How Should I Dressss Tonight? Improving the Pantherophis guttatus Genome for the Study of Skin and Coloration Traits in Snakes

Very few genomic resources are available for reptiles considering the impressive variety of phenotypes present in the more than 10,000 species of this clade. Hence, additional genome sequencing projects are vital to improve our understanding of their evolution, development and diversification. We promote the corn snake (Pantherophis guttatus), an oviparous snake with a wide range of colour and colour pattern morphs, as an appropriate model species for evolutionary developmental studies in squamates. Besides our developmental work and our color trait mapping studies, we have also published a draft genome of this species (Ullate-Agote & al, 2014). Here, we present a higher quality assembly that combines: (i) 250bp Illumina paired-end reads for contig assembly with DISCOVAR de novo, (ii) multiple long-fragment size mate pair libraries for initial scaffolding, (iii) transcriptomic data to improve gene connectivity and (iv) BioNano genome maps to generate megabase long superscaffolds and to correct mis-assemblies and gap length estimations. We built a final genome assembly of 1.94Gbp, matching a 1.85Gbp expected genome size. With an N50 of 1.38Mbp (L50 = 279 sequences), we achieved a more than 300-fold improvement compared to the first version, making the corn snake genome the highest quality snake genome currently available. We retrieved 245 of the 248 CEGMA core genes and recovered the Hox genes clusters, both indicators of high gene completeness and contiguity. Combined with our on-going genome annotation and comparative transcriptomic projects (made available at www.reptilomics.org), this genome should prove useful for the genomics, transcriptomics, proteomics and herpetology communities alike.