An end-to-end assembly of the Aedes aegypti genome

2016/05/16 by Daisy E. Pagete, Olga Dudchenko, Sanjit S. Batra +10 · 1 voice · 3,024 citations
Agricultural and Biological Sciences · Biochemistry, Genetics and Molecular Biology · #Aedes #Aedes aegypti #Biology #Botany #Chromosomal and Genetic Variations #Chromosome #Computational biology #Dengue fever #Gene #Genetics #Genome #Genomics and Phylogenetic Studies #Plant Virus Research Studies #Sequence assembly #Virology #q-bio.GN

paper · pdf · open access · doi:10.1126/science.aal3327

published in Science 356(6333), 92-95 (American Association for the Advancement of Science) · 5 pages, 2 figures. Admin note: withdrawn by arXiv admin because of the use of a pseudonym, in violation of arXiv policy [This does not reflect on the quality of the assembly linked from arXiv:1605.04619v1 , which still can and should be assessed independently]

arxiv published 2016/05/16 · arxiv created 2016/06/13 · arxiv updated 2016/06/13 · openalex publication_date 2017/03/24 · openalex created_date 2025/10/10 · openalex updated_date 2026/08/05

Abstract

We present an end-to-end genome assembly of a female Aedes aegypti mosquito, which spreads viral diseases such as yellow fever, dengue, chikungunya, and Zika to humans. The assembly is based on an earlier genome published in 2007 and improved in 2013. The new assembly has a scaffold N50 of 419Mb, with 96.9% of the ungapped sequence anchored to chromosomes. We used the new assembly to examine the conservation of A. aegypti chromosomes. Our results suggest that synteny is strongly conserved between Ae. aegypti and An. gambiae. Comparison to D. melanogaster highlights the extent to which the identity of entire chromosome arms is preserved across dipterans.

Citations

• On the shortest spanning subtree of a graph and the traveling salesman problem

Cited by

• Coexisting With Humans: Genomic and Behavioral Consequences in a Small and Isolated Bear Population
• Structural Rearrangements and Selection Promote Phenotypic Evolution in Anolis Lizards
• Linking Measures of Inbreeding and Genetic Load to Demographic Histories Across Three Species of Bears
• Chromosome-Level Sex-Specific Genome Assemblies of Onthophagus binodis Provide Insight into Scarab Sex Chromosomes
• Transcriptomic Data Reveal Divergent Paths of Chitinase Evolution Underlying Dietary Convergence in Anteaters and Pangolins
• The Distribution and Dispersal of Large Haploblocks in a Superspecies
• Allopolyploidy expanded gene content but not pangenomic variation in the hexaploid oilseed Camelina sativa
• Deep origins, distinct adaptations and species level status indicated for a glacial relict seal
• Insights into bear evolution from a Pleistocene polar bear genome
• Population genetic structure of wild Malayan tapirs (Tapirus indicus) in Peninsular Malaysia revealed by nine cross-species microsatellite markers
• Molecular Evidence for Relaxed Selection on the Enamel Genes of Toothed Whales (Odontoceti) with Degenerative Enamel Phenotypes
• The sterlet sturgeon genome sequence and the mechanisms of segmental rediploidization
• Genomic signatures of high-altitude adaptation and chromosomal polymorphism in geladas
• Genome Assembly of a Living Fossil, the Atlantic Horseshoe Crab Limulus polyphemus, Reveals Lineage-Specific Whole-Genome Duplications, Transposable Element-Based Centromeres, and a ZW Sex Chromosome System
• Pervasive Conservation of Intron Number and Other Genetic Elements Revealed by a Chromosome-level Genome Assembly of the Hyper-polymorphic Nematode Caenorhabditis brenneri
• Range‐Wide Genomic Analysis Reveals Regional and Meta‐Population Dynamics of Decline and Recovery in the Grey Seal
• Multiple types of genomic variation contribute to adaptive traits in the mustelid subfamily Guloninae
• Genome‐Wide Analysis Successfully Resolves Population Structure Shaped by Recent Divergence in the Endangered Bagrid Catfish Pseudobagrus ichikawai
• Brachiopod genome unveils the evolution of BMP signalling in bilaterian body patterning
• Breath to genome: Whole genome sequencing of large whales from blow sampling
• Comparative Genomics and Phylogenomics of the Mustelinae Lineage (Mustelidae, Carnivora)
• The architecture of resilience: a genome assembly of Myrothamnus flabellifolia sheds light on desiccation tolerance and sex determination
• Bryophytes hold a larger gene family space than vascular plants
• Microsynteny Analysis Clarifies the Early Diversification of Cypriniform Fishes
• Ancient hybridization underlies tuberization and radiation of the potato lineage
• Evidence for evolution of a new sex chromosome within the haploid‐dominant Marchantiales plant lineage
• Evolutionary origin of genomic structural variations in domestic yaks
• Gene and genome duplications have contrasting impacts on biosynthetic and flower developmental pathways in California poppy
• Chromosome-length genome assembly of the stone marten (Martes foina, Mustelidae): A new view on one of the cornerstones in carnivore cytogenetics
• Chromosome-Level Assemblies of Three Candidatus Liberibacter solanacearum Vectors: Dyspersa apicalis (Förster, 1848), Dyspersa pallida (Burckhardt, 1986), and Trioza urticae (Linnaeus, 1758) (Hemiptera: Psylloidea)
• Chromosome-level reference genome for the Jonah crab, Cancer borealis
• Structural variation drives rhizome innovation and adaptive divergence in sister Medicago species
• Pressure-tolerant Evolution in Rhodopsin of Deep-diving Whales
• Sex without crossovers mimics clonal reproduction in the holocentric plant Rhynchospora tenuis
• Extensive Recombination Suppression and Genetic Degeneration of a Young ZW Sex Chromosome System in Halfbeak Fish
• Genome Sequence and Analysis ofNicotiana benthamiana, the Model Plant for Interactions between Organisms
• High‐quality genome of elite peanut cultivar ZH05 reveals subgenome asymmetry, pan‐genome diversity, and breeding insights
• Evolutionary genomic basis of mimicry diversity of Epicopeiidae moths
• Ancient but dynamic: structural expansion, massive gene duplication, and transposable element colonization in a supergene controlling ant social organization
• A holocentric pangenome links karyotype evolution to meiotic recombination
• Chromosomal‐scale genome assembly of Dendrobium tangerinum provides new insights into orchid genome resources
• Transposons drove the evolution of a male sex-determining gene from a female gene with deep introgression across cichlids
• Chromosome-Level Genome Assembly and Annotation of the Amur Rat Snake Elaphe schrenckii
• The genome of Eleocharis vivipara elucidates the genetics of C3–C4 photosynthetic plasticity and karyotype evolution in the Cyperaceae
• Genomic underpinnings of floral scent and ecological adaptation of the endangered Orchidantha insularis
• Chromosome‐scale assembly of Salix integra reveals a conserved sex‐determination mechanism in 15ZW clade I willows
• Sequential origin of an alternative colony founding strategy driven by two supergenes in Temnothorax ants
• That's So Last Season: Unraveling the Genomic Consequences of Fur Farming in Arctic Foxes ( Vulpes lagopus )
• Robust Seriation and Applications to Cancer Genomics
• A Shift to Metapopulation Genetic Management for Persistence of a Species Threatened by Fragmentation: The Case of an Endangered Australian Freshwater Fish
• A Genomic Perspective on the Evolutionary Diversification of Turtles
• Evaluation of improved separator material in large silver zinc cells. Final report
• The Sensory Shark: High-quality Morphological, Genomic and Transcriptomic Data for the Small-spotted Catshark Scyliorhinus Canicula Reveal the Molecular Bases of Sensory Organ Evolution in Jawed Vertebrates
• Pangenome analysis provides insight into the evolution of the orange subfamily and a key gene for citric acid accumulation in citrus fruits
• Quantifying the Influence of Genetic Context on Duplicated Mammalian Genes
• Genomics of Sable ( Martes zibellina) × Pine Marten ( Martes martes ) Hybridization
• Resolving the Stasis-Dynamism Paradox: Genome Evolution in Tree Ferns
• Adaptive radiation and social evolution of the ants
• Uncovering the Genetic Basis of Heterodichogamy in Pterocarya and Cyclocarya Using a Low-Input Pan-Genomic Approach
• The genome of the Australian water dragon (Intellagama lesueurii), an agamid model for urban adaptation
• Differential Conservation and Loss of CR1 Retrotransposons in Squamates Reveals Lineage-Specific Genome Dynamics across Reptiles
• The chromosome‐level genome of Hemiboea subcapitata provides new insights into karst adaptation
• Chromosome-level genome assembly of the Vermilion Snapper (Rhomboplites aurorubens)
• Daya Cerna Lemak Pakan pada Avam Broiler setelah Pemberian Perasan Buah Pare (Momordica charantia L.)
• Elevated retrocopy burden and sloth-specific expansions illuminate mammalian genome evolution
• Chromosome‐level genome of the green odorous frog ( Odorrana margaretae ) provides insights into the evolution of transposable elements and olfaction‐related gene families in frogs
• Chromosome-Scale Reference Genome Assemblies for Two Anoplophora Longhorned Beetle Species (Coleoptera: Cerambycidae)
• Pan-genome analysis of 33 genetically diverse rice accessions reveals hidden genomic variations
• Genomic insights into chromosomal fusion and its evolutionary implications for zokors
• Multi‐omics analyses shed lights on the evolution and fruit development of Chinese raspberries ( Rubus spp.)
• Chromosome‐level genome assembly and resequencing reveal the genomic basis of two ornamental traits in White Cloud Mountain minnow ( Tanichthys albonubes )
• A chromosome-level Mitragyna parvifolia genome unveils spirooxindole alkaloid diversification and mitraphylline biosynthesis
• Genome and Tissue‐Specific Transcriptome of the Tropical Milkweed ( Asclepias curassavica )
• Retracted and Replaced: Telomere-to-telomere genome and resequencing of 254 individuals reveal evolution, genomic footprints in Asian icefish, Protosalanx chinensis
• The gold-ringed octopus (Amphioctopus fangsiao) genome and cerebral single-nucleus transcriptomes provide insights into the evolution of karyotype and neural novelties
• Cultural transmission and genomic co-divergence in the willow tit across the Palearctic
• Genomic architecture and evolution of heterostyly: new insights from Cordia subcordata (Boraginaceae)
• A Chromosome-Level Reference Assembly and Annotation for the White-Faced Plover ( Charadrius dealbatus ) Genome
• A comprehensive omics resource and genetic tools for genetic research and precision breeding of Cucumis melo ssp. agrestis
• The telomere-to-telomere (T2T) genome provides insights into the evolution of specialized centromere sequences in sandalwood
