Publications by authors named "Evgeny M Zdobnov"

95 Publications

: A Small but Versatile Species.

Microorganisms 2021 Aug 17;9(8). Epub 2021 Aug 17.

Department of Microbiology and Molecular Medicine, University of Geneva, 1206 Geneva, Switzerland.

Enteroviruses (EVs) from the D species are the causative agents of a diverse range of infectious diseases in spite of comprising only five known members. This small clade has a diverse host range and tissue tropism. It contains types infecting non-human primates and/or humans, and for the latter, they preferentially infect the eye, respiratory tract, gastrointestinal tract, and nervous system. Although several members, in particular EV-D68, have been associated with neurological complications, including acute myelitis, there is currently no effective treatment or vaccine against any of them. This review highlights the peculiarities of this viral species, focusing on genome organization, functional elements, receptor usage, and pathogenesis.
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http://dx.doi.org/10.3390/microorganisms9081758DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8400195PMC
August 2021

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

Mol Biol Evol 2021 Sep;38(10):4647-4654

Department of Genetic Medicine and Development, University of Geneva, Geneva, Switzerland.

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.
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http://dx.doi.org/10.1093/molbev/msab199DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8476166PMC
September 2021

The genome of the stable fly, Stomoxys calcitrans, reveals potential mechanisms underlying reproduction, host interactions, and novel targets for pest control.

BMC Biol 2021 03 10;19(1):41. Epub 2021 Mar 10.

Department of Computer Science & Engineering, Department of Biochemistry & Biophysics, Texas A & M University, College Station, TX, USA.

Background: The stable fly, Stomoxys calcitrans, is a major blood-feeding pest of livestock that has near worldwide distribution, causing an annual cost of over $2 billion for control and product loss in the USA alone. Control of these flies has been limited to increased sanitary management practices and insecticide application for suppressing larval stages. Few genetic and molecular resources are available to help in developing novel methods for controlling stable flies.

Results: This study examines stable fly biology by utilizing a combination of high-quality genome sequencing and RNA-Seq analyses targeting multiple developmental stages and tissues. In conjunction, 1600 genes were manually curated to characterize genetic features related to stable fly reproduction, vector host interactions, host-microbe dynamics, and putative targets for control. Most notable was characterization of genes associated with reproduction and identification of expanded gene families with functional associations to vision, chemosensation, immunity, and metabolic detoxification pathways.

Conclusions: The combined sequencing, assembly, and curation of the male stable fly genome followed by RNA-Seq and downstream analyses provide insights necessary to understand the biology of this important pest. These resources and new data will provide the groundwork for expanding the tools available to control stable fly infestations. The close relationship of Stomoxys to other blood-feeding (horn flies and Glossina) and non-blood-feeding flies (house flies, medflies, Drosophila) will facilitate understanding of the evolutionary processes associated with development of blood feeding among the Cyclorrhapha.
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http://dx.doi.org/10.1186/s12915-021-00975-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7944917PMC
March 2021

OrthoDB in 2020: evolutionary and functional annotations of orthologs.

Nucleic Acids Res 2021 01;49(D1):D389-D393

Department of Genetic Medicine and Development, University of Geneva Medical School, rue Michel-Servet 1, 1211 Geneva, Switzerland, and Swiss Institute of Bioinformatics, rue Michel-Servet 1, 1211 Geneva, Switzerland.

