Journal of Heredity Advance Access originally published online on November 29, 2006
Journal of Heredity 2006 97(6):541-548; doi:10.1093/jhered/esl040
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Tuatara (Sphenodon) Genomics: BAC Library Construction, Sequence Survey, and Application to the DMRT Gene Family
From the Department of Biology, University of Washington, Box 351800, Seattle, WA 98195 (Wang, Edwards, and Amemiya); and the Benaroya Research Institute at Virginia Mason, 1201 Ninth Avenue, Seattle, WA 98101 (Miyake and Amemiya). Edwards is now at the Department of Organismic and Evolutionary Biology, Harvard University, 26 Oxford Street, Cambridge, MA 02138. Wang is now at the Department of Pharmacology, University of Washington, Box 357280, Seattle, WA 98195
Address correspondence to Z. Wang at the address above, or e-mail: zhenshan{at}u.washington.edu.
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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