the crocodilian genomics Consortium

16 October 2014Posted by David Ray

 

The International Crocodilian Genomes Working Group (ICGWG) is leading a large-scale effort to use genomic methods to examine crocodilian biology. We have targeted the American alligator (Alligator mississippiensis), saltwater crocodile (Crocodylus porosus), and gharial (Gavialis gangeticus) for genome sequencing and have produced preliminary genome assemblies.

To complement these efforts we and others have  collected (or are planning to collect) related data that can be used to enrich our knowledge of crocodilian genomes. These data include:

  • Transcriptome data for various tissues
  • BAC-end sequences for all three taxa (and some complete BAC sequences)

We expect the combinination of these data to result in a high quality genome assembly with rich annotation that will bring these fascinating reptiles into the genomic era.

why reptilian genomics?

12 October 2011Posted by Edward Braun

 

Reptiles (class Reptilia) represent one of the most diverse vertebrate groups they have largely been excluded from the genomics revolution. Extant reptiles comprise four major groups, traditionally assigned the rank of order:

  • Crocodylia (crocodiles and alligators; ~30 species)
  • Sphenodontia (tuataras; 2 species)
  • Squamata (lizards and snakes; ~7,900 species)
  • Testudines (turtles; ~300 species).

The reptile clade also includes class Aves (birds; ~10,000 species), the sister group of crocodilians. Birds and crocodilians are the extant members of the Archosauria ("ruling reptiles"), the clade that also includes the extinct dinosaurs and pterosaurs. Given the public interest in these spectacular animals (and their extinct relatives) they are also ideal for education and efforts that bridge genomics and organismal biology.

why crocodilian genomes?

12 October 2011Posted by Edward Braun

 

Crocodilians have long been a part of the human experience, making appearences in pop culture and providing sources of prized commodities such as leather and meat.  In fact, crocodilians are a source of trade worth over $US 500 million worldwide.  Some crocodilians, like the gharial, are critically endangered and their genome sequence may provide tools for genetic monitoring. Crocodilians are also important for human health; their immune systems may provide antimicrobial agents and they have been used to monitor the environment for contaminants, such as endocrine disruptiors.

Although crocodilians  represent important model organisms for fields as diverse as developmental biology, osmoregulation, cardiophysiology, sex determination, and functional morphology. The ICGWG plans to provide the genomic resources needed to expand our knowledge of these fascinating organisms. Since cocodilians are a pivotal lineage in the vertebrate tree of life this effort will also provide fascinating information for comparative genomics.