Int. J. Dev. Biol. 58: 881 - 888 (2014)
doi: 10.1387/ijdb.150060at
© UPV/EHU Press

The genome sequence of the corn snake (Pantherophis guttatus), a valuable resource for EvoDevo studies in squamates

Asier Ullate-Agote1,2,3, Michel C. Milinkovitch1,2,3 and Athanasia C. Tzika1,2,3,*

1Laboratory of Artificial & Natural Evolution (LANE), Dept. of Genetics & Evolution, University of Geneva, 2SIB Swiss Institute of Bioinformatics and 3Institute of Genetics and Genomics of Geneva (iGE3), University of Geneva, Geneva, Switzerland

ABSTRACT Squamates (snakes and lizards) exhibit a striking variety of phenotypes, with little known on their generative mechanisms. Studies aiming to understand the genetic basis of this wide diversity in morphology, physiology and ecology will greatly benefit from whole genome sequencing initiatives, as they provide the foundation for comparative analyses and improve our understanding of the evolution, development and diversification of traits. Here, we present the first draft genome of the corn snake Pantherophis guttatus, an oviparous snake that we promote as a particularly appropriate model species for evolutionary developmental studies in squamates. We sequenced 100-base paired-end reads from multiple individuals of a single family (parents and offspring) that produced a genome assembly of 1.53 gigabases (Gb), roughly covering 75% of the expected total genome size, and 297,768 scaffolds >1 Kb. We were able to fully retrieve 86, and partially another 106, of the 248 CEGMA core genes, indicating that a high genome completeness was achieved, even though the assembly is fragmented. Using MAKER2, we annotated 10,917 genes with high confidence (Annotation Edit Distance (AED)<1) and an additional 5,263 predicted genes matched with the species’ transcriptome. Numerous colour and colour pattern morphs exist in P. guttatus, making it an ideal model to study the genetic determinism, development, and evolution of adaptive colour traits in reptiles. Using our draft genome and a Single-Nucleotide Polymorphism (SNP) calling approach, we confirmed the interval with the causative mutation for the amelanistic phenotype, a result supported by a parallel exome-based study.

Keywords:

Pantherophis guttatus, corn snake, reptile, genome, amelanistic, SNP calling

*Corresponding author e-mail: Athanasia.Tzika@unige.ch