Sequencing three crocodilian genomes to illuminate the evolution of archosaurs and amniotes
- John A St John1,
- Edward L Braun2,
- Sally R Isberg3, 5,
- Lee G Miles5,
- Amanda Y Chong5,
- Jaime Gongora5,
- Pauline Dalzell4, 5,
- Christopher Moran5,
- Bertrand Bed'Hom6,
- Arkhat Abzhanov7,
- Shane C Burgess8,
- Amanda M Cooksey8,
- Todd A Castoe9,
- Nicholas G Crawford10,
- Llewellyn D Densmore11,
- Jennifer C Drew12,
- Scott V Edwards7,
- Brant C Faircloth13,
- Matthew K Fujita7,
- Matthew J Greenwold14,
- Federico G Hoffmann8, 15,
- Jonathan M Howard16,
- Taisen Iguchi17,
- Daniel E Janes18, 19,
- Shahid Yar Khan1,
- Satomi Kohno20,
- AP Jason de Koning9,
- Stacey L Lance21,
- Fiona M McCarthy22,
- John E McCormack23,
- Mark E Merchant24,
- Daniel G Peterson8, 25,
- David D Pollock9,
- Nader Pourmand1,
- Brian J Raney26,
- Kyria A Roessler1,
- Jeremy R Sanford16,
- Roger H Sawyer14,
- Carl J Schmidt27,
- Eric W Triplett28,
- Tracey D Tuberville21,
- Miryam Venegas-Anaya11,
- Jason T Howard29,
- Erich D Jarvis29,
- Louis J GuilletteJr20,
- Travis C Glenn30,
- Richard E Green1 and
- David A Ray8, 15Email author
© BioMed Central Ltd. 2012
Published: 31 January 2012
The International Crocodilian Genomes Working Group (ICGWG) will sequence and assemble the American alligator (Alligator mississippiensis), saltwater crocodile (Crocodylus porosus) and Indian gharial (Gavialis gangeticus) genomes. The status of these projects and our planned analyses are described.
KeywordsGenomics evolution Crocodylia Archosauria amniote
The importance of reptilian genomics
Order Crocodylia is a key group within Reptilia and genome drafts from crocodilians would provide insights into ancestral reptilian and amniote genomes. These genome assemblies will also enable more detailed inferences on the evolution of three additional lineages of substantial interest to vertebrate biologists: dinosaurs, pterosaurs and birds. Crocodilians and birds are the only extant members of Archosauria (a clade that also includes dinosaurs and pterosaurs along with several extinct lineages) . Among archosaurs, only the genomes of chicken (Gallus gallus ), turkey (Meleagris gallopavo ) and zebra finch (Taeniopygia guttata ) have been sequenced, although several additional avian genomes, such as the Mallard duck (Anas platyrhynchos , budgerigar (Melopsittacus undulatus, a type of parrot) and a set of other avian taxa  are currently underway . Crocodilians are the best extant outgroup for comparative analysis of avian genomes, and, as such, would substantially enhance analyses of the large set of bird genomes that are expected to be available shortly. Avian and crocodilian genomes provide the best hope for elucidating the gene and genomic properties of dinosaurs and other extinct archosaurs, about which we have learned surprising amounts (for example, genome size and limited protein sequences) considering we have no access to the DNA of these organisms [15–19]. In the broadest sense, Crocodylia represent an important vertebrate clade, and their genomes hold information that will illuminate the underlying relationships among all amniotes. In addition, crocodilians present several interesting biological questions that can be approached from a genomic perspective, many of these will be discussed below.
Background on crocodilians and project justification
The order Crocodylia, which typically refers to the clade that includes the extant crocodilians , is an ecologically successful group of reptiles that originated in the mid- to upper-Cretaceous period (approximately100 Mya) [21, 22]. Crocodilians are apex predators in the marine and freshwater habitats where they reside. They play a major role in warm-water ecosystems throughout the world. Extant crocodilians are members of a larger group, termed the Crocodylomorpha, that appeared in the fossil record by the upper Triassic (about 200-250 Mya) [8, 1], a date coincident with molecular estimates of the avian-crocodilian divergence [2, 22, 23]. Crocodylia is divided into three families with extant members, Alligatoridae (alligators and caimans), Crocodylidae (crocodiles) and Gavialidae (gharials) [21, 23]; the Gavialidae are traditionally thought to be the outgroup of a clade comprising Alligatoridae and Crocodylidae . However, recent phylogenetic analyses of both molecular data [22, 24] and combined molecular and morphological data  support a closer relationship between Crocodylidae and Gavialidae (Figure 1).