• Assembling genomes of non‐model plants: A case study with evolutionary insights from Ranunculus (Ranunculaceae)
• Gene family rearrangements and transcriptional priming drive the evolution of vegetative desiccation tolerance in Selaginella
• Genomics of sable ( Martes zibellina) × pine marten ( Martes martes ) hybridization
• Efficient assembly of plant genomes: A case study with evolutionary implications in Ranunculus (Ranunculaceae)
• Microhaplotype Methods Enable Relationship Inference in a Bottlenecked Mammalian Species
• Pan-Genome Analysis Reveals Local Adaptation to Climate Driven by Introgression in Oak Species
• Genomic insights into drought adaptation of the forage shrub Caragana korshinskii (Fabaceae) widely planted in drylands
• A Ball Python Colour Morph Implicates MC1R in Melanophore–Xanthophore Distribution and Pattern Formation
• The chromosome-level genome assembly of the red swamp crayfish Procambarus clarkii
• Population genomics highlights structural variations in local adaptation to saline coastal environments in woolly grape
• Modified meiosis in the tardigrade Hypsibius exemplaris maintains heterozygosity across the genome
• Effective Purging and Conservation of Heterozygous Regions During Independent Evolution to High‐Level Inbreeding in Wild Paradise Fishes
• The I gene defines a dynamic NLR cluster conferring broad potyvirus resistance in common bean
• Modified meiosis in the tardigrade Hypsibius exemplaris maintains heterozygosity across the genome
• Transposable Element-Mediated Cis-Regulation Drives the Evolution of dmrt1 as a Candidate Master Sex-Determining Gene in Black Carp
• The telomere-to-telomere (T2T) genome of Peucedanum praeruptorum Dunn provides insights into the genome evolution and coumarin biosynthesis
• Living on the Rocks: Genomic Analysis of Limestone Langurs Provides Novel Insights into the Adaptive Evolution in Extreme Karst Environments
• Unraveling genome- and immunome-wide genetic diversity in modern and historical Jaguars
• Origin and de novo domestication of sweet orange
• Chromosome-Level Assembly and Annotation of the Grey Reef Shark (Carcharhinus amblyrhynchos) Genome
• Chromosome-level genome assembly of the sand martin (Riparia riparia)
• Haplotype-resolved telomere-to-telomere reference genome of sweet cherry 'Tieton’ v3.0 characterized the large fragment deletion associated with yellow-skinned variety
• The telomere-to-telomere gap-free reference genome and taxonomic reassessment of Siniperca roulei
• The telomere-to-telomere gapless genome of grass carp provides insights for genetic improvement
• Three-dimensional genome architecture persists in a 52,000-year-old woolly mammoth skin sample
• Telomere-to-telomere genome of common bean (Phaseolus vulgaris L., YP4)
• Chromosomal fusions reshape gene expression and environmental responses in Corbicula Clams
• A Chromosome-scale Genome Assembly of Meloidogyne hapla Reveals Localized Recombination Hotspots Enriched with Effector Proteins
• Evolution and genetic adaptation of fishes to the deep sea
• A chromosome-level genome assembly of the Chinese herring ( Ilisha elongata ) uncovered its population dynamics and genes related to lipid metabolism
• Palaeoproteomic identification of a whale bone tool from Bronze Age Heiloo, the Netherlands
• Population genomics of Vitis pseudoreticulata reveals the genetic basis of fungal resistance in grapevine
• Genomic and transcriptomic analyses of Heteropoda venatoria reveal the expansion of P450 family for starvation resistance in spiders
• The telomere-to-telomere genome of flowering cherry (Prunus campanulata) reveals genomic evolution of the subgenus Cerasus
• Evolution of 3D Chromatin Folding
• Enhancing inbreeding estimation and global conservation insights through chromosome-level assemblies of the Chinese and Malayan pangolin
• Grapevine pangenome facilitates trait genetics and genomic breeding
• Unlocking plant genetics with telomere-to-telomere genome assemblies
• An improved chromosome-level genome assembly of perennial ryegrass (Lolium perenne L.)
• A high-quality chromosomal genome assembly of the sea cucumber Chiridota heheva and its hydrothermal adaptation
• Haplotype-resolved assemblies provide insights into genomic makeup of the oldest grapevine cultivar (Munage) in China
• YaHS: yet another Hi-C scaffolding tool
• Telomere-to-telomere African wild rice (Oryza longistaminata) reference genome reveals segmental and structural variation