OrthoDB provides evolutionary and functional annotations of orthologs, inferred for a vast number of available organisms. OrthoDB is leading in the coverage and genomic diversity sampling of Eukaryotes, Prokaryotes and Viruses, and the sampling of Bacteria is further set to increase three-fold. The user interface has been enhanced in response to the massive growth in data. OrthoDB provides three views on the data: (i) a list of orthologous groups related to a user query, which are now arranged to visualize their hierarchical relations, (ii) a detailed view of an orthologous group, now featuring a Sankey diagram to facilitate navigation between the levels of orthology, from more finely-resolved to more general groups of orthologs, as well as an arrangement of orthologs into an interactive organism taxonomy structure, and (iii) we added a gene-centric view, showing the gene functional annotations and the pair-wise orthologs in example species. The OrthoDB standalone software for delineation of orthologs, Orthologer, is freely available. Online BUSCO assessments and mapping to OrthoDB of user-uploaded data enable interactive exploration of related annotations and generation of comparative charts. OrthoDB strives to predict orthologs from the broadest coverage of species, as well as to extensively collate available functional annotations, and to compute evolutionary annotations such as evolutionary rate and phyletic profile. OrthoDB data can be assessed via SPARQL RDF, REST API, downloaded or browsed online from https://orthodb.org.
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http://dx.doi.org/10.1093/nar/gkaa1009DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7779051PMC
January 2021

A Novel Anphevirus in Mosquitoes Is Distributed Worldwide and Interacts with the Host RNA Interference Pathway.

Viruses 2020 11 6;12(11). Epub 2020 Nov 6.

Department of Genetic Medicine and Development, University of Geneva Medical School, Rue Michel-Servet 1, 1206 Geneva, Switzerland.

The Asian tiger mosquito is a competent vector for several human arboviruses including dengue, chikungunya and Zika viruses. Mosquitoes also harbor insect-specific viruses (ISVs) that may modulate host physiology and potentially affect the transmission of viruses that are pathogenic to vertebrates, thus representing a potential tool for vector control strategies. In we identified a novel anphevirus (family order ) provisionally designated here as Aedes albopictus anphevirus (AealbAV). AealbAV contains a ~12.4 kb genome that is highly divergent from currently known viruses but displays gene content and genomic organization typical of known anpheviruses. We identified AealbAV in several publicly available RNA-Seq datasets from different geographical regions both in laboratory colonies and field collected mosquitoes. Coding-complete genomes of AealbAV strains are highly similar worldwide (>96% nucleotide identity) and cluster according to the geographical origin of their hosts. AealbAV appears to be present in various body compartments and mosquito life stages, including eggs. We further detected AealbAV-derived vsiRNAs and vpiRNAs in publicly available miRNA-Seq libraries of and in samples experimentally coinfected with chikungunya virus. This suggests that AealbAV is targeted by the host RNA interference (RNAi) response, consistent with persistent virus replication. The discovery and characterization of AealbAV in will now allow us to identify its infection in mosquito populations and laboratory strains, and to assess its potential impact on physiology and ability to transmit arboviruses.
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http://dx.doi.org/10.3390/v12111264DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7694661PMC
November 2020

Genome-enabled insights into the biology of thrips as crop pests.

BMC Biol 2020 10 19;18(1):142. Epub 2020 Oct 19.

Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St. Lucia, QLD, 4072, Australia.

Background: The western flower thrips, Frankliniella occidentalis (Pergande), is a globally invasive pest and plant virus vector on a wide array of food, fiber, and ornamental crops. The underlying genetic mechanisms of the processes governing thrips pest and vector biology, feeding behaviors, ecology, and insecticide resistance are largely unknown. To address this gap, we present the F. occidentalis draft genome assembly and official gene set.

Results: We report on the first genome sequence for any member of the insect order Thysanoptera. Benchmarking Universal Single-Copy Ortholog (BUSCO) assessments of the genome assembly (size = 415.8 Mb, scaffold N50 = 948.9 kb) revealed a relatively complete and well-annotated assembly in comparison to other insect genomes. The genome is unusually GC-rich (50%) compared to other insect genomes to date. The official gene set (OGS v1.0) contains 16,859 genes, of which ~ 10% were manually verified and corrected by our consortium. We focused on manual annotation, phylogenetic, and expression evidence analyses for gene sets centered on primary themes in the life histories and activities of plant-colonizing insects. Highlights include the following: (1) divergent clades and large expansions in genes associated with environmental sensing (chemosensory receptors) and detoxification (CYP4, CYP6, and CCE enzymes) of substances encountered in agricultural environments; (2) a comprehensive set of salivary gland genes supported by enriched expression; (3) apparent absence of members of the IMD innate immune defense pathway; and (4) developmental- and sex-specific expression analyses of genes associated with progression from larvae to adulthood through neometaboly, a distinct form of maturation differing from either incomplete or complete metamorphosis in the Insecta.

