Amniote phylogeny emphasizing the crocodilians. The geographic ranges of the three crocodilians of interest are shown, along with approximate times of divergence of each group based upon the Timetree of Life [1]. On the basis of the fossil record, the origins of dinosaurs and birds were Triassic and upper Jurassic, respectively [86], and birds from within dinosaurs [86,87]. The phylogenetic position of turtles is unclear [2,88,89], however for simplicity we chose the consensus estimated position and divergence time presented in the Timetree of Life [1]. The photos of the American alligator (Alligator mississippiensis), the saltwater crocodile (Crocodylus porosus) were kindly provided by Louis Guillette and the photo of the Indian gharial (Gavialis gangeticus) was provided by Alan Wolf. Mya; million years ago.

The distribution of repeats of different length in the alligator and crocodile assemblies. Overlaid are some of the library insert size or fragment sizes we have made for the various assemblies. Note however that the current crocodile assembly in this figure does not include the 454 data.

The size of different repeat families classified in our current alligator and crocodile assemblies. Despite more long-distance insert libraries for alligator, more repeats were found in the crocodile assembly. This strongly suggests that crocodiles have more repeats than do alligators, and perhaps the difference will become even more striking as the crocodile assembly improves.

The distribution of GC proportion across several species. Note that alligators and crocodiles have a higher overall proportion of GC than many other vertebrates, as predicted by early BAC-end scans [42]. Abbreviation: SD; standard deviation.

Using de novo assembled alligator transcripts, the level of gene presence and fragmentation in two alternate alligator assemblies were compared. These results suggest that the new assembly (assembly B) is an improvement over the earlier effort (assembly A).

Using gene regions in a whole genome alignment to the chicken reference genome (galGal3), we compared the number of scaffolds of each assembly that the alignment of each gene is split between. Although many genomic rearrangements may exist between chicken and crocodile, assuming that breakpoints tend to happen between genes rather than within genes, this method allows us to assess the relative quality of assemblies in the same manner as Figure 5 when assembled and verified transcripts are not yet available.