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Adaptive genomic signatures of globally invasive populations of the yellow fever mosquito Aedes aegypti
<p><strong>* These authors contributed equally: </strong>Alejandro N. Lozada-Chávez, Irma Lozada-Chávez.</p> <h3> </h3> <h1>Supplementary Dataset</h1> <p> </p> <p>This repository contains the <strong> Supplementary Data (from 1 to 12) </strong>cited in our paper "Adaptive genomic signatures of globally invasive populations of the yellow fever mosquito Aedes aegypti" in <em>Nature Ecology and Evolution</em>: <a title="Aedes aegypti domestication." href="https://doi.org/10.1038/s41559-025-02643-5">https://doi.org/10.1038/s41559-025-02643-5</a></p> <p>These datasets are available in the section "Supplementary Information" of our paper, but with the absence of the SD-9 due its large big size (~3Gb after decompressed). Here you can find the complete set of datasets in a single ZIP file:</p> <p><strong>41559_2025_2643_MOESM5_ESM_Supplementary_Data.zip</strong></p> <p> </p> <p><strong>LIST OF DATASETS:</strong></p> <p>1) Supplementary Data 1. SNP statistics for populations through genomic regions (TXT). <br>2) Supplementary Data 2. Sequences of new detected nrEVEs (FASTA). <br>3) Supplementary Data 3. Phylogenetic trees for populations and individuals (NEWICK). <br>4) Supplementary Data 4. Information for 8,120 hard selective sweeps detected with RAiSD in out-of-Africa populations (TXT). <br>5) Supplementary Data 5. Information for 1,030 SNP outliers detected with PCAdapt within 2,266 genes (VCF format). <br>6) Supplementary Data 6. Matrix with DoS scores for 11,651 orthologous protein-coding genes in AaegL5 and each Ae. aegypti population (TXT). <br>7) Supplementary Data 7. Matrix with MKT scores for 11,651 orthologous protein-coding genes in AaegL5 and each Ae. aegypti population (TXT). <br>8) Supplementary Data 8. Matrix with DoS scores used to estimate relaxed selection (TXT). <br>9) Supplementary Data 9. Matrix with SNPs and genomic coordinates within adaptive protein-coding genes and ncRNAs that are shared or private for out-of-Africa populations against African populations (TXT). <br>10) Supplementary Data 10. Matrix with 483 nonsynonymous SNPs and their allele frequencies for our 40 populations Florida and Colombia (TXT).<br>11) Supplementary Data 11. Genomic coordinates of SNPs in AaegL5 obtained from the literature and VectorBase (TXT). <br>12) Supplementary Data 12. Source data of metrics used to plot Figure 4b (TXT).</p> <p> </p> <p><strong>UPDATES NOTE:</strong></p> <ul> <li><strong>Repository version 3.</strong> Final version of datasets for the accepted manuscript.</li> <li><strong>Repository version 2.</strong> Incomplete datasets: Files as prelimary versions and their content may vary. The SD-10 is not present (matrix with 483 SNPs) was added. The SD-7 is a broken file (cannot be opened).</li> <li><strong>Repository version 1. </strong> Incomplete datasets: Files as prelimary versions and their content may vary. Two final SD files are not present.</li> </ul> <p> </p> <p><strong>CITATION OF THIS REPOSITORY:</strong></p> <p>Lozada-Chávez, A. N., Lozada-Chávez, I., Alfano, N., Palatini, U., Sogliani, D., Elfekih, S., Degefa, T., Sharakhova, M. V., Badolo, A., Patchara, S., Casas-Martinez, M., Carlos, B. C., Carballar-Lejarazú, R., Lambrechts, L., Souza-Neto, J. A., & Bonizzoni, M. (2024). Adaptive genomic signatures of globally invasive populations of the yellow fever mosquito Aedes aegypti [Data set]. Zenodo. https://doi.org/10.5281/zenodo.14948092</p> <p> </p> <p> </p>
Comprehensive characterisation of the genomic insertion site of a transgene in highly repetitive, centromeric region of Anopheles mosquitoes
<p>The availability of the genomic sequence of the malaria mosquito <em>Anopheles</em> <em>gambiae</em> has sparked in recent years the development of transgenic technologies with the potential to be used as novel tools for vector control. These technologies rely on genome editing that confers features able to affect vector capacity. This can be achieved by either reducing the mosquito population or by making mosquitoes refractory to the parasite infection. Although sophisticated molecular techniques such as those based on AttB/AttP site-specific recombination and CRISPR/Cas9 systems can lead to the integration of transgenes in specific sites of the genome, methods that allow semi-random integration are still in use due to their high efficiency; PiggyBac transposon-mediated integrations fall in this category. Characterization of the insertion site of transgenes in transgenic strains generated via PiggyBac integration can be hampered when the transgene is inserted in regions of the genome rich in repetitive sequences. Here we describe a number of techniques that were used to identify the genomic location of the transgene in a repetitive region in the <em>Anopheles gambiae</em> strain Ag(PMB)1 which was initially reported on Chromosome 3R 36D. Whilst Inverse PCR used in previous analysis was unable to distinguish between multiple genomic locations as potential insertion sites of the transgene, here we demonstrate that the use of FISH identifies clearly the integration of the transgene in a poorly annotated centromeric region of Chromosome 2R 19D. This study emphasises the need for accuracy in sequencing data for the genome of organisms of medical importance such as <em>Anopheles </em>mosquitoes. An effort to further improve reference genomes is of paramount importance to support and facilitate vector control interventions based on genome editing.</p>
