Comparative genomic analysis of the whale (Pseudorca crassidens) PRNP locus.
There have been many studies of the morphology, behavioral audiograms, and population structure of the false killer whale (Pseudorca crassidens), but sequencing, mapping, and functional and comparative genomics studies are still largely unknown. In this paper, we sequenced three novel BAC clones corresponding to a total length of 308 kb and spanning the PRNP, PRND, and RASSF2 loci, and conducted comparative genomic analysis to examine the genomic structure of the false killer whale PRNP locus. We determined that the three genes show a high degree of conservation in their syntenic regions with respect to gene order, gene orientation, and the predicted coding sequence (CDS) between human and whale, whereas PRNT was not detected in whale. Interestingly, the predicted CDS in whale PRNP contained a novel type of 4-copy octarepeat resulting from a 24 bp deletion when compared with the human sequence. In addition, we identified a novel 1869 bp repeat unit in a region that is non-syntenic to human and cow sequences and is therefore considered to be whale-specific sequence. Our results will provide novel insights into the genomic changes that have occurred during evolution of mammalian PRNP loci, and may also have implications for research into prion disease.
Genome Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon 305-806, Korea.
Dae-Won
DW
Kim
Sung-Hwa
SH
Chae
Bo-Ra
BR
Kang
Sang-Haeng
SH
Choi
Aeri
A
Kim
Seonock
S
Woo
Hong-Seog
HS
Park
D000595:Amino Acid Sequence; D000818:Animals; D004289:Dolphins / Q000235:genetics*; D005091:Exons / Q000235:genetics; D023281:Genomics; D006801:Humans; D007438:Introns / Q000235:genetics; D008969:Molecular Sequence Data; D016133:Polymerase Chain Reaction; D011328:Prions / Q000235:genetics*; D017386:Sequence Homology, Amino Acid
D011328:Prions