and not-so-early-career researchers working in the global and public health fields.

Genomic signatures accompanying the dietary shift to phytophagy in polyphagan beetles.

BACKGROUND: The diversity and evolutionary success of beetles (Coleoptera) are proposed to be related to the diversity of plants on which they feed. Indeed, the largest beetle suborder, Polyphaga, mostly includes plant eaters among its approximately 315,000 species. In particular, plants defend themselves with a diversity of specialized toxic chemicals. These may impose selective pressures that drive genomic diversification and speciation in phytophagous beetles. However, evidence of changes in beetle gene repertoires driven by such interactions remains largely anecdotal and without explicit hypothesis testing. RESULTS: We explore the genomic consequences of beetle-plant trophic interactions by performing comparative gene family analyses across 18 species representative of the two most species-rich beetle suborders. We contrast the gene contents of species from the mostly plant-eating suborder Polyphaga with those of the mainly predatory Adephaga. We find gene repertoire evolution to be more dynamic, with significantly more adaptive lineage-specific expansions, in the more speciose Polyphaga. Testing the specific hypothesis of adaptation to plant feeding, we identify families of enzymes putatively involved in beetle-plant interactions that underwent adaptive expansions in Polyphaga. There is notable support for the selection hypothesis on large gene families for glutathione S-transferase and carboxylesterase detoxification enzymes. CONCLUSIONS: Our explicit modeling of the evolution of gene repertoires across 18 species identifies putative adaptive lineage-specific gene family expansions that accompany the dietary shift towards plants in beetles. These genomic signatures support the popular hypothesis of a key role for interactions with plant chemical defenses, and for plant feeding in general, in driving beetle diversification.

BUSCO: Assessing Genome Assembly and Annotation Completeness.

Genomics drives the current progress in molecular biology, generating unprecedented volumes of data. The scientific value of these sequences depends on the ability to evaluate their completeness using a biologically meaningful approach. Here, we describe the use of the BUSCO tool suite to assess the completeness of genomes, gene sets, and transcriptomes, using their gene content as a complementary method to common technical metrics. The chapter introduces the concept of universal single-copy genes, which underlies the BUSCO methodology, covers the basic requirements to set up the tool, and provides guidelines to properly design the analyses, run the assessments, and interpret and utilize the results.

Using BUSCO to Assess Insect Genomic Resources.

The increasing affordability of sequencing technologies offers many new and exciting opportunities to address a diverse array of biological questions. This is evidenced in entomological research by numerous genomics and transcriptomics studies that attempt to decipher the often complex relationships among different species or orders and to build "omics" resources to drive advancement of the molecular understanding of insect biology. Being able to gauge the quality of the sequencing data is of critical importance to understanding the potential limitations on the types of questions that these data can be reliably used to address. This chapter details the use of the Benchmarking Universal Single-Copy Orthologue (BUSCO) assessment tool to estimate the completeness of transcriptomes, genome assemblies, and annotated gene sets in terms of their expected gene content.

Validation d'un questionnaire auto-administré sur les valeurs en politique publique de santé.

OBJECTIVES: The aims of this article are to describe the development of a self-administered questionnaire assessing the core values in the field of public health ( radardesvaleurs.com ) and to report the results of a study testing the questionnaire's test-retest reliability, internal consistency and construct validity. METHOD: A 24-item questionnaire grounded in the conceptual framework of Shalom H. Schwartz (2000) was developed by a group of international experts in public health. Six scores were generated, each linked to a specific value and put on three axes: individualism-equity, autonomy-conformity and risk-security. The questionnaire was submitted to students attending the School of Public Health of the Université de Montréal (ESPUM) (n = 700). A total of 401 students completed the questionnaire, 52 of whom completed it again one month later. RESULTS: For the test-retest reliability, all percentages of agreement were equal or superior to 60% except for a single question (50%). All Cohen's kappa coefficients of individual items were strong (> 0.60) except for three questions which presented a very high percentage of agreement. The Intraclass Correlation coefficients of the values' scores varied between 0.27 and 0.77. The three axes' internal consistency was estimated by Cronbach's alphas (between 0.46 and 0.74). The exploratory factorial analysis only partially confirmed the questionnaire's theoretical structure. CONCLUSION: Despite the limits of the results, the questionnaire has an interesting level of reliability and validity, which makes its pedagogical use pertinent to pursue. The limitation to four items/value, as well as the representativeness of the sampling (ESPUM students), could explain certain empirical shortcomings of the questionnaire.

BUSCO Applications from Quality Assessments to Gene Prediction and Phylogenomics.

Genomics promises comprehensive surveying of genomes and metagenomes, but rapidly changing technologies and expanding data volumes make evaluation of completeness a challenging task. Technical sequencing quality metrics can be complemented by quantifying completeness of genomic data sets in terms of the expected gene content of Benchmarking Universal Single-Copy Orthologs (BUSCO, http://busco.ezlab.org). The latest software release implements a complete refactoring of the code to make it more flexible and extendable to facilitate high-throughput assessments. The original six lineage assessment data sets have been updated with improved species sampling, 34 new subsets have been built for vertebrates, arthropods, fungi, and prokaryotes that greatly enhance resolution, and data sets are now also available for nematodes, protists, and plants. Here, we present BUSCO v3 with example analyses that highlight the wide-ranging utility of BUSCO assessments, which extend beyond quality control of genomics data sets to applications in comparative genomics analyses, gene predictor training, metagenomics, and phylogenomics.

Donor-funded project's sustainability assessment: a qualitative case study of a results-based financing pilot in Koulikoro region, Mali.

BACKGROUND: Results-based financing (RBF) is emerging as a new alternative to finance health systems in many African countries. In Mali, a pilot project was conducted to improve demand and supply of health services through financing performance in targeted services. No study has explored the sustainability process of such a project in Africa. This study's objectives were to understand the project's sustainability process and to assess its level of sustainability. METHODS: Sustainability was examined through its different determinants, phases, levels and contexts. These were explored using qualitative interviews to discern, via critical events, stakeholders' ideas regarding the project's sustainability. Data collection sites were chosen with the participation of different stakeholders, based on a variety of criteria (rural/urban settings, level of participation, RBF participants still present, etc.). Forty-nine stakeholders were then interviewed in six community health centres and two referral health centres (from 11/12/15 to 08/03/16), including health practitioners, administrators, and those involved in implementing and conceptualizing the program (government and NGOs). A theme analysis was done with the software © QDA Miner according to the study's conceptual framework. RESULTS: The results of this project show a weak level of sustainability due to many factors. While some gains could be sustained (ex.: investments in long-term resources, high compatibility of values and codes, adapted design to the implementations contexts, etc.) other intended benefits could not (ex.: end of investments, lack of shared cultural artefacts around RBF, loss of different tasks and procedures, need of more ownership of the project by the local stakeholders). A lack of sustainability planning was observed, and few critical events were associated to phases of sustainability. CONCLUSIONS: While this RBF project aimed at increasing health agents' motivation through different mechanisms (supervision, investments, incentives, etc.), these results raise questions on what types of motivation could be more stable and what could be the place of local stakeholders in the project; all this with the aim of more sustained and efficient results.

Genomic Features of the Damselfly Calopteryx splendens Representing a Sister Clade to Most Insect Orders.

Insects comprise the most diverse and successful animal group with over one million described species that are found in almost every terrestrial and limnic habitat, with many being used as important models in genetics, ecology, and evolutionary research. Genome sequencing projects have greatly expanded the sampling of species from many insect orders, but genomic resources for species of certain insect lineages have remained relatively limited to date. To address this paucity, we sequenced the genome of the banded demoiselle, Calopteryx splendens, a damselfly (Odonata: Zygoptera) belonging to Palaeoptera, the clade containing the first winged insects. The 1.6 Gbp C. splendens draft genome assembly is one of the largest insect genomes sequenced to date and encodes a predicted set of 22,523 protein-coding genes. Comparative genomic analyses with other sequenced insects identified a relatively small repertoire of C. splendens detoxification genes, which could explain its previously noted sensitivity to habitat pollution. Intriguingly, this repertoire includes a cytochrome P450 gene not previously described in any insect genome. The C. splendens immune gene repertoire appears relatively complete and features several genes encoding novel multi-domain peptidoglycan recognition proteins. Analysis of chemosensory genes revealed the presence of both gustatory and ionotropic receptors, as well as the insect odorant receptor coreceptor gene (OrCo) and at least four partner odorant receptors (ORs). This represents the oldest known instance of a complete OrCo/OR system in insects, and provides the molecular underpinning for odonate olfaction. The C. splendens genome improves the sampling of insect lineages that diverged before the radiation of Holometabola and offers new opportunities for molecular-level evolutionary, ecological, and behavioral studies.