Genotypes of Aedes aegypti mosquitoes derived from SNP chip and low-coverage whole genome sequencing for platform cross-validation
<p>The mosquito <em>Aedes aegypti </em>is the primary vector of many human arboviruses such as dengue, yellow fever, chikungunya, and Zika, which affect millions of people world-wide. Population genetics studies on this mosquito have been important in understanding its invasion pathways and success as a vector of human disease. The Axiom aegypti1 SNP chip was developed from a sample of geographically diverse <em>Ae. aegypti </em>populations to facilitate genomic studies on this species. Here we evaluate the utility of the Axiom aegypti1 SNP chip for population genetics and compare it with a low-depth shot-gun sequencing approach using mosquitoes from the species' native (Africa) and invasive range (outside Africa). These analyses indicate that the results from the SNP chip are highly reproducible and have a higher sensitivity to capture alternative alleles than a low-coverage whole-genome sequencing approach. Although the SNP chip suffers from ascertainment bias, results from population structure, ancestry, demographic, and phylogenetic analyses using the SNP chip were congruent with those derived from low coverage whole genome sequencing, and consistent with previous reports on Africa and outside Africa populations using microsatellites. More importantly, we identified a subset of SNPs that can be reliably used to generate merged databases, opening the door to combined analyses. We conclude that the Axiom aegypti1 SNP chip is a convenient, more accurate, low-cost alternative to low-depth whole genome sequencing for population genetic studies of <em>Ae. aegypti</em> that do not rely on full allelic frequency spectra. Whole genome sequencing and SNP chip data can be easily merged, extending the usefulness of both approaches. </p>
Genome-wide association analysis identifies naturally segregating genetic variation associated with the rapid evolution of diapause in Aedes albopictus, an invasive vector mosquito.
<p>The raw data for genotype calls, the output files from the genotype calls, the code to replicate the analysis, and the output of the analysis.</p>
Genotypes of Aedes aegypti mosquitoes derived from SNP chip and low-coverage whole genome sequencing for platform cross-validation
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Data from: Extensive genetic diversity among populations of the malaria mosquito Anopheles moucheti revealed by population genomics
Malaria vectors are exposed to intense selective pressures due to large-scale intervention programs that are underway in most African countries. One of the current priorities is therefore to clearly assess the adaptive potential of Anopheline populations, which is critical to understand and anticipate the response mosquitoes can elicit against such adaptive challenges. The development of genomic resources that will empower robust examinations of evolutionary changes in all vectors including currently understudied species is an inevitable step toward this goal. Here we constructed double-digest Restriction Associated DNA (ddRAD) libraries and generated 6461 Single Nucleotide Polymorphisms (SNPs) that we used to explore the population structure and demographic history of wild-caught Anopheles moucheti from Cameroon. The genome-wide distribution of allelic frequencies among samples best fitted that of an old population at equilibrium, characterized by a weak genetic structure and extensive genetic diversity, presumably due to a large long term effective population size. Estimates of FST and Linkage Disequilibrium (LD) across SNPs reveal a very low genetic differentiation throughout the genome and the absence of segregating LD blocks among populations, suggesting an overall lack of local adaptation. Our study provides the first investigation of the genetic structure and diversity in An. moucheti at the genomic scale. We conclude that, despite a weak genetic structure, this species has the potential to challenge current vector control measures and other rapid anthropogenic and environmental changes thanks to its great genetic diversity.