Crocodilians have been a part of the human narrative for centuries, appearing in modern popular culture (for example, the wildlife documentary series The Crocodile Hunter), scientific documentaries, as ancient mummies and in cave paintings. They are prized for their hides and meat, and some species, such as the American alligator, the Nile crocodile (Crocodylus niloticus) and the saltwater crocodile, are ranched (that is their eggs are brought in from the wild) and/or farmed (in which captive breeding stock produce the eggs). Globally, crocodilians are a source of trade worth more than $US500 million . However, crocodilians likely have their most profound economic impact as tourist attractions [27, 28]. Thoughtful ecotourism could be the best hope for saving endangered crocodilians, such as the critically endangered gharial, from extinction and their habitats from destruction.
Given their popularity, their status as the sister group of dinosaurs, and their inherent public fascination, efforts focused on crocodilian genomics are ideally suited for education and outreach focused on evolution and comparative genomics. Indeed, the preliminary data from our efforts has been used in a pilot genomics course at the University of Florida that integrates with undergraduate research. The consortium plans to make material for genomics pedagogy and public outreach available in parallel with the release of the genome assemblies.
In addition to their ecological, sociological and economic significance, crocodilians have genomes that will be useful sources of data for biological and biomedical research. Alligator serum has been shown to contain broad spectrum antibiotic peptides [29–32]. The American alligator has been used extensively as a model for examining the environmental impact of various contaminants, including endocrine disrupting xenobiotics [33–36]. Crocodilians represent important research organisms for diverse fields that include evolution and phylogenetics [25, 37–39], functional morphology [37, 40], osmoregulation , sex determination [41–45], hybridization [46–48] and population genetics [49–51]. To provide the genomic resources necessary to expand our understanding of these fascinating organisms, the ICGWG is obtaining and assembling genome sequences for the American alligator, saltwater crocodile, and gharial, one representative from each of the extant crocodilian families. For further information about the project and preliminary assemblies, see Ref. .
Properties of crocodilian genomes and available genomic resources
Short of whole genome sequencing, much work has been done on crocodilian genomes, especially the American alligator and Australian saltwater crocodile. The genome of the American alligator is approximately 2.5 gigabases  comprising 16 pairs of chromosomes [54, 55]. The genome size of the saltwater crocodile is around 2.78 gigabases  with 17 pairs of chromosomes [54, 57]. The genome size of the gharial is currently unknown, although it is likely to be approximately 2-3 gigabases, given the genome sizes of other crocodilians. Like the American alligator, the gharial has 16 chromosomes . Unlike organisms with genetic sex-determination systems, crocodilians are not thought to have sex chromosomes . Instead sex is determined by incubation temperature of the egg . Although microchromosomes are common among other reptiles (including birds), and there is striking variation in chromosome sizes within crocodilians, the smallest crocodilian chromosomes are not generally regarded as small enough to be classified as microchromosomes [54, 58, 57, 55].
Libraries of bacterial artificial chromosomes (BACs) are available for all three species of interest and these will be used for each genome project. The American alligator BAC library currently has about 10× clone coverage , the saltwater crocodile library has approximately 3.7× clone coverage  and the gharial library has about 5.7× clone coverage, assuming it is a 2.7 gigabase genome (X. Shan, unpublished data). Several large-scale nucleotide datasets have been collected for the American alligator, including 21 assembled BAC sequences completed through the NISC Comparative Sequencing Initiative , and 3,276 Sanger BAC-end reads . A linkage map based on microsatellite loci  for the saltwater crocodile is also available. Additionally some saltwater crocodile microsatellite loci have been mapped by fluorescence in situ hybridization (FISH) to physical chromosomes using fosmids and BACs ( and P. Dalzell unpublished data), which will facilitate anchoring portions of the genome assembly to chromosomes.