Conclusions: Analysis of the F. occidentalis genome offers insights into the polyphagous behavior of this insect pest that finds, colonizes, and survives on a widely diverse array of plants. The genomic resources presented here enable a more complete analysis of insect evolution and biology, providing a missing taxon for contemporary insect genomics-based analyses. Our study also offers a genomic benchmark for molecular and evolutionary investigations of other Thysanoptera species.
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http://dx.doi.org/10.1186/s12915-020-00862-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7570057PMC
October 2020

LEMMI: a continuous benchmarking platform for metagenomics classifiers.

Genome Res 2020 08 2;30(8):1208-1216. Epub 2020 Jul 2.

Department of Genetic Medicine and Development, University of Geneva Medical School and Swiss Institute of Bioinformatics, 1211 Geneva, Switzerland.

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.
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http://dx.doi.org/10.1101/gr.260398.119DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7462069PMC
August 2020

ATLAS: a Snakemake workflow for assembly, annotation, and genomic binning of metagenome sequence data.

BMC Bioinformatics 2020 Jun 22;21(1):257. Epub 2020 Jun 22.

Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, 99352, USA.

Background: Metagenomics studies provide valuable insight into the composition and function of microbial populations from diverse environments; however, the data processing pipelines that rely on mapping reads to gene catalogs or genome databases for cultured strains yield results that underrepresent the genes and functional potential of uncultured microbes. Recent improvements in sequence assembly methods have eased the reliance on genome databases, thereby allowing the recovery of genomes from uncultured microbes. However, configuring these tools, linking them with advanced binning and annotation tools, and maintaining provenance of the processing continues to be challenging for researchers.

Results: Here we present ATLAS, a software package for customizable data processing from raw sequence reads to functional and taxonomic annotations using state-of-the-art tools to assemble, annotate, quantify, and bin metagenome data. Abundance estimates at genome resolution are provided for each sample in a dataset. ATLAS is written in Python and the workflow implemented in Snakemake; it operates in a Linux environment, and is compatible with Python 3.5+ and Anaconda 3+ versions. The source code for ATLAS is freely available, distributed under a BSD-3 license.

Conclusions: ATLAS provides a user-friendly, modular and customizable Snakemake workflow for metagenome data processing; it is easily installable with conda and maintained as open-source on GitHub at https://github.com/metagenome-atlas/atlas.
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http://dx.doi.org/10.1186/s12859-020-03585-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7310028PMC
June 2020

Sawfly Genomes Reveal Evolutionary Acquisitions That Fostered the Mega-Radiation of Parasitoid and Eusocial Hymenoptera.

Genome Biol Evol 2020 07;12(7):1099-1188

Human Genome Sequencing Center, Department of Human and Molecular Genetics, Baylor College of Medicine, Houston, Texas.

The tremendous diversity of Hymenoptera is commonly attributed to the evolution of parasitoidism in the last common ancestor of parasitoid sawflies (Orussidae) and wasp-waisted Hymenoptera (Apocrita). However, Apocrita and Orussidae differ dramatically in their species richness, indicating that the diversification of Apocrita was promoted by additional traits. These traits have remained elusive due to a paucity of sawfly genome sequences, in particular those of parasitoid sawflies. Here, we present comparative analyses of draft genomes of the primarily phytophagous sawfly Athalia rosae and the parasitoid sawfly Orussus abietinus. Our analyses revealed that the ancestral hymenopteran genome exhibited traits that were previously considered unique to eusocial Apocrita (e.g., low transposable element content and activity) and a wider gene repertoire than previously thought (e.g., genes for CO2 detection). Moreover, we discovered that Apocrita evolved a significantly larger array of odorant receptors than sawflies, which could be relevant to the remarkable diversification of Apocrita by enabling efficient detection and reliable identification of hosts.
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http://dx.doi.org/10.1093/gbe/evaa106DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7455281PMC
July 2020

Phigaro: high-throughput prophage sequence annotation.

Bioinformatics 2020 06;36(12):3882-3884

Department of Molecular Biology and Genetics, Federal Research and Clinical Centre of Physical-Chemical Medicine, Moscow 119435, Russia.

Summary: Phigaro is a standalone command-line application that is able to detect prophage regions taking raw genome and metagenome assemblies as an input. It also produces dynamic annotated 'prophage genome maps' and marks possible transposon insertion spots inside prophages. It is applicable for mining prophage regions from large metagenomic datasets.

Availability And Implementation: Source code for Phigaro is freely available for download at https://github.com/bobeobibo/phigaro along with test data. The code is written in Python.

Supplementary Information: Supplementary data are available at Bioinformatics online.
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http://dx.doi.org/10.1093/bioinformatics/btaa250DOI Listing
June 2020

Brown marmorated stink bug, Halyomorpha halys (Stål), genome: putative underpinnings of polyphagy, insecticide resistance potential and biology of a top worldwide pest.

BMC Genomics 2020 Mar 14;21(1):227. Epub 2020 Mar 14.

URGI, INRA, Université Paris-Saclay, 78026, Versailles, France.

Background: Halyomorpha halys (Stål), the brown marmorated stink bug, is a highly invasive insect species due in part to its exceptionally high levels of polyphagy. This species is also a nuisance due to overwintering in human-made structures. It has caused significant agricultural losses in recent years along the Atlantic seaboard of North America and in continental Europe. Genomic resources will assist with determining the molecular basis for this species' feeding and habitat traits, defining potential targets for pest management strategies.

Results: Analysis of the 1.15-Gb draft genome assembly has identified a wide variety of genetic elements underpinning the biological characteristics of this formidable pest species, encompassing the roles of sensory functions, digestion, immunity, detoxification and development, all of which likely support H. halys' capacity for invasiveness. Many of the genes identified herein have potential for biomolecular pesticide applications.

Conclusions: Availability of the H. halys genome sequence will be useful for the development of environmentally friendly biomolecular pesticides to be applied in concert with more traditional, synthetic chemical-based controls.
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http://dx.doi.org/10.1186/s12864-020-6510-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7071726PMC
March 2020

Gene content evolution in the arthropods.

Genome Biol 2020 01 23;21(1):15. Epub 2020 Jan 23.

Department of Genetic Medicine and Development and Swiss Institute of Bioinformatics, University of Geneva, 1211, Geneva, Switzerland.

Background: Arthropods comprise the largest and most diverse phylum on Earth and play vital roles in nearly every ecosystem. Their diversity stems in part from variations on a conserved body plan, resulting from and recorded in adaptive changes in the genome. Dissection of the genomic record of sequence change enables broad questions regarding genome evolution to be addressed, even across hyper-diverse taxa within arthropods.

Results: Using 76 whole genome sequences representing 21 orders spanning more than 500 million years of arthropod evolution, we document changes in gene and protein domain content and provide temporal and phylogenetic context for interpreting these innovations. We identify many novel gene families that arose early in the evolution of arthropods and during the diversification of insects into modern orders. We reveal unexpected variation in patterns of DNA methylation across arthropods and examples of gene family and protein domain evolution coincident with the appearance of notable phenotypic and physiological adaptations such as flight, metamorphosis, sociality, and chemoperception.

Conclusions: These analyses demonstrate how large-scale comparative genomics can provide broad new insights into the genotype to phenotype map and generate testable hypotheses about the evolution of animal diversity.
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http://dx.doi.org/10.1186/s13059-019-1925-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6977273PMC
January 2020

The Genome of the Blind Soil-Dwelling and Ancestrally Wingless Dipluran Campodea augens: A Key Reference Hexapod for Studying the Emergence of Insect Innovations.

