A CRISPR-Cas9 gene drive system targeting female reproduction in the malaria mosquito vector Anopheles gambiae.

Gene drive systems that enable super-Mendelian inheritance of a transgene have the potential to modify insect populations over a timeframe of a few years. We describe CRISPR-Cas9 endonuclease constructs that function as gene drive systems in Anopheles gambiae, the main vector for malaria. We identified three genes (AGAP005958, AGAP011377 and AGAP007280) that confer a recessive female-sterility phenotype upon disruption, and inserted into each locus CRISPR-Cas9 gene drive constructs designed to target and edit each gene. For each targeted locus we observed a strong gene drive at the molecular level, with transmission rates to progeny of 91.4 to 99.6%. Population modeling and cage experiments indicate that a CRISPR-Cas9 construct targeting one of these loci, AGAP007280, meets the minimum requirement for a gene drive targeting female reproduction in an insect population. These findings could expedite the development of gene drives to suppress mosquito populations to levels that do not support malaria transmission

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 amongst 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

Standardized metadata for human pathogen/vector genomic sequences

High throughput sequencing has accelerated the determination of genome sequences for thousands of human infectious disease pathogens and dozens of their vectors. The scale and scope of these data are enabling genotype-phenotype association studies to identify genetic determinants of pathogen virulence and drug/insecticide resistance, and phylogenetic studies to track the origin and spread of disease outbreaks. To maximize the utility of genomic sequences for these purposes, it is essential that metadata about the pathogen/vector isolate characteristics be collected and made available in organized, clear, and consistent formats. Here we report the development of the GSCID/BRC Project and Sample Application Standard, developed by representatives of the Genome Sequencing Centers for Infectious Diseases (GSCIDs), the Bioinformatics Resource Centers (BRCs) for Infectious Diseases, and the U.S. National Institute of Allergy and Infectious Diseases (NIAID), part of the National Institutes of Health (NIH), informed by interactions with numerous collaborating scientists. It includes mapping to terms from other data standards initiatives, including the Genomic Standards Consortium's minimal information (MIxS) and NCBI's BioSample/BioProjects checklists and the Ontology for Biomedical Investigations (OBI). The standard includes data fields about characteristics of the organism or environmental source of the specimen, spatial-temporal information about the specimen isolation event, phenotypic characteristics of the pathogen/vector isolated, and project leadership and support. By modeling metadata fields into an ontology-based semantic framework and reusing existing ontologies and minimum information checklists, the application standard can be extended to support additional project-specific data fields and integrated with other data represented with comparable standards. The use of this metadata standard by all ongoing and future GSCID sequencing projects will provide a consistent representation of these data in the BRC resources and other repositories that leverage these data, allowing investigators to identify relevant genomic sequences and perform comparative genomics analyses that are both statistically meaningful and biologically relevant

Transcriptomic analysis of insecticide resistance in the lymphatic filariasis vector Culex quinquefasciatus

Culex quinquefasciatus plays an important role in transmission of vector-borne diseases of public health importance, including lymphatic filariasis (LF), as well as many arboviral diseases. Currently, efforts to tackle C. quinquefasciatus vectored diseases are based on either mass drug administration (MDA) for LF, or insecticide-based interventions. Widespread and intensive insecticide usage has resulted in increased resistance in mosquito vectors, including C. quinquefasciatus. Herein, the transcriptome profile of Ugandan bendiocarb-resistant C. quinquefasciatus was explored to identify candidate genes associated with insecticide resistance. High levels of insecticide resistance were observed for five out of six insecticides tested, with the lowest mortality (0.97%) reported to permethrin, while for DDT, lambdacyhalothrin, bendiocarb and deltamethrin the mortality rate ranged from 1.63–3.29%. Resistance to bendiocarb in exposed mosquitoes was marked, with 2.04% mortality following 1 h exposure and 58.02% after 4 h. Genotyping of the G119S Ace-1 target site mutation detected a highly significant association (p 8-fold increase vs unexposed controls). These results provide evidence that bendiocarb resistance in Ugandan C. quinquefasciatus is mediated by both target-site mechanisms and over-expression of detoxification enzymes

Corrigendum: Whole genome analysis of a schistosomiasis-transmitting freshwater snail

This corrects the article DOI: 10.1038/ncomms15451

MIReAD, a minimum information standard for reporting arthropod abundance data

Arthropods play a dominant role in natural and human-modified terrestrial ecosystem dynamics. Spatially-explicit arthropod population time-series data are crucial for statistical or mathematical models of these dynamics and assessment of their veterinary, medical, agricultural, and ecological impacts. Such data have been collected world-wide for over a century, but remain scattered and largely inaccessible. In particular, with the ever-present and growing threat of arthropod pests and vectors of infectious diseases, there are numerous historical and ongoing surveillance efforts, but the data are not reported in consistent formats and typically lack sufficient metadata to make reuse and re-analysis possible. Here, we present the first-ever minimum information standard for arthropod abundance, Minimum Information for Reusable Arthropod Abundance Data (MIReAD). Developed with broad stakeholder collaboration, it balances sufficiency for reuse with the practicality of preparing the data for submission. It is designed to optimize data (re)usability from the “FAIR,” (Findable, Accessible, Interoperable, and Reusable) principles of public data archiving (PDA). This standard will facilitate data unification across research initiatives and communities dedicated to surveillance for detection and control of vector-borne diseases and pests

A sensory appendage protein protects malaria vectors from pyrethroids

Pyrethroid-impregnated bednets have driven significant reductions in malaria morbidity and mortality in Africa since the beginning of the century 1. The intense selection pressure exerted by bednets has precipitated widespread and escalating pyrethroid resistance in African Anopheles populations, threatening to reverse gains made by malaria control 2. Here we show that a leg-enriched sensory appendage protein, SAP2, confers pyrethroid resistance in Anopheles gambiae. SAP2 expression is elevated in insecticide-resistant populations and is further induced upon mosquito contact with pyrethroids. SAP2 silencing fully restores mosquito mortality, whilst its overexpression results in increased resistance, likely due to the high-affinity SAP2 binding to pyrethroid insecticides. Mining of genome sequence data reveals a selective sweep near the SAP2 locus in three West African countries, with the observed increase in haplotype associated SNPs mirroring increasing resistance reported in Burkina Faso. Our study identifies a new insecticide resistance mechanism that is likely highly relevant to malaria control efforts