Here we outline major questions, types of analyses and analytical goals that will be included in the core publication of these completed genomes. The Toronto Statement  suggests these questions should be articulated to identify these topics as embargoed during preparation of the genome publication. The ICGWG will address a number of research questions at both the level of genome evolution and crocodilian biology that we describe below.
A crucial step in making genome resources useful to the scientific community is generating gene annotations. We will perform gene finding for crocodilians using the Ensembl  and Augustus  annotation pipelines and combine the output. We will also partner with groups sequencing additional avian genomes and update the crocodile annotations as needed. Gene finders will initially be trained using the chicken genome and the results from the pipelines will be compared to identify accuracy at both the gene and exon level. Genes will be assigned standardized gene nomenclature based on chicken gene names where there is an unambiguous 1:1 functional ortholog, or a gene identifier in cases where this is not possible. We will also provide preliminary functional annotation for proteins and transcripts using standard Gene Ontology Consortium methods, including functional analysis of motifs and domains and manual curation of orthologs. The ICGWG will perform these analyses to complement and extend those performed by NCBI and Ensembl once the draft genomes are submitted to those organizations.
One major focus will be the large-scale structure of crocodilian genomes, focusing on the degree of syntenic conservation at different scales within these genomes. Karyotype analysis suggests a remarkable conservation of synteny among crocodilians, with the alligator and crocodile having undergone fewer than five chromosomal rearrangements visible at the microscopic level  despite 80 million years of evolutionary divergence. However, the level of syntenic conservation at small scales within these genomes remains unclear, and we expect our genome assemblies to illuminate this topic. Microchromosomes are absent in crocodilians [54, 55, 59] but present in birds, lizards and snakes, tuatara, and turtles [4, 84]. This absence in crocodilians almost certainly represents a derived feature of crocodilians. We will examine the fate of these genetic units within crocodilian genomes. Do microchromosomes comprise linked components within the genomes of the only major reptilian clade without microchromosomes?
Recent work showed that the lizard, Anolis carolinensis, unlike other amniotes sequenced to date (with the possible exception of turtles ), has a homogeneous genome that lacks GC-rich isochores [76, 4]. Our preliminary analyses indicate that crocodilians have a higher GC-content and greater heterogeneity than Anolis (Figure 4), but these analyses are less clear regarding the scale of the observed GC-content variation. Do crocodilians have GC-rich isochores that are similar to those in mammals and birds or do the patterns of GC-content heterogeneity appear distinct?
We will also carry out a number of traditional analyses of genome content using the crocodilian genomes, focusing on repeated sequences and gene families. These analyses include the evolution of repeat families and patterns of TE proliferation. We will compare the repeat family content within crocodilian genomes and with other reptiles and amniotes. Additionally, we will conduct analyses of gene family evolution within reptiles and crocodilians to identify specific genes and other functional elements, including the identification of ultra-conserved regions and potential micro RNA sequences, with a special focus on those sequences that could have been gained or lost both within the crocodilians and in comparison to the other relevant lineages that are now available for investigation.
We will use these three crocodilian genomes to infer their ancestral genome. This, combined with existing and soon to be released bird genomes, will enable some inference of the ancestral archosaur genome. Reconstructing the ancestral archosaur genome has obvious implications for expanding our understanding of the genomes of extinct archosaurs, like the non-bird dinosaurs and pterosaurs (Figure 1).
There are also several biological questions specific to crocodilians that we will address by analyzing genomic and RNA-seq data and via experimental techniques. For example, despite having a temperature-dependent sex-determination system seemingly without sex chromosomes, the sexes of crocodilians have been shown to have very different recombination rates . Identification of the genes that are differentially expressed in the male and female crocodilian gonads might provide insight into the perplexing observation.
SNP discovery arising from the genome sequencing is particularly relevant to farm-bred saltwater crocodiles. Large panels of SNP markers will enable more refined linkage maps , more precise mapping of quantitative trait loci (QTL) than is currently possible with microsatellite markers  and eventually the implementation of genomic selection in crocodile breeding programs.
Eventually members of the ICGWG hope to address additional questions beyond the scope of the initial genome paper. These might be presented in satellite publications. One of these involves the sex determination system of American alligators. Which genes are the initial temperature sensitive regulators that trigger the downstream, largely conserved  sex-determination system? Having the genome sequences available for these three crocodilians will enable a new wave of discoveries about the evolutionary histories of crocodilians, non-avian reptiles and birds, and amniotes generally.