Genome Biol Evol 2020 01;12(1):3534-3549

Department of Genetic Medicine and Development, Swiss Institute of Bioinformatics, University of Geneva Medical School, Switzerland.

The dipluran two-pronged bristletail Campodea augens is a blind ancestrally wingless hexapod with the remarkable capacity to regenerate lost body appendages such as its long antennae. As sister group to Insecta (sensu stricto), Diplura are key to understanding the early evolution of hexapods and the origin and evolution of insects. Here we report the 1.2-Gb draft genome of C. augens and results from comparative genomic analyses with other arthropods. In C. augens, we uncovered the largest chemosensory gene repertoire of ionotropic receptors in the animal kingdom, a massive expansion that might compensate for the loss of vision. We found a paucity of photoreceptor genes mirroring at the genomic level the secondary loss of an ancestral external photoreceptor organ. Expansions of detoxification and carbohydrate metabolism gene families might reflect adaptations for foraging behavior, and duplicated apoptotic genes might underlie its high regenerative potential. The C. augens genome represents one of the key references for studying the emergence of genomic innovations in insects, the most diverse animal group, and opens up novel opportunities to study the under-explored biology of diplurans.
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http://dx.doi.org/10.1093/gbe/evz260DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6938034PMC
January 2020

Viral Sequences Detection by High-Throughput Sequencing in Cerebrospinal Fluid of Individuals with and without Central Nervous System Disease.

Genes (Basel) 2019 08 19;10(8). Epub 2019 Aug 19.

Laboratory of Virology, Laboratory Medicine Division, Diagnostic Department, Geneva University Hospitals, 1205 Geneva, Switzerland.

Meningitis, encephalitis, and myelitis are various forms of acute central nervous system (CNS) inflammation, which can coexist and lead to serious sequelae. Known aetiologies include infections and immune-mediated processes. Despite advances in clinical microbiology over the past decades, the cause of acute CNS inflammation remains unknown in approximately 50% of cases. High-throughput sequencing was performed to search for viral sequences in cerebrospinal fluid (CSF) samples collected from 26 patients considered to have acute CNS inflammation of unknown origin, and 10 patients with defined causes of CNS diseases. In order to better grasp the clinical significance of viral sequence data obtained in CSF, 30 patients without CNS disease who had a lumbar puncture performed during elective spinal anaesthesia were also analysed. One case of human astrovirus (HAstV)-MLB2-related meningitis and disseminated infection was identified. No other viral sequences that can easily be linked to CNS inflammation were detected. Viral sequences obtained in all patient groups are discussed. While some of them reflect harmless viral infections, others result from reagent or sample contamination, as well as index hopping. Altogether, this study highlights the potential of high-throughput sequencing in identifying previously unknown viral neuropathogens, as well as the interpretation issues related to its application in clinical microbiology.
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http://dx.doi.org/10.3390/genes10080625DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6723360PMC
August 2019

Comparative genomics groups phages of Negativicutes and classical Firmicutes despite different Gram-staining properties.

Environ Microbiol 2019 11 31;21(11):3989-4001. Epub 2019 Jul 31.

Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva, Switzerland.

Negativicutes are gram-negative bacteria characterized by two cell membranes, but they are phylogenetically a side-branch of gram-positive Firmicutes that contain only a single membrane. We asked whether viruses (phages) infecting Negativicutes were horizontally acquired from gram-negative Proteobacteria, given the shared outer cell structure of their bacterial hosts, or if Negativicute phages co-evolved vertically with their hosts and thus resemble gram-positive Firmicute prophages. We predicted and characterized 485 prophages (mostly Caudovirales) from gram-negative Firmicute genomes plus 2977 prophages from other bacterial clades, and we used virome sequence data from 183 human stool samples to support our predictions. The majority of identified Negativicute prophages were lambdoids closer related to prophages from other Firmicutes than Proteobacteria by sequence relationship and genome organization (position of the lysis module). Only a single Mu-like candidate prophage and no clear P2-like prophages were identified in Negativicutes, both common in Proteobacteria. Given this collective evidence, it is unlikely that Negativicute phages were acquired from Proteobacteria. Sequence-related prophages, which occasionally harboured antibiotic resistance genes, were identified in two distinct Negativicute orders (Veillonellales and Acidaminococcales), possibly suggesting horizontal cross-order phage infection between human gut commensals. Our results reveal ancient genomic signatures of phage and bacteria co-evolution despite horizontal phage mobilization.
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http://dx.doi.org/10.1111/1462-2920.14746DOI Listing
November 2019

BUSCO: Assessing Genome Assembly and Annotation Completeness.

