Corn snake genome v1

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 con dence (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.

Associated Publications
Ullate-Agote A., Milinkovitch M.C. & A.C. Tzika
The genome sequence of the corn snake (Pantherophis guttatus), a valuable resource for EvoDevo studies in squamates
Int. J. Dev. Biol. 58: 881-888 (2014)

Saenko S.V., Lamichhaney S., Martinez Barrio A., Rafati N., Andersson L. & M. C. Milinkovitch
Amelanism in the corn snake is associated with the insertion of an LTR-retrotransposon in the OCA2 gene
Scientific Reports 5, 17118 (2015)

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You can perform BLAST searches against the corn snake genome v1 using our WWWBLAST server.

Download the data
All files are compressed (zipped).

Supplementary File 1
‣ Supplementary table 1 with the Hox genes location and table 2 with the SNP calling filters (PDF file)

Supplementary File 2
‣ An XLS table with MAKER2 information on the annotated P. guttatus proteins (AED < 1) (XLS file)

Supplementary File 3
‣ A FASTA file with sequences of predicted proteins (AED < 1) (FASTA file)

Supplementary File 4
‣ A FASTA file with sequences of predicted transcripts (AED < 1) (FASTA file)

Supplementary File 5
‣ An XLS file listing the SNPs selected for mapping of the amelanistic mutation (XLS file)