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

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.

Progressive Loss of Function in a Limb Enhancer during Snake Evolution

“…To explore the potential role of the ZRS limb enhancer in snake evolution, we examined the draft genomes of six snake species including the Burmese python ( Python molurus bivittatus ) (Castoe et al, 2013), boa constrictor ( Boa constrictor constrictor ), king cobra ( Ophiophagus hannah ) (Vonk et al, 2013), speckled rattlesnake ( Crotalus mitchellii pyrrhus ), viper ( Vipera berus berus ), and corn snake ( Pantherophis guttatus ) (Ullate-Agote et al, 2014). These species represent different morphological stages within the evolutionary history of snakes (Apesteguía and Zaher, 2006; Martill et al, 2015), from basal snakes (boa and python) that retained a vestigial pelvic girdle and rudimentary hindlimbs, to advanced snakes (viper, rattlesnake, king cobra, and corn snake) that completely lost all skeletal limb structures and represent the majority (>85%) of all extant snake species (Lawson et al, 2005; Pyron et al, 2013).…”

The Mobilome of Reptiles: Evolution, Structure, and Function

“…Despite these fascinating aspects of squamate biology and their obvious utility as a research tool, only a limited number of highquality squamate genome assemblies are available and have been analyzed for their repeat content. High-quality genome assemblies exist for the green anole A. carolinensis [Alföldi et al, 2011]; the Burmese python, Python molurus bivittatus [Castoe et al, 2013]; the king cobra, Ophiophagus hannah [Vonk et al, 2013], and the five-pace viper, Deinagkistrodon acutus [Yin et al, 2016] in addition to high-coverage assemblies of the Australian dragon lizard, Pogona vitticeps [Georges et al, 2015] and the Chinese crocodile lizard, Shinisaurus crocodilurus [Gao J et al, 2017] as well as draft assemblies of the Burmese glass lizard, Ophisaurus gracilis , a legless anguid lizard [Song et al, 2015]; the leopard gecko, Eublepharis macularius [Xiong et al, 2016], and the corn snake, Pantherophis guttatus [Ullate-Agote et al, 2014]. This collection of genomes, when considered together, reveals that squamates are as diverse in TE content as they are diverse morphologically, physiologically, or ecologically.…”

Morphological specializations of the yolk sac for yolk processing in embryonic corn snakes (Pantherophis guttatus: Colubridae)

“…The present study draws on light microscopy (LM) and scanning electron microscopy (SEM) to reveal details of the mechanism of yolk cellularization and vascularization in the corn snake, P. guttatus (Colubridae). Corn snakes have been developed as a model squamate species (Di-Poï et al, 2010;Milinkovitch & Tzika, 2007) and their genome has been sequenced (Ullate-Agote, Milinkovitch, & Tzika, 2014). They also are one of the few oviparous snakes in which fetal membrane development has been studied in detail (Blackburn, Johnson, & Petzold, 2003;Knight & Blackburn, 2008).…”