Methods Mol Biol 2019 ;1962:227-245

Department of Genetic Medicine and Development, Swiss Institute of Bioinformatics, University of Geneva Medical School, Geneva, Switzerland.

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.
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http://dx.doi.org/10.1007/978-1-4939-9173-0_14DOI Listing
August 2019

Molecular evolutionary trends and feeding ecology diversification in the Hemiptera, anchored by the milkweed bug genome.

Genome Biol 2019 04 2;20(1):64. Epub 2019 Apr 2.

Department of Biological Sciences, University of Cincinnati, Cincinnati, OH, 45221, USA.

Background: The Hemiptera (aphids, cicadas, and true bugs) are a key insect order, with high diversity for feeding ecology and excellent experimental tractability for molecular genetics. Building upon recent sequencing of hemipteran pests such as phloem-feeding aphids and blood-feeding bed bugs, we present the genome sequence and comparative analyses centered on the milkweed bug Oncopeltus fasciatus, a seed feeder of the family Lygaeidae.

Results: The 926-Mb Oncopeltus genome is well represented by the current assembly and official gene set. We use our genomic and RNA-seq data not only to characterize the protein-coding gene repertoire and perform isoform-specific RNAi, but also to elucidate patterns of molecular evolution and physiology. We find ongoing, lineage-specific expansion and diversification of repressive C2H2 zinc finger proteins. The discovery of intron gain and turnover specific to the Hemiptera also prompted the evaluation of lineage and genome size as predictors of gene structure evolution. Furthermore, we identify enzymatic gains and losses that correlate with feeding biology, particularly for reductions associated with derived, fluid nutrition feeding.

Conclusions: With the milkweed bug, we now have a critical mass of sequenced species for a hemimetabolous insect order and close outgroup to the Holometabola, substantially improving the diversity of insect genomics. We thereby define commonalities among the Hemiptera and delve into how hemipteran genomes reflect distinct feeding ecologies. Given Oncopeltus's strength as an experimental model, these new sequence resources bolster the foundation for molecular research and highlight technical considerations for the analysis of medium-sized invertebrate genomes.
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http://dx.doi.org/10.1186/s13059-019-1660-0DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6444547PMC
April 2019

Using BUSCO to Assess Insect Genomic Resources.

Methods Mol Biol 2019 ;1858:59-74

University of Geneva and Swiss Institute of Bioinformatics, Geneva, Switzerland.

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.
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http://dx.doi.org/10.1007/978-1-4939-8775-7_6DOI Listing
July 2019

OrthoDB v10: sampling the diversity of animal, plant, fungal, protist, bacterial and viral genomes for evolutionary and functional annotations of orthologs.

Nucleic Acids Res 2019 01;47(D1):D807-D811

Department of Genetic Medicine and Development, University of Geneva Medical School, rue Michel-Servet 1, 1211 Geneva, Switzerland.

