Ag Data Commons
Browse

Genome sequencing of Curculio caryae adult female principal pseudohaplotype

dataset
posted on 2025-08-07, 21:28 authored by LINDSEY PERKINLINDSEY PERKIN, ZACHARY COHENZACHARY COHEN, SHEINA SIMSHEINA SIM, Scott GeibScott Geib, Anna ChildersAnna Childers, Tim Smith, J. Spencer Johnston, Perot saelaoPerot saelao, Charles P-C. Suh
<p dir="ltr">The pecan weevil, <i>Curculio caryae </i>(Horn), is an obligate feeder of pecan and native hickory throughout North America. Subsequently it is a significant agricultural pest in commercial pecan orchards. In this study, we present a reference quality genome using deep-coverage, ~50x PacBio HiFi genome sequence reads, and chromatic confirmation, Hi-C, scaffolding. The final genome assembly is approximately 2.1 Gb, which was confirmed with flow cytometry. The primary genome scaffolds have an N50 of 132 Mb and a BUSCO completeness of 99.1% [S:97.5%, D:1.6%]. Furthermore, we employed PacBio long-read RNA, Iso-seq, for <i>de novo </i>annotation, followed by InterProscan to identify approximately 16,000 protein coding genes. Repeat content is extensive, contributing to >75% of the total genome. This data set provides a valuable resource for use in comparative genomics and evolutionary studies for an economically impactful group of insect pests that currently lack genomic resources.</p>

Funding

Texas Pecan Board: 58-3091-0-019

USDA-ARS: 3091-22000-038-000D

USDA-ARS: 2040-22430-028-000-D

History

Data contact name

Perkin, Lindsey, C.

Data contact email

lindsey.perkin@usda.gov

Publisher

NCBI

Temporal Extent Start Date

2020-09-05

Temporal Extent End Date

2023-12-31

Theme

  • Non-geospatial

ISO Topic Category

  • biota

Ag Data Commons Group

  • Insects - i5K

National Agricultural Library Thesaurus terms

Curculio caryae; males; females; head; pecans; indigenous species; Carya; North America; orchards; nucleotide sequences; genome assembly; flow cytometry; RNA; genes; genomics; insect pests

OMB Bureau Code

  • 005:18 - Agricultural Research Service

OMB Program Code

  • 005:040 - National Research

ARS National Program Number

  • 304

ARIS Log Number

427165

Pending citation

  • No

Public Access Level

  • Public

Usage metrics

    Licence

    Exports

    RefWorks
    BibTeX
    Ref. manager
    Endnote
    DataCite
    NLM
    DC