OrthoDB v9.1: cataloging evolutionary and functional annotations for animal, fungal, plant, archaeal, bacterial and viral orthologs.

OrthoDB is a comprehensive catalog of orthologs, genes inherited by extant species from a single gene in their last common ancestor. In 2016 OrthoDB reached its 9th release, growing to over 22 million genes from over 5000 species, now adding plants, archaea and viruses. In this update we focused on usability of this fast-growing wealth of data: updating the user and programmatic interfaces to browse and query the data, and further enhancing the already extensive integration of available gene functional annotations. Collating functional annotations from over 100 resources, and enabled us to propose descriptive titles for 87% of ortholog groups. Additionally, OrthoDB continues to provide computed evolutionary annotations and to allow user queries by sequence homology. The OrthoDB resource now enables users to generate publication-quality comparative genomics charts, as well as to upload, analyze and interactively explore their own private data. OrthoDB is available from http://orthodb.org.

The Genome of the Toluene-Degrading Pseudomonas veronii Strain 1YdBTEX2 and Its Differential Gene Expression in Contaminated Sand.

The natural restoration of soils polluted by aromatic hydrocarbons such as benzene, toluene, ethylbenzene and m- and p-xylene (BTEX) may be accelerated by inoculation of specific biodegraders (bioaugmentation). Bioaugmentation mainly involves introducing bacteria that deploy their metabolic properties and adaptation potential to survive and propagate in the contaminated environment by degrading the pollutant. In order to better understand the adaptive response of cells during a transition to contaminated material, we analyzed here the genome and short-term (1 h) changes in genome-wide gene expression of the BTEX-degrading bacterium Pseudomonas veronii 1YdBTEX2 in non-sterile soil and liquid medium, both in presence or absence of toluene. We obtained a gapless genome sequence of P. veronii 1YdBTEX2 covering three individual replicons with a total size of 8 Mb, two of which are largely unrelated to current known bacterial replicons. One-hour exposure to toluene, both in soil and liquid, triggered massive transcription (up to 208-fold induction) of multiple gene clusters, such as toluene degradation pathway(s), chemotaxis and toluene efflux pumps. This clearly underlines their key role in the adaptive response to toluene. In comparison to liquid medium, cells in soil drastically changed expression of genes involved in membrane functioning (e.g., lipid composition, lipid metabolism, cell fatty acid synthesis), osmotic stress response (e.g., polyamine or trehalose synthesis, uptake of potassium) and putrescine metabolism, highlighting the immediate response mechanisms of P. veronii 1YdBTEX2 for successful establishment in polluted soil.

The role of transportation to access maternal care services for women in rural Bangladesh and Burkina Faso: A mixed methods study.

OBJECTIVE: To understand the role of transportation in accessing health care during pregnancy, delivery, and the postpartum period among women in rural Bangladesh and Burkina Faso. METHODS: An exploratory mixed methods study was conducted in Mymensingh district in Bangladesh and Kaya district in Burkina Faso. We recruited 300 women from Bangladesh and 340 from Burkina Faso with a delivery outcome within one year of interview. Key informant interviews were conducted with 19 participants and 12 focus group discussions took place with attendees in selected community clinics. RESULTS: Of the interviewees, 45.7% in Bangladesh and 73.2% in Burkina Faso reported having had health complications during their last pregnancy, delivery, or postpartum period. Of all women, 42.7% in Bangladesh and 67.4% in Burkina Faso sought facility care for their complications. Facility-based delivery was much higher in Burkina Faso (87.7%) than Bangladesh (38.2%). Literacy, transport availability, transportation costs, and travel time were associated with care seeking behavior. CONCLUSION: Lack of reliable transportation was reported as a significant barrier to accessing care during pregnancy, delivery, and postpartum by women in Bangladesh and Burkina Faso. Effort should be made to improve access to emergency obstetric care, and transport intervention should be strengthened.