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Journal of Heredity Advance Access published online on November 29, 2006
Journal of Heredity, doi:10.1093/jhered/esl040
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© The American Genetic Association. 2006. All rights reserved. For permissions, please email: journals.permissions@oxfordjournals.org.
Received May 5, 2006
Accepted October 13, 2006

Article

Tuatara (Sphenodon) Genomics: BAC Library Construction, Sequence Survey, and Application to the DMRT Gene Family

Zhenshan Wang 1 *, Tsutomu Miyake 2, Scott V. Edwards 3, and Chris T. Amemiya 4

1 From the Department of Biology, University of Washington, Box 351800, Seattle, WA 98195; Wang is now at the Department of Pharmacology, University of Washington, Box 357280, Seattle, WA 98195
2 The Benaroya Research Institute at Virginia Mason, 1201 Ninth Avenue, Seattle, WA 98101
3 From the Department of Biology, University of Washington, Box 351800, Seattle, WA 98195; Edwards is now at the Department of Organismic and Evolutionary Biology, Harvard University, 26 Oxford Street, Cambridge, MA 02138
4 From the Department of Biology, University of Washington, Box 351800, Seattle, WA 98195; The Benaroya Research Institute at Virginia Mason, 1201 Ninth Avenue, Seattle, WA 98101

* To whom correspondence should be addressed.
Zhenshan Wang, E-mail: zhenshan{at}u.washington.edu


  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 (http://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.


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