title: Tuatara (Sphenodon) genomics: BAC library construction, sequence survey, and application to the DMRT gene family.
abstract: The tuatara (Sphenodon punctatus) is of "extraordinary biological interest" as the most distinctive surviving reptilian lineage (Rhyncocephalia) in the world. To provide a genomic resource for an understanding of genome evolution in reptiles, and as part of a larger project to produce genomic resources for various reptiles (evogen.jgi.doe.gov/second_levels/BACs/our_libraries.html), a large-insert bacterial artificial chromosome (BAC) library from a male tuatara was constructed. The library consists of 215 424 individual clones whose average insert size was empirically determined to be 145 kb, yielding a genomic coverage of approximately 6.3x. A BAC-end sequencing analysis of 121 420 bp of sequence revealed a genomic GC content of 46.8%, among the highest observed thus far for vertebrates, and identified several short interspersed repetitive elements (mammalian interspersed repeat-type repeats) and long interspersed repetitive elements, including chicken repeat 1 element. Finally, as a quality control measure the arrayed library was screened with probes corresponding to 2 conserved noncoding regions of the candidate sex-determining gene DMRT1 and the DM domain of the related DMRT2 gene. A deep coverage contig spanning nearly 300 kb was generated, supporting the deep coverage and utility of the library for exploring tuatara genomics.
authors.affiliation: Department of Biology, University of Washington, Seattle, WA 98195, USA. zhenshan@u.washington.edu
authors.forename: Zhenshan
authors.initials: Z
authors.lastname: Wang
authors.forename: Tsutomu
authors.initials: T
authors.lastname: Miyake
authors.forename: Scott V
authors.initials: SV
authors.lastname: Edwards
authors.forename: Chris T
authors.initials: CT
authors.lastname: Amemiya
mesh_terms: D000818:Animals; D001499:Bayes Theorem; D022202:Chromosomes, Artificial, Bacterial; D015723:Gene Library; D016678:Genome; D023281:Genomics / Q000379:methods; D008297:Male; D005810:Multigene Family; D010802:Phylogeny; D012104:Reptiles / Q000235:genetics*; D014157:Transcription Factors / Q000145:classification / Q000235:genetics*
chemical_list: D014157:Transcription Factors