• Telomere-to-telomere chromosome-scale genome assemblies of black and golden koi carp variants support construction of an ancient karyotype of Cypriniformes
• A new subgenome of the Camelina genus reveals genome dominance is controlled by chromosomal proximity
• Genomic analyses reveal the stepwise domestication and genetic mechanism of curd biogenesis in cauliflower
• Telomere-to-telomere genome assembly of yellow-fruited allotetraploid American ginseng ( Panax quinquefolius L . ) provides insights into flavonoid biosynthesis
• WITHDRAWN: ChromPhaser: A HiFi Read Phasing Framework Integrating SNPmers and Hi-C Data
• Telomere to telomere flax (Linum usitatissimum L.) genome assembly unlocks insights beyond fatty acid metabolism pathways
• Chromosome-level genome assembly of the small snakehead ( Channa asiatica ) provides insights into the genetic basis for its pelvic fin loss
• Pangenomics and single-cell transcriptomics uncover the genetic basis of continuous bearing trait in grapevine
• Complex Genomic Structural Variation Underlies Climate Adaptation across Eucalyptus species
• Novel chromosome-length genome assemblies of three distinct subspecies of pine marten, sable, and yellow-throated marten (genus Martes , family Mustelidae)
• De novo genome assembly, inversion detection, and worldwide adaptation on the invasive species Styela plicata
• Construction of the super pan-genome for the genus Actinidia reveals structural variations linked to phenotypic diversity
• A chromosome-level genome assembly of the snow leopard, Panthera uncia
• Deep origins, distinct adaptations, and species-level status indicated for a glacial relict seal
• Haplotype-resolved T2T gap-free genomes of the winegrape cultivar ‘Cabernet Sauvignon’
• T2T Gap-free Genome Assembly of Gp03, a Soybean Cultivar with High Genetic Transformation Efficiency
• A genome assembly for a textbook mammalian study species, the California ground squirrel ( Otospermophilus beecheyi )
• Chromosome-scale genome assembly for Yellow Wood sorrel, Oxalis stricta
• The architecture of resilience: a genome assembly of Myrothamnus flabellifolia sheds light on desiccation tolerance and sex determination
• From macro to micro: De novo genomes of Aedes mosquitoes enable comparative genomics among close and distant relatives
• Chromosome-scale assemblies of three Ormosia species: repetitive sequences distribution and structural rearrangement
• Chromosome-level genome assemblies of five Sinocyclocheilus species
• Telomere-to-telomere genome assembly of Electrophorus electricus provides insights into the evolution of electric eels
• Deciphering the Sequence Basis and Application of Transcriptional Initiation Regulation in Plant Genomes Through Deep Learning
• A chromosome-level reference genome facilitates the discovery of clubroot-resistant gene Crr5 in Chinese cabbage
• Hidden Hamiltonian Cycle Recovery via Linear Programming
• Moderate introgression in a single individual genome is sufficient to mislead phylogenomic inference of Triplophysa
• Parameterizing Pantherinae: De Novo Mutation Rate Estimates from Panthera and Neofelis Pedigrees
• Telomere-to-telomere, gap-free genome of mung bean ( Vigna radiata ) provides insights into domestication under structural variation
• The mixed auto‐/allooctoploid genome of Japanese knotweed (Reynoutria japonica) provides insights into its polyploid origin and invasiveness
• Phased T2T genome assemblies facilitate the mining of disease-resistance genes in Vitis davidii
• Long reads: their purpose and place
• Origin and stepwise evolution of vertebrate lungs
• A high-quality assembly revealing the PMEL gene for the unique plumage phenotype in Liancheng ducks
• Chromosome-level echidna genome illuminates evolution of multiple sex chromosome system in monotremes
• Chromosome-level genome assembly of the king horseshoe bat (Rhinolophus rex) provides insights into its conservation status and chromosomal evolution of Rhinolophus
• De novo assembly and characterization of a highly degenerated ZW sex chromosome in the fish Megaleporinus macrocephalus
• Genus-Wide Characterization of Bumblebee Genomes Provides Insights into Their Evolution and Variation in Ecological and Behavioral Traits
• Genome and tissue-specific transcriptome of the tropical milkweed ( Asclepias curassavica )
• An unusually large genome from an unusually large stonefly: A chromosome-length genome assembly for the giant salmonfly, Pteronarcys californica (Plecoptera: Pteronarcyidae)