Comparative mitochondrial genome and phylogenetic analysis of malaria mosquitoes Anopheles hyrcanus and Anopheles messeae supplementary files
<p><strong>T</strong><strong><span>able</span></strong><strong> S1.</strong> This study encompassed 105 species, along with their corresponding taxonomy and GenBank registration numbers.</p> <p><strong>Figure S1</strong> Inferred secondary structures of tRNAs in the mt genome of <em>An. </em><em><span>h</span></em><em>yrcanus</em><em> </em><span>(A)</span><em> </em><span>and </span><em>An. </em><em><span>m</span></em><em>esseae</em><em> </em><span>(B)</span>, with corresponding amino acids labeled next to the tRNAs.</p>
Genomic shifts, phenotypic clines and fitness costs associated with cold-tolerance in the Asian tiger mosquito
<p>Climatic variation is a key driver of genetic differentiation and phenotypic traits evolution, and local adaptation to temperature is expected in widespread species. We investigated phenotypic and genomic changes in the native range of the Asian tiger mosquito, <em>Aedes</em> <em>albopictus</em>. We first refine the phylogeographic structure based on genome-wide regions (1,901 double-digest restriction-site associated DNA single nucleotide polymophisms [ddRAD SNPs]) from 41 populations. We then explore the patterns of cold adaptation using phenotypic traits measured in common garden (wing size and cold tolerance) and genotype–temperature associations at targeted candidate regions (51,706 exon-capture SNPs) from nine populations. We confirm the existence of three evolutionary lineages including clades A (Malaysia, Thailand, Cambodia, and Laos), B (China and Okinawa), and C (South Korea and Japan). We identified temperature-associated differentiation in 15 out of 221 candidate regions but none in ddRAD regions, supporting the role of directional selection in detected genes. These include genes involved in lipid metabolism and a circadian clock gene. Most outlier SNPs are differently fixed between clades A and C, whereas clade B has an intermediate pattern. Females are larger at higher latitudes yet produce no more eggs, which might favor the storage of energetic reserves in colder climates. Nondiapausing eggs from temperate populations survive better to cold exposure than those from tropical populations, suggesting they are protected from freezing damages but this cold tolerance has a fitness cost in terms of egg viability. Altogether, our results provide strong evidence for the thermal adaptation of <em>A</em>. <em>albopictus</em> across its wide temperature range.</p>
Data from: Whole genome sequencing reveals absence of recent gene-flow and separate demographic histories for Anopheles punctulatus mosquitoes in Papua New Guinea
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Data from: Extensive genetic diversity among populations of the malaria mosquito Anopheles moucheti revealed by population genomics
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Data from: Composite linkage map and enhanced genome map for Culex pipiens complex mosquitoes
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Genomic shifts, phenotypic clines and fitness costs associated with cold-tolerance in the Asian tiger mosquito
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A linkage-based genome assembly for the mosquito Aedes albopictus and identification of chromosomal regions affecting diapause
<p>The Asian tiger mosquito, Aedes albopictus, is an invasive vector mosquito of substantial public health concern. The large genome size (~1.19-1.28 Gb by cytofluorometric estimates), comprised of ~68% repetitive DNA sequences, has made it difficult to produce a high-quality genome assembly for this species. We constructed a high-density linkage map for Ae. albopictus based on 111,328 informative SNPs obtained by RNAseq. We then performed a linkage-map anchored reassembly of AalbF2, the genome assembly produced by Palatini et al. (2020). Our re-assembled genome sequence, AalbF3, represents several improvements relative to AalbF2. First, the size of the AalbF3 assembly is 1.45 Gb, almost half the size of AalbF2. Furthermore, relative to AalbF2, AalbF3 contains a higher proportion of complete and single-copy BUSCO genes (84.3%) and a higher proportion of aligned RNAseq reads that map concordantly to a single location of the genome (46%). We demonstrate the utility of AalbF3 by using it as reference for a bulk segregant-based comparative genomics analysis which identifies chromosomal regions with clusters of candidate SNPs putatively associated with photoperiodic diapause, a crucial ecological adaptation underpinning the rapid range expansion and climatic adaptation of Ae. albopictus.</p>
Selection and exploitation of prevalent, tandemly repeated genomic targets for improved real-time PCR-based detection of Wuchereria bancrofti and Plasmodium falciparum in mosquitoes
