ChIP-Seq-Annotated Heliconius erato Genome Highlights Patterns of cis-Regulatory Evolution in Lepidoptera.
Uncovering phylogenetic patterns of cis-regulatory evolution remains a fundamental goal for evolutionary and developmental biology. Here, we characterize the evolution of regulatory loci in butterflies and moths using chromatin immunoprecipitation sequencing (ChIP-seq) annotation of regulatory elements across three stages of head development. In the process we provide a high-quality, functionally annotated genome assembly for the butterfly, Heliconius erato. Comparing cis-regulatory element conservation across six lepidopteran genomes, we find that regulatory sequences evolve at a pace similar to that of protein-coding regions. We also observe that elements active at multiple developmental stages are markedly more conserved than elements with stage-specific activity. Surprisingly, we also find that stage-specific proximal and distal regulatory elements evolve at nearly identical rates. Our study provides a benchmark for genome-wide patterns of regulatory element evolution in insects, and it shows that developmental timing of activity strongly predicts patterns of regulatory sequence evolution.
Department of Ecology and Evolutionary Biology, Cornell University, 215 Tower Road, Ithaca, NY 14853-7202, USA. Electronic address: jjl336@cornell.edu.
James J
JJ
Lewis
Department of Ecology and Evolutionary Biology, Cornell University, 215 Tower Road, Ithaca, NY 14853-7202, USA.
Karin R L
KRL
van der Burg
Department of Ecology and Evolutionary Biology, Cornell University, 215 Tower Road, Ithaca, NY 14853-7202, USA.
Anyi
A
Mazo-Vargas
Department of Ecology and Evolutionary Biology, Cornell University, 215 Tower Road, Ithaca, NY 14853-7202, USA.
Robert D
RD
Reed
D000818:Animals; D001483:Base Sequence; D002080:Butterflies / Q000235:genetics* / Q000254:growth & development; D047369:Chromatin Immunoprecipitation / Q000379:methods*; D019143:Evolution, Molecular; D049750:Genome, Insect; D006257:Head; D008018:Life Cycle Stages / Q000235:genetics; D058977:Molecular Sequence Annotation; D012045:Regulatory Sequences, Nucleic Acid / Q000235:genetics*; D017423:Sequence Analysis, RNA / Q000379:methods*