Outbred genome sequencing and CRISPR/Cas9 gene editing in butterflies

Nat Commun. 2015 Sep 10;6:8212. doi: 10.1038/ncomms9212.


Butterflies are exceptionally diverse but their potential as an experimental system has been limited by the difficulty of deciphering heterozygous genomes and a lack of genetic manipulation technology. Here we use a hybrid assembly approach to construct high-quality reference genomes for Papilio xuthus (contig and scaffold N50: 492 kb, 3.4 Mb) and Papilio machaon (contig and scaffold N50: 81 kb, 1.15 Mb), highly heterozygous species that differ in host plant affiliations, and adult and larval colour patterns. Integrating comparative genomics and analyses of gene expression yields multiple insights into butterfly evolution, including potential roles of specific genes in recent diversification. To functionally test gene function, we develop an efficient (up to 92.5%) CRISPR/Cas9 gene editing method that yields obvious phenotypes with three genes, Abdominal-B, ebony and frizzled. Our results provide valuable genomic and technological resources for butterflies and unlock their potential as a genetic model system.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Animals
  • Base Sequence
  • Butterflies / genetics*
  • CRISPR-Cas Systems
  • DNA-Binding Proteins / genetics*
  • Frizzled Receptors / genetics*
  • Gene Expression Profiling
  • Genetic Techniques
  • Genetic Variation
  • Genome, Insect / genetics*
  • Homeodomain Proteins / genetics*
  • Insect Proteins / genetics*
  • Molecular Sequence Data
  • Phenotype


  • DNA-Binding Proteins
  • Frizzled Receptors
  • Homeodomain Proteins
  • Insect Proteins

Associated data

  • GENBANK/LADI00000000
  • GENBANK/LADJ00000000
  • GEO/GSE65280
  • GEO/GSE65281
  • SRA/SRA230220
  • SRA/SRA230221
  • SRA/SRA272689