De novo assembly of a chromosome-scale reference genome for the northern flicker Colaptes auratus

Jack P. Hruska, Joseph D. Manthey

Research output: Contribution to journalArticlepeer-review

Abstract

The northern flicker, Colaptes auratus, is a widely distributed North American woodpecker and a long-standing focal species for the study of ecology, behavior, phenotypic differentiation, and hybridization. We present here a highly contiguous de novo genome assembly of C. auratus, the first such assembly for the species and the first published chromosome-level assembly for woodpeckers (Picidae). The assembly was generated using a combination of short-read Chromium 10× and long-read PacBio sequencing, and further scaffolded with chromatin conformation capture (Hi-C) reads. The resulting genome assembly is 1.378 Gb in size, with a scaffold N50 of 11 and a scaffold L50 of 43.948 Mb. This assembly contains 87.4-91.7% of genes present across four sets of universal single-copy orthologs found in tetra-pods and birds. We annotated the assembly both for genes and repetitive content, identifying 18,745 genes and a prevalence of ∼28.0% repetitive elements. Lastly, we used fourfold degenerate sites from neutrally evolving genes to estimate a mutation rate for C. auratus, which we estimated to be 4.007 × 10-9 substitutions/site/year, about 1.5× times faster than an earlier mutation rate estimate of the family. The highly contiguous assembly and annotations we report will serve as a resource for future studies on the genomics of C. auratus and comparative evolution of woodpeckers.

Original languageEnglish
Article numberjkaa026
JournalG3: Genes, Genomes, Genetics
Volume11
Issue number1
DOIs
StatePublished - Jan 26 2021

Keywords

  • Colaptes auratus
  • Genome assembly
  • Hi-C
  • PacBio
  • Woodpeckers

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