Data from: Haplotype-resolved genome assemblies for the New World screwworm, <i>Cochliomyia hominivorax</i> (Diptera: Calliphoridae), using the trio binning approach
These are supplemental data for producing haplotype-resolved genome assemblies of C. hominivorax using the trio-binning approach. Briefly, a single male progeny from the cross of a Panama line male with a production strain female was sequenced using PacBio HiFi and scaffolded using Hi-C chromatin conformation, while Illumina NextSeq 2000 was used for short read sequencing of both parents to facilitate trio-binning. We produced a linear haploid reference assembly by transferring a copy of the X chromosome and mitochondrial genome to the paternal haplotype. This assembly is comprised of five autosomes, two sex chromosomes, the mitogenome, and 75 unplaced scaffolds spanning 455.6 Mb, which is closer to the predicted size based on flow cytometry (443.8 Mb) than the previous assembly of 534.4 Mb. NCBI’s external Eukaryotic Genome Annotation Pipeline (EGAPx) was used to annotate the protein coding and non-coding genes in the linear haploid reference and the maternal haplotype assembly.This research used resources provided by the SCINet project and/or the AI Center of Excellence of the USDA Agricultural Research Service, ARS project numbers 0201-88888-003-000D and 0201-88888-002-000D.
Resources
10 resources available
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blob.sh
SH -
busco5.sh
SH -
hic_yahs.sh
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hifiadapterfiltFCS.sh
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hifiasm.sh
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yak.sh
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fcs_genome.sh
SH -
Chom_hap2.gff
GFF -
Chom_ref.gff
GFF -
final.dna.phy
PHY
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Complete Metadata
| @type | dcat:Dataset |
|---|---|
| accessLevel | public |
| bureauCode |
[ "005:18", "005:32" ] |
| contactPoint |
{ "fn": "Hickner, Paul, V.", "hasEmail": "mailto:paul.hickner@usda.gov" } |
| description | <p dir="ltr">These are supplemental data for producing haplotype-resolved genome assemblies of <i>C. hominivorax </i>using the trio-binning approach. Briefly, a single male progeny from the cross of a Panama line male with a production strain female was sequenced using PacBio HiFi and scaffolded using Hi-C chromatin conformation, while Illumina NextSeq 2000 was used for short read sequencing of both parents to facilitate trio-binning. We produced a linear haploid reference assembly by transferring a copy of the X chromosome and mitochondrial genome to the paternal haplotype. This assembly is comprised of five autosomes, two sex chromosomes, the mitogenome, and 75 unplaced scaffolds spanning 455.6 Mb, which is closer to the predicted size based on flow cytometry (443.8 Mb) than the previous assembly of 534.4 Mb. NCBI’s external Eukaryotic Genome Annotation Pipeline (EGAPx) was used to annotate the protein coding and non-coding genes in the linear haploid reference and the maternal haplotype assembly.</p><p dir="ltr">This research used resources provided by the SCINet project and/or the AI Center of Excellence of the USDA Agricultural Research Service, ARS project numbers 0201-88888-003-000D and 0201-88888-002-000D.</p> |
| distribution |
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| identifier | 10.15482/USDA.ADC/31071736.v1 |
| keyword |
[ "blow fly", "livestock pest", "myiasis", "obligate parasite", "screwworm", "sterile insect technique" ] |
| license | https://creativecommons.org/publicdomain/zero/1.0/ |
| modified | 2026-07-28 |
| programCode |
[ "005:040" ] |
| publisher |
{ "name": "Agricultural Research Service", "@type": "org:Organization" } |
| temporal | 2025-06-04/2025-06-04 |
| title | Data from: Haplotype-resolved genome assemblies for the New World screwworm, <i>Cochliomyia hominivorax</i> (Diptera: Calliphoridae), using the trio binning approach |