In addition to genomic sequences and mapping information, both Sanger and 454 transcriptome data for the crocodile and alligator are available [63, 64]. Transcriptome data will be further augmented by a diversity of tissue-specific cDNA libraries from multiple species that will be sequenced using Illumina RNA-seq to assist gene annotations. The cDNA sequences will also enable further scaffold ordering and orientation for transcripts that are split between multiple genomic fragments . We will use these legacy and new data to further improve the initial de novo assemblies. To view the preliminary assemblies, see Ref. .
Sequencing strategy for the three crocodilian genomes
Owing to the availability of diverse legacy data, we are pursuing different strategies for the sequencing and assembly of each genome, as described below.
For the American alligator genome, we are following the Allpaths-LG recommended pipeline  of a combination of high coverage pairs of overlapping reads with a second, moderate coverage, longer insert mate-pair library. This pipeline has yielded good results with a variety of assemblies including de novo reassemblies of mouse and human , and was successfully employed in an independently evaluated genome assembly contest . We have combined approximately 50× coverage from an overlapping, Illumina, short-insert library with about 20× coverage from an Illumina 2 kbp mate-pair library. To investigate genetic variation and increase coverage, we will combine these reads with a set of short, non-overlapping 2 × 100 bp Illumina reads at approximately 50× coverage. In addition to providing deeper coverage, these data will also provide information about genetic variation in American alligators due to single nucleotide polymorphism differences between the diploid chromosomes of an individual. We will further scaffold the assembly using low coverage BAC-end sequences, and we will carry out FISH mapping to assign scaffolds to chromosomes.
To sequence the saltwater crocodile genome, we are combining high coverage Illumina short insert sequencing with low coverage 454 libraries in a hybrid approach, similar to that used for the turkey genome . We currently have about 80× coverage from a non-overlapping, short-insert library and an additional 40× from an overlapping short-insert library. We also plan to generate about 20× coverage from an Illumina 2 kbp mate-pair library. To supplement the Illumina data, we have generated 1× coverage of unpaired 454 reads (about 700 bp in length), and plan to generate an additional 2× coverage from 3 kbp and 6 kbp paired 454 reads. We will also end-sequence the crocodile BAC library using a method similar to the fosmid-based ShARC method described by Gnerre et al. . Some of these BACs are known to contain microsatellite DNA markers used in the crocodile linkage map  and others have already been FISH mapped to chromosomes in the crocodile . We will integrate this information for scaffolding and assigning scaffolds to chromosomes. As with the American alligator genome, we are also generating transcriptome data for the saltwater crocodile for both annotation and scaffolding purposes. We will also use the 454 brain transcriptome data that exists for the American alligator  and the Nile crocodile  in our analyses. We will use these EST and RNA-seq data, along with the other resources described above, to further order and orient scaffolds within the assembly.
Finally, we will assemble the gharial genome using a hybrid approach similar to that used for the saltwater crocodile. To do this, we have generated 40× coverage from an overlapping short-insert library. This will be combined with sequences from 400 bp and 700 bp paired-end Illumina libraries sequenced to give approximately 30× coverage, as well as 2-3× genome coverage consisting of 454 shotgun reads and 3 kbp and 6 kbp paired-end 454 libraries with FLX+ reads. Finally we will generate approximately 20× coverage from an Illumina 2 kbp mate-pair library. The gharial is a critically endangered species, making it nearly impossible to collect a wide variety of tissues for transcriptome data. Nonetheless, we have collected blood, which will be used to generate Illumina RNA-seq data. As with the American alligator and saltwater crocodile, we will use de novo assembled transcripts to improve the assembly.
