Annotation and analysis of three crocodilian genomes

Crocodilians are important model organisms in fields as diverse as developmental biology, osmoregulation, cardiophysiology, paleoclimatology, sex determination, population genetics, paleobiogeography, and functional morphology. Crocodilians, birds, dinosaurs, and pterosaurs comprise a monophyletic group known as the archosaurs. Crocodilians and birds are the only extant members and thus crocodilians (alligators, caimans, crocodiles, and gharials) are the closest living relatives of all birds. To provide context for the diversifications of archosaurs, we generated draft genomes of three crocodilians, Alligator mississippiensis (the American alligator), Crocodylus porosus (the saltwater crocodile), and Gavialis gangeticus (the Indian gharial). We generated high-coverage Illumina sequence data from paired-end and mate-pair libraries from each species. The assembly strategy for each taxon differed due to varying legacy data and developments in library preparation methods during the course of the project. Gene annotation was accomplished using a combination of RNASeq data and homology-based analyses. We identified 23,323 protein-coding genes in the alligator compared to 13,321 and 14,043 in crocodile and gharial, respectively. Transposable elements (TEs) were identified de novo in all three crocodilians and analyses resulted in a library of 1269 different TEs.