• High quality genome assembly and annotation (v1) of the eukaryotic terrestrial microalga Coccomyxa viridis SAG 216-4
• A reference genome of Commelinales provides insights into the commelinids evolution and global spread of water hyacinth (Pontederia crassipes)
• Insight into the adaptive role of arachnid genome-wide duplication through chromosome-level genome assembly of the Western black widow spider
• The whole-genome assembly of an endangered Salicaceae species: Chosenia arbutifolia (Pall.) A. Skv
• Inference of evolution of vertebrate genomes and chromosomes from genomic and cytogenetic analyses using amphibians
• Chromosome-length genome assembly and structural variations of the primal Basenji dog (Canis lupus familiaris) genome
• The Cathaya argyrophylla Genome Reveals the Evolutionary Trade-offs of a Living Fossil
• The Cycas genome and the early evolution of seed plants
• Near-chromosomal de novo assembly of Bengal tiger genome reveals genetic hallmarks of apex predation
• Genetics and Evolution of Mammalian Coat Pigmentation
• Genome of an iconic Australian bird: High‐quality assembly and linkage map of the superb fairy‐wren ( Malurus cyaneus )
• The Diversity, Structure, and Function of Heritable Adaptive Immunity Sequences in the Aedes aegypti Genome. [europepmc]
• Vector biology meets disease control: using basic research to fight vector-borne diseases. [europepmc]
• Chromosome-level reference genome and alternative splicing atlas of moso bamboo (Phyllostachys edulis). [europepmc]
• Improved reference genome of Aedes aegypti informs arbovirus vector control. [europepmc]
• A chromosome-scale genome assembly of cucumber (Cucumis sativus L.). [europepmc]
• Integrating Hi-C links with assembly graphs for chromosome-scale assembly. [europepmc]
• RaGOO: fast and accurate reference-guided scaffolding of draft genomes. [europepmc]
• Long walk to genomics: History and current approaches to genome sequencing and assembly. [europepmc]
• Eight high-quality genomes reveal pan-genome architecture and ecotype differentiation of Brassica napus. [europepmc]
• Development of a confinable gene drive system in the human disease vector Aedes aegypti . [europepmc]
• Chromatin Organization in Early Land Plants Reveals an Ancestral Association between H3K27me3, Transposons, and Constitutive Heterochromatin. [europepmc]
• The sterlet sturgeon genome sequence and the mechanisms of segmental rediploidization. [europepmc]
• Genome assembly of wild tea tree DASZ reveals pedigree and selection history of tea varieties. [europepmc]
• Construction of a chromosome-scale long-read reference genome assembly for potato. [europepmc]
• Chromosome-scale, haplotype-resolved assembly of human genomes. [europepmc]
• Fully phased human genome assembly without parental data using single-cell strand sequencing and long reads. [europepmc]
• The Taxus genome provides insights into paclitaxel biosynthesis. [europepmc]
• Haplotype-resolved genome assembly provides insights into evolutionary history of the tea plant Camellia sinensis. [europepmc]
• InsectBase 2.0: a comprehensive gene resource for insects. [europepmc]
• Deeply conserved synteny and the evolution of metazoan chromosomes. [europepmc]
• Non-cell-autonomous disruption of nuclear architecture as a potential cause of COVID-19-induced anosmia. [europepmc]
• Genome evolution and diversity of wild and cultivated potatoes. [europepmc]
• A super pan-genomic landscape of rice. [europepmc]
• Telomere-to-telomere assembly of diploid chromosomes with Verkko. [europepmc]
• Integrating gene annotation with orthology inference at scale. [europepmc]

Discussions

• New #Aedes genome N50=419Mb 96.9% chromosome-mapped from #TAGC "we choose to share this assembly ... without delay" http://arxiv.org/abs/1605.04619 [bsky, 0 points, 0 comments]

Related

• From macro to micro: De novo genomes of Aedes mosquitoes enable comparative genomics among close and distant relatives
• Two chromosome-scale genomes of wild Aedes aegypti aegypti mosquitoes from North America and South-East Asia
• Chromosomal Inversions and Their Potential Impact on the Evolution of Arboviral Vector Aedes aegypti
• SHARCGS, a fast and highly accurate short-read assembly algorithm for de novo genomic sequencing
• ERGA-BGE Genomes of Culex laticinctus, Culex modestus, Culex perexiguus, and Culex theileri: Unveiling the Genomes of the Key Vectors of West Nile Virus in the Mediterranean Basin.