<p><b>Background</b></p> <p>Optimization of polymerase chain reaction (PCR)-based diagnostics requires the careful selection of molecular targets that are both highly repetitive and pathogen-specific. Advances in both next-generation sequencing (NGS) technologies and bioinformatics-based analysis tools are facilitating this selection process, informing target choices and reducing labor. Once developed, such assays provide disease control and elimination programs with an additional set of tools capable of evaluating and monitoring intervention successes. The importance of such tools is heightened as intervention efforts approach their endpoints, as accurate and complete information is an essential component of the informed decision-making process. As global efforts for the control and elimination of both lymphatic filariasis and malaria continue to make significant gains, the benefits of diagnostics with improved analytical and clinical/field-based sensitivities and specificities will become increasingly apparent.</p> <p><b>Methodology/Principal Findings </b></p> <p>Coupling Illumina-based NGS with informatics approaches, we have successfully identified the tandemly repeated elements in both the <i>Wuchereria bancrofti </i>and <i>Plasmodium falciparum </i>genomes of putatively greatest copy number. Utilizing these sequences as quantitative real-time PCR (qPCR)-based targets, we have developed assays capable of exploiting the most abundant tandem repeats for both organisms. For the detection of <i>P. falciparum</i>, analysis and development resulted in an assay with improved analytical and field-based sensitivity vs. an established ribosomal sequence-targeting assay. Surprisingly, analysis of the <i>W. bancrofti </i>genome predicted a ribosomal sequence to be the genome's most abundant tandem repeat. While resulting cycle quantification values comparing a qPCR assay targeting this ribosomal sequence and a commonly targeted repetitive DNA sequence from the literature supported our finding that this ribosomal sequence was the most prevalent tandemly repeated target in the <i>W. bancrofti </i>genome, the resulting assay did not significantly improve detection sensitivity in conjunction with field sample testing. </p> <p><b>Conclusions/Significance </b></p> <p>Examination of pathogen genomes facilitates the development of PCR-based diagnostics targeting the most abundant and specific genomic elements. While in some instances currently available tools may deliver equal or superior performance, systematic analysis of potential targets provides confidence that the selected assays represent the most advantageous options available and that informed assay selection is occurring in the context of a particular study's objectives.</p>
Data from: Genome annotation improvements from cross-phyla proteogenomics and time-of-day differences in malaria mosquito proteins using untargeted quantitative proteomics
The malaria mosquito, Anopheles stephensi, and other mosquitoes modulate their biology to match the time-of-day. In the present work, we used a non-hypothesis driven approach (untargeted proteomics) to identify proteins in mosquito tissue, and then quantified the relative abundance of the identified proteins from An. stephensi bodies. Using these quantified protein levels, we then analyzed the data for proteins that were only detectable at certain times-of-the day, highlighting the need to consider time-of-day in experimental design. Further, we extended our time-of-day analysis to look for proteins which cycle in a rhythmic 24-hour ("circadian") manner, identifying 31 rhythmic proteins. Finally, to maximize the utility of our data, we performed a proteogenomic analysis to improve the genome annotation of An. stephensi. We compare peptides that were detected using mass spectrometry but are 'missing' from the An. stephensi predicted proteome, to reference proteomes from 38 other primarily human disease vector species. We found 239 such peptide matches and reveal that genome annotation can be improved using proteogenomic analysis from taxonomically diverse reference proteomes. Examination of 'missing' peptides revealed reading frame errors, errors in gene-calling, overlapping gene models, and suspected gaps in the genome assembly.
Data from: Identifying insecticide resistance genes in mosquito by combining AFLP genome scan and 454 pyrosequencing
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Data from: Genome annotation improvements from cross-phyla proteogenomics and time-of-day differences in malaria mosquito proteins using untargeted quantitative proteomics
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Data from: "Identification and assessment of single nucleotide polymorphisms (SNPs) between Culex complex mosquitoes." in Genomic Resources Notes Accepted 1 August 2014-30 September 2014
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Selection and exploitation of prevalent, tandemly repeated genomic targets for improved real-time PCR-based detection of Wuchereria bancrofti and Plasmodium falciparum in mosquitoes
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A linkage-based genome assembly for the mosquito Aedes albopictus and identification of chromosomal regions affecting diapause
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