Chamaeleo calyptratus Genome Assembly

Squamates define the largest order of reptiles and have radiated and adapted to every niche on the planet. Chameleons have numerous interesting morphological features including a cranial casque, forelimb and hindlimb syndactyly and zygodactyly, a projectile tongue, prehensile tail and the ability to color change. However, little is known about how any of these adaptations evolved. We therefore sequenced and annotated the veiled chameleon (Chamaeleo calyptratus) genome at a chromosomal level. Examination of the Hox gene clusters revealed 41 genes with retention of HoxC1, which was lost in most amniotes. Interestingly, veiled chameleons lay eggs when embryos are at pre-gastrulation stages of development, contrary to other squamates, which are mid-organogenesis at the time of oviposition, thus allowing for the study of early development. Analysis of the Nodal left-right patterning cascade revealed both ancestral paralogs of the Nodal gene, but loss of Dand5 and several other genes, likely in conjunction with loss of motile cilia during left-right patterning in reptiles. We also identified the XX/XY sex determination region, which appears to be unique to genus Chamaeleo. Further synteny analysis revealed a remarkable chromosomal conservation across squamates, but comparisons to more distant genomes revealed GC peaks correlating with ancestral fusion events. This chameleon genome can therefore provide novel insights into the evolution of squamate genomes and the molecular mechanisms driving phenotypic variation and ecological adaptation.