Comparative genomic analysis of the false killer whale ( Pseudorca crassidens ) LMBR1 locus
The sequencing and comparative genomic analysis of LMBR1 loci in mammals or other species, including human, would be very important in understanding evolutionary genetic changes underlying the evolution of limb development. In this regard, comparative genomic annotation of the false killer whale LMB...
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crcansciencepubl:10.1139/g10-043 2024-04-07T07:53:48+00:00 Comparative genomic analysis of the false killer whale ( Pseudorca crassidens ) LMBR1 locus Kim, Dae-Won Choi, Sang-Haeng Kim, Ryong Nam Kim, Sun-Hong Paik, Sang-Gi Nam, Seong-Hyeuk Kim, Dong-Wook Kim, Aeri Kang, Aram Park, Hong-Seog Danzmann, Roy 2010 http://dx.doi.org/10.1139/g10-043 http://www.nrcresearchpress.com/doi/full-xml/10.1139/G10-043 http://www.nrcresearchpress.com/doi/pdf/10.1139/G10-043 en eng Canadian Science Publishing http://www.nrcresearchpress.com/page/about/CorporateTextAndDataMining Genome volume 53, issue 9, page 658-666 ISSN 0831-2796 1480-3321 Genetics Molecular Biology General Medicine Biotechnology journal-article 2010 crcansciencepubl https://doi.org/10.1139/g10-043 2024-03-08T00:37:44Z The sequencing and comparative genomic analysis of LMBR1 loci in mammals or other species, including human, would be very important in understanding evolutionary genetic changes underlying the evolution of limb development. In this regard, comparative genomic annotation of the false killer whale LMBR1 locus could shed new light on the evolution of limb development. We sequenced two false killer whale BAC clones, corresponding to 156 kb and 144 kb, respectively, harboring the tightly linked RNF32, LMBR1, and NOM1 genes. Our annotation of the false killer whale LMBR1 gene showed that it consists of 17 exons (1473 bp), in contrast to 18 exons (1596 bp) in human, and it displays 93.1% and 95.6% nucleotide and amino acid sequence similarity, respectively, compared with the human gene. In particular, we discovered that exon 10, deleted in the false killer whale LMBR1 gene, is present only in primates, and this fact strongly implies that exon 10 might be crucial in determining primate-specific limb development. ZRS and TFBS sequences have been well conserved across 11 species, suggesting that these regions could be involved in an important function of limb development and limb patterning. The neighboring gene RNF32 showed several lineage-conserved exons, such as exons 2 through 9 conserved in eutherian mammals, exons 3 through 9 conserved in mammals, and exons 5 through 9 conserved in vertebrates. The other neighboring gene, