Abstract
The pecan weevil, Curculio caryae (Horn), is an obligate feeder of pecan and native hickory trees (genus Carya) throughout North America. Subsequently it is a significant agricultural pest in pecan orchards. In this study, we present a reference quality genome using deep-coverage, ~40x PacBio HiFi genome sequence reads, and chromatin confirmation, Hi-C, scaffolding. The final genome assembly is approximately 2.2 Gb, which was confirmed by flow cytometry. The primary genome scaffolds have an N50 of 132 Mb and a BUSCO completeness of 95.4% [S:94.3%, D:1.1%]. Furthermore, we employed PacBio long-read RNA, Iso-seq, for de novo gene annotation, in conjunction with InterProscan to identify approximately 19,000 protein coding genes. Repeat content is extensive, contributing at least >80% of the total genome. This data set provides a valuable resource for comparative genomics and evolutionary studies of an economically impactful group of insect pests that currently lack extensive genomic resources.
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Data availability
The raw sequencing data, genome assembly, transcripts, and mitochondrial genome of Curculio caryae have been deposited at the National Center Biotechnology under project number PRJNA813156 and at the National Ag Library https://hdl.handle.net/10779/USDA.ADC.29329910. The custom annotations can be found at the National Ag Library https://doi.org/10.15482/USDA.ADC/30234490.
Code availability
Data processing was executed using published programs and default parameters unless otherwise specified in the Methods section. No custom code was used for these analyses.
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Acknowledgements
This work was partially supported through funds from the Texas Pecan Board (Agreement # 58-3091-0-019) and the U.S. Department of Agriculture, Agricultural Research Service (USDA-ARS, CRIS Projects 3091-22000-038-000D and 2040-22430-028-000-D). The genome assembly was generated as part of the USDA-ARS Ag100Pest Initiative. The authors thank members of the USDA-ARS Ag100Pest Team for sequencing and analysis support. This research used resources provided by the SCINet project of the USDA-ARS project number 0500-00093-001-00-D. Mention of trade names or commercial products in this publication is solely for the purpose of providing specific information and does not imply recommendation or endorsement by the U.S. Department of Agriculture. USDA is an equal opportunity provider and employer. Special thanks to Mike Barry (Comanche Co., TX, Extension Agent), and Patrick Dudley (Texas Department of Agriculture) for their assistance in setting up Circle traps. The US Department of Agriculture, Agricultural Research Service is an equal opportunity/affirmative action employer, and all agency services are available without discrimination.
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Designed research: Lindsey C. Perkin, Zachary P. Cohen, and Charles P.-C. Suh. Collection of samples: Lindsey C Perkin and Charles P.-C. Suh. Genome assembly and data analysis: Zachary P. Cohen, Sheina B. Sims, Scott M. Geib. Flow Cytometry: J. Spencer Johnston. Resources: Timothy P.L. Smith and Perot Saelao. Manuscript writing: Lindsey C. Perkin and Zachary P. Cohen. All authors provided suggestions for the final manuscript.
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Perkin, L.C., Cohen, Z.P., Sim, S.B. et al. A chromosome level reference genome for the pecan weevil, Curculio caryae. Sci Data (2026). https://doi.org/10.1038/s41597-026-07030-8
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DOI: https://doi.org/10.1038/s41597-026-07030-8
