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Accession: PRJNA661545 ID: 661545

Culex quinquefasciatus JHB Genome sequencing and assembly

See Genome Information for Culex quinquefasciatus
Culex quinquefasciatus is a major vector of West Nile virus, which is now the leading cause of mosquito-borne disease in the continental US. The JHB strain of Culex quinquefasciatus, the strain from which previous genome assemblies were derived, maintained high heterozygosity, which presented a challenge to obtaining a high-quality reference assembly. In this project we obtained long Oxford Nanopore (ONT) sequences from F1 male siblings and separated them into paternal and maternal reads by TrioCanu according to paternal-specific and maternal-specific k-mers identified from the paternal and maternal Illumina reads (F0 father and mother, ~100x coverage each). All paternal-specific reads plus unseparated reads were used to obtain a paternal assembly by Canu and then polished using the F0 Illumina reads by Pilon. The assembly was further scaffolded using a Bionano optical map and HiC.
AccessionPRJNA661545
TypeUmbrella project
OrganismCulex quinquefasciatus[Taxonomy ID: 7176]
Eukaryota; Metazoa; Ecdysozoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Endopterygota; Diptera; Nematocera; Culicoidea; Culicidae; Culicinae; Culicini; Culex; Culex; Culex quinquefasciatus
Grants
  • "Mechanism and application of male determination in aedine mosquitoes" (Grant ID R01 AI123338, National Institute of Allergy and Infectious Diseases Extramural Activities)
  • "The male-determining locus of Culex quinquefasciatus" (Grant ID R21 AI154871, National Institute of Allergy and Infectious Diseases Extramural Activities)
SubmissionRegistration date: 4-Sep-2020
None
RelevanceMedical
Project Data:
Resource NameNumber
of Links
Sequence data
Nucleotide (total)27263
WGS master2
Transcript27199
SRA Experiments5
Protein Sequences24518
Publications
PubMed1
PMC1
Other datasets
BioSample6
Assembly2
SRA Data Details
ParameterValue
Data volume, Gbases326
Data volume, Tbytes0.16
This project encompasses the following 3 sub-projects:
Project TypeNumber of Projects
Genome sequencing
Highest level of assembly :
Chromosomes
Scaffolds
Total

2
1
3
BioProject
accession
Assembly
level
OrganismTitle
PRJNA644878 ChromosomesCulex quinquefasciatusCulex quinquefasciatus JHB principal haplotype Genome sequencing and assembly (None)
PRJNA661262 ScaffoldsCulex quinquefasciatusCulex quinquefasciatus alternate haplotype Genome sequencing and assembly (None)
PRJNA684067 ChromosomesCulex quinquefasciatusCulex quinquefasciatus strain:JHB RefSeq Genome sequencing and assembly (NCBI)

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