In-house annotated gene set for the pecan weevil, <i>Curculio caryae</i>

This in-house annotated gene set was created using the following methods. RNA was isolated from the head and thorax segments of one adult male and one adult female pecan weevil using the NucleoMag RNA Kit (Macherey-Nagel, Düren, Germany, 744350.1) according to kit protocols. Isolated RNA was processed into PacBio Kinnex sequencing libraries using the Iso-Seq express 2.0 kit (Pacific Biosciences, Menlo Park, CA, USA 103-071-500) and Kinnex full-length RNA kit (Pacific Biosciences, Menlo Park, CA, USA,103-072-000). The prepared library was bound and sequenced at the USDA-ARS Veterinary Pest Genetics Research Unit in Kerrville, Texas, on two Pacific Biosciences SMRT cell trays with a Revio system (Pacific Biosciences, Menlo Park, CA, USA, 102-202-200) beginning with a 2-h pre-extension followed by a 30-h movie collection time. After sequencing, circular consensus sequences from the PacBio Sequel Revio subreads were obtained using the SMRTLink v13.0 software. Reads were subsequently mapped to the repeat-masked genome assembly using minimap2 with arguments for spliced nucleotide sequences (-ax splice:hq) to generate sam mapping files. These were then compressed into bam files using samtools view -bS and used as input for gene model prediction with the Braker version 3.0.8 program (https://github.com/Gaius-Augustus/BRAKER), generating 72,879 gene models. These gene models and amino acid protein predictions were further curated and annotated with gene ontologies and protein domains using InterProScan-5.73-104.0 with PANTHER-19.0 and Pfam-37.2 databases (https://github.com/ebi-pf-team/interproscan), resulting in 19,508 InterProScan results.

                                            [
  "005:18"
]
                                        

                                            {
  "fn": "Perkin, Lindsey, C.",
  "hasEmail": "mailto:lindsey.perkin@usda.gov"
}
                                        

                                            [
  {
    "@type": "dcat:Distribution",
    "title": "curated_genes.fasta",
    "format": "fasta",
    "mediaType": "text/plain",
    "downloadURL": "https://ndownloader.figshare.com/files/58362277"
  }
]
                                        

                                            [
  "gene annotation",
  "pecan weevil"
]
                                        

                                            [
  "005:040"
]
                                        

                                            {
  "name": "Agricultural Research Service",
  "@type": "org:Organization"
}