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, This statement should provide the following information, where applicable:-Accession codes, unique identifiers, or web links for publicly available datasets-A list of figures that have associated raw data-A description of any restrictions on data availability Data availability statement. All raw data have been deposited at NCBI under the following BioProject Accession numbers: PRJNA318737 (Primary Pacific Biosciences data, Hi-C sequencing primary data and processed contact maps, whole-genome sequencing data from a single male (Fig. 4d), and pools of male and females (Fig. 3d), Bionano optical mapping data (Fig. 3c and Fig. 4c), and 10X linked-read sequences, Peer J, vol.6, p.4958, 2018.
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, PRJNA393466 (full-length Pacific Biosciences Iso-Seq transcript sequencing)
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, merge) and have been uploaded to GEO (GEO Record: GSE113256). The Hi-C maps are available via http://aidenlab.org/juicebox. The complete mitochondrial genome is available as Genbank accession MF194022.1, RefSeq accession NC_035159.1. The final genome assembly and annotation are available from the NCBI Assembly Resource under accession GCF_002204515.2. Field-specific reporting Please select the best fit for your research. If you are not sure, read the appropriate sections before making your selection, PRJNA393171 (exome sequencing data Fig. 5e-g). Intermediate results related to the AaegL5 assembly are also available via GitHub
, For a reference copy of the document with all sections, see nature.com/authors/policies/ReportingSummary-flat
, Sample sizes for genome size determination (Fig. 1d) were determined according to the standards of the field (see Hare and Johnston, 2011 PMID 22065429). Samples sizes for FISH were determined according to the standards of the field (see Timoshevskiy et al., 2012 PMID 23007640). Sample sizes for dengue virus competence (Fig. 5b-d and Extended Data Fig. 10a), pyrethroid resistance (Fig. 5e-g) and larval motility Ext. Data Figure 10c) were determined by the limited availability of animals, Sample sizes for genome variability analysis via SNP-chip (Fig. 1c) were determined according to previously published work, 2015.
, Data exclusions None Replication Replication does not apply to the primary results of this paper-it was not feasible to independently resequence/reassemble the genome twice within the scope of the funding available to us
, Randomization Randomization was not performed in this study. Samples were divided into experimental groups based on species, strain or biological phenotype according to the criteria listed in the methods
, Blinding Blinding was not performed for this study. The diversity of sourcing of samples and data precluded centralized collection and blinding of biological material or sequencing data