Project timeline and goals
The first phase of our sequencing effort, in which we generate high coverage short insert and overlapping libraries, has been completed for American alligator and saltwater crocodile and is ongoing for the Indian gharial. The data generated for alligator and crocodile were used to generate early draft assemblies for those genomes. The second phase will involve generating longer distance mate-pair libraries and BAC-end sequences to improve the assemblies. We plan to have the data gathered for this phase by mid-March 2012. The third and final phase will involve FISH mapping the BACs to assign scaffolds to chromosomes. When all three phases are completed the assemblies should be as contiguous as possible, given the combination of high coverage short distance information generated in phase one with lower coverage long distance information generated in phase two. The third phase is not critical for the most pressing questions involving crocodilian genomics; individual genes and their regulatory regions will be of primary interest, as opposed to the long-range linkage required for identifying selective sweeps. Thus we will proceed with this third phase in parallel with our other comparative genomic analyses. Once the three genomes are assembled, we will perform comparative genomic analyses both within Order Crocodylia, and among crocodilians and other members of Reptilia.
The completion of each of these phases will be publicly communicated via the website, and links to the data and assemblies will be available to researchers with restrictions as detailed below. We anticipate data collection and initial analyses to be complete by June 2012, and we plan to submit the genome paper within one year of finalizing these initial analyses. The Toronto Statement  suggests that there be a one-year period of initial analyses and publication, after which the broader community would be free to use this data in an unrestricted manner. Precise dates at which we complete data collection and initial analysis, and thus the beginning of the embargo period on the genome data, will be promptly posted on the website .
Status of the current preliminary genome assemblies
Overview of the current draft assembliesa.
Estimated Length (Gbp)
Assembly Length (Gbp)
Estimated % Coverage
Contig N50 (Kbp)
Contig N90 (Kbp)
Scaffold N50 (Kbp)
Scaffold N90 (Kbp)
Quality control of intermediate assemblies and raw data
We will employ additional quality metrics to detect and describe the collapse of segmental duplications within our assemblies. Specifically, read-depth is a sensitive measure of this assembly artifact. Preliminary analysis suggests that such artifacts are not common in alligator or crocodile genomes (data not shown). We will employ a final form of quality control by examining the relative synteny of our three crocodilian candidate assemblies. Because alligators, crocodiles, and gharials appear to have undergone few chromosome-level rearrangements , we expect a high level of synteny between accurate assemblies. Once we begin scaffolding all of our assemblies with longer mate-pair and BAC data, we will assess their relative quality by measuring the effect on overall crocodilian synteny.
Planned analyses and experiments
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.
How other groups can join the consortium, or publish independently with our early release data
This project is affiliated with the Genome 10 K (G10K) initiative . We invite other G10K affiliates and the broader scientific community to access and make use of the draft assembly and raw read data that we have produced. Any group performing non-genome-scale analyses that are sufficiently independent of the analyses described above are welcome to use these data without restriction. As a matter of courtesy and to avoid duplicated effort, we request that competing genome-scale projects or analyses that overlap with the areas stated above disclose their status to the ICGWG consortium (formal inquiries and requests to join the working group should be made to D.A.R.) and cite this and subsequent papers that provide the data. Versioned assemblies, further project description, and a complete list of current ICGWG members can be accessed on the website dedicated to this project .
This work was supported by grants to D.A.R. (MCB-1052500, MCB-0841821, DEB-1020865 from the U.S. National Science Foundation) and funds from the Institute for Genomics, Biocomputing and Biotechnology at Mississippi State University. E.L.B., E.W.T., and collaborators at the University of Florida were supported by funds from the U.S. National Science Foundation (DUE-0920151). T.I. received financial support from the National Institute for Basic Biology and Grants-in-Aid for Scientific Research from the Ministry of Education, Culture, Sports, Science and Technology of Japan. S.R.I., L.G.M., J.G., P.D. and C.M. were supported by Australian Rural Industries Research and Development Corporation grants (RIRDC PRJ-000549, RIRDC PRJ-005355, RIRDC PRJ-002461). M.K.F. received financial support from a U.S. National Science Foundation Biological Informatics Postdoctoral Fellowship (DBI-0905714). R.E.G. is a Searle Scholar and a Sloan Fellow. E.D.J. was supported by the Howard Hughes Medical Institute and the National Institutes of Health. We are grateful to Kent Vliet (University of Florida) and the Alligator Farm (St. Augustine, Florida) for providing access to fresh gharial blood.
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