OrthoDB (https://www.orthodb.org) provides evolutionary and functional annotations of orthologs. This update features a major scaling up of the resource coverage, sampling the genomic diversity of 1271 eukaryotes, 6013 prokaryotes and 6488 viruses. These include putative orthologs among 448 metazoan, 117 plant, 549 fungal, 148 protist, 5609 bacterial, and 404 archaeal genomes, picking up the best sequenced and annotated representatives for each species or operational taxonomic unit. OrthoDB relies on a concept of hierarchy of levels-of-orthology to enable more finely resolved gene orthologies for more closely related species. Since orthologs are the most likely candidates to retain functions of their ancestor gene, OrthoDB is aimed at narrowing down hypotheses about gene functions and enabling comparative evolutionary studies. Optional registered-user sessions allow on-line BUSCO assessments of gene set completeness and mapping of the uploaded data to OrthoDB to enable further interactive exploration of related annotations and generation of comparative charts. The accelerating expansion of genomics data continues to add valuable information, and OrthoDB strives to provide orthologs from the broadest coverage of species, as well as to extensively collate available functional annotations and to compute evolutionary annotations. The data can be browsed online, downloaded or assessed via REST API or SPARQL RDF compatible with both UniProt and Ensembl.
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http://dx.doi.org/10.1093/nar/gky1053DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6323947PMC
January 2019

ACI-1 beta-lactamase is widespread across human gut microbiomes in Negativicutes due to transposons harboured by tailed prophages.

Environ Microbiol 2018 06 7;20(6):2288-2300. Epub 2018 Aug 7.

Department of Genetic Medicine and Development, University of Geneva Medical School and Swiss Institute of Bioinformatics, Geneva, Switzerland.

Antibiotic resistance is increasing among pathogens, and the human microbiome contains a reservoir of antibiotic resistance genes. Acidaminococcus intestini is the first Negativicute bacterium (Gram-negative Firmicute) shown to be resistant to beta-lactam antibiotics. Resistance is conferred by the aci1 gene, but its evolutionary history and prevalence remain obscure. We discovered that ACI-1 proteins are phylogenetically distinct from beta-lactamases of Gram-positive Firmicutes and that aci1 occurs in bacteria scattered across the Negativicute clade, suggesting lateral gene transfer. In the reference A. intestini RyC-MR95 genome, we found transposons residing within a tailed prophage context are likely vehicles for aci1's mobility. We found aci1 in 56 (4.4%) of 1,267 human gut metagenomes, mostly hosted within A. intestini, and, where could be determined, mostly within a consistent mobile element constellation. These samples are from Europe, China and the USA, showing that aci1 is distributed globally. We found that for most Negativicute assemblies with aci1, the prophage observed in A. instestini is absent, but in all cases aci1 is flanked by varying transposons. The chimeric mobile elements we identify here likely have a complex evolutionary history and potentially provide multiple complementary mechanisms for antibiotic resistance gene transfer both within and between cells.
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http://dx.doi.org/10.1111/1462-2920.14276DOI Listing
June 2018

BUSCO Applications from Quality Assessments to Gene Prediction and Phylogenomics.

Mol Biol Evol 2018 Mar;35(3):543-548

Department of Genetic Medicine and Development, University of Geneva Medical School and Swiss Institute of Bioinformatics, Geneva, Switzerland.

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.
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http://dx.doi.org/10.1093/molbev/msx319DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5850278PMC
March 2018

Metagenomics analysis of red blood cell and fresh-frozen plasma units.

Transfusion 2017 07 11;57(7):1787-1800. Epub 2017 May 11.

Department of Medical Specialties, Division of Infectious Diseases and Division of Laboratory Medicine, University Hospitals of Geneva, Geneva.

Background: Although the risk of transmitting infectious agents by blood transfusion is dramatically reduced after donor selection, leukoreduction, and laboratory testing, some could still be present in donor's blood. A description of metagenomes in blood products eligible for transfusion represents relevant information to evaluate the risk of pathogen transmission by transfusion.

Study Design And Methods: Detection of viruses, bacteria, and fungi genomes was made by high-throughput sequencing (HTS) of 600 manufactured blood products eligible for transfusion: 300 red blood cell (RBC) and 300 fresh-frozen plasma (FFP) units.

Results: Anelloviruses and human pegivirus, frequent in the blood of healthy individuals, were found. Human papillomavirus type 27 and Merkel cell polyomavirus, present on the skin, were also detected. Unexpectedly, astrovirus MLB2 was identified and characterized in a FFP unit. The presence of astrovirus MLB2 was confirmed in donor's blood and corresponded to an asymptomatic acute viremia. Sequences of bacteria and fungi were also detected; they are likely the result of environmental contamination.

Conclusion: This study demonstrates that HTS is a promising tool for detecting common and less frequent infectious pathogens in blood products.
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http://dx.doi.org/10.1111/trf.14148DOI Listing
July 2017

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

Genome Biol Evol 2017 02;9(2):415-430

Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva, Switzerland.

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.
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http://dx.doi.org/10.1093/gbe/evx006DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5381652PMC
February 2017

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

Nucleic Acids Res 2017 01 28;45(D1):D744-D749. Epub 2016 Nov 28.

Department of Genetic Medicine and Development, University of Geneva Medical School, rue Michel-Servet 1, 1211 Geneva, Switzerland, and Swiss Institute of Bioinformatics, rue Michel-Servet 1, 1211 Geneva, Switzerland

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.
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http://dx.doi.org/10.1093/nar/gkw1119DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5210582PMC
January 2017

Genome of the Asian longhorned beetle (Anoplophora glabripennis), a globally significant invasive species, reveals key functional and evolutionary innovations at the beetle-plant interface.

Genome Biol 2016 11 11;17(1):227. Epub 2016 Nov 11.

School of Biology, Georgia Institute of Technology, Atlanta, GA, 30332, USA.

Background: Relatively little is known about the genomic basis and evolution of wood-feeding in beetles. We undertook genome sequencing and annotation, gene expression assays, studies of plant cell wall degrading enzymes, and other functional and comparative studies of the Asian longhorned beetle, Anoplophora glabripennis, a globally significant invasive species capable of inflicting severe feeding damage on many important tree species. Complementary studies of genes encoding enzymes involved in digestion of woody plant tissues or detoxification of plant allelochemicals were undertaken with the genomes of 14 additional insects, including the newly sequenced emerald ash borer and bull-headed dung beetle.

Results: The Asian longhorned beetle genome encodes a uniquely diverse arsenal of enzymes that can degrade the main polysaccharide networks in plant cell walls, detoxify plant allelochemicals, and otherwise facilitate feeding on woody plants. It has the metabolic plasticity needed to feed on diverse plant species, contributing to its highly invasive nature. Large expansions of chemosensory genes involved in the reception of pheromones and plant kairomones are consistent with the complexity of chemical cues it uses to find host plants and mates.

Conclusions: Amplification and functional divergence of genes associated with specialized feeding on plants, including genes originally obtained via horizontal gene transfer from fungi and bacteria, contributed to the addition, expansion, and enhancement of the metabolic repertoire of the Asian longhorned beetle, certain other phytophagous beetles, and to a lesser degree, other phytophagous insects. Our results thus begin to establish a genomic basis for the evolutionary success of beetles on plants.
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http://dx.doi.org/10.1186/s13059-016-1088-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5105290PMC
November 2016

Astrovirus MLB2, a New Gastroenteric Virus Associated with Meningitis and Disseminated Infection.

Emerg Infect Dis 2016 May;22(5):846-53

Next-generation sequencing has identified novel astroviruses for which a pathogenic role is not clearly defined. We identified astrovirus MLB2 infection in an immunocompetent case-patient and an immunocompromised patient who experienced diverse clinical manifestations, notably, meningitis and disseminated infection. The initial case-patient was identified by next-generation sequencing, which revealed astrovirus MLB2 RNA in cerebrospinal fluid, plasma, urine, and anal swab specimens. We then used specific real-time reverse transcription PCR to screen 943 fecal and 424 cerebrospinal fluid samples from hospitalized patients and identified a second case of meningitis, with positive results for the agent in the patient's feces and plasma. This screening revealed 5 additional positive fecal samples: 1 from an infant with acute diarrhea and 4 from children who had received transplants. Our findings demonstrate that astrovirus MLB2, which is highly prevalent in feces, can disseminate outside the digestive tract and is an unrecognized cause of central nervous system infection.
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http://dx.doi.org/10.3201/eid2205.151807DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4861523PMC
May 2016
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