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 c...
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crcansciencepubl:10.1139/g08-029 2023-12-17T10:32:53+01:00 Comparative genomic analysis of the whale ( Pseudorca crassidens ) PRNP locus Kim, Dae-Won Chae, Sung-Hwa Kang, Bo-Ra Choi, Sang-Haeng Kim, Aeri Woo, Seonock Park, Hong-Seog Bell, John 2008 http://dx.doi.org/10.1139/g08-029 http://www.nrcresearchpress.com/doi/full-xml/10.1139/G08-029 http://www.nrcresearchpress.com/doi/pdf/10.1139/G08-029 en eng Canadian Science Publishing http://www.nrcresearchpress.com/page/about/CorporateTextAndDataMining Genome volume 51, issue 6, page 452-464 ISSN 0831-2796 1480-3321 Genetics Molecular Biology General Medicine Biotechnology journal-article 2008 crcansciencepubl https://doi.org/10.1139/g08-029 2023-11-19T13:38:26Z 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. Article in Journal/Newspaper Killer Whale Canadian Science Publishing (via Crossref) Genome 51 6 452 464 |
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Open Polar |
collection |
Canadian Science Publishing (via Crossref) |
op_collection_id |
crcansciencepubl |
language |
English |
topic |
Genetics Molecular Biology General Medicine Biotechnology |
spellingShingle |
Genetics Molecular Biology General Medicine Biotechnology Kim, Dae-Won Chae, Sung-Hwa Kang, Bo-Ra Choi, Sang-Haeng Kim, Aeri Woo, Seonock Park, Hong-Seog Comparative genomic analysis of the whale ( Pseudorca crassidens ) PRNP locus |
topic_facet |
Genetics Molecular Biology General Medicine Biotechnology |
description |
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. |
author2 |
Bell, John |
format |
Article in Journal/Newspaper |
author |
Kim, Dae-Won Chae, Sung-Hwa Kang, Bo-Ra Choi, Sang-Haeng Kim, Aeri Woo, Seonock Park, Hong-Seog |
author_facet |
Kim, Dae-Won Chae, Sung-Hwa Kang, Bo-Ra Choi, Sang-Haeng Kim, Aeri Woo, Seonock Park, Hong-Seog |
author_sort |
Kim, Dae-Won |
title |
Comparative genomic analysis of the whale ( Pseudorca crassidens ) PRNP locus |
title_short |
Comparative genomic analysis of the whale ( Pseudorca crassidens ) PRNP locus |
title_full |
Comparative genomic analysis of the whale ( Pseudorca crassidens ) PRNP locus |
title_fullStr |
Comparative genomic analysis of the whale ( Pseudorca crassidens ) PRNP locus |
title_full_unstemmed |
Comparative genomic analysis of the whale ( Pseudorca crassidens ) PRNP locus |
title_sort |
comparative genomic analysis of the whale ( pseudorca crassidens ) prnp locus |
publisher |
Canadian Science Publishing |
publishDate |
2008 |
url |
http://dx.doi.org/10.1139/g08-029 http://www.nrcresearchpress.com/doi/full-xml/10.1139/G08-029 http://www.nrcresearchpress.com/doi/pdf/10.1139/G08-029 |
genre |
Killer Whale |
genre_facet |
Killer Whale |
op_source |
Genome volume 51, issue 6, page 452-464 ISSN 0831-2796 1480-3321 |
op_rights |
http://www.nrcresearchpress.com/page/about/CorporateTextAndDataMining |
op_doi |
https://doi.org/10.1139/g08-029 |
container_title |
Genome |
container_volume |
51 |
container_issue |
6 |
container_start_page |
452 |
op_container_end_page |
464 |
_version_ |
1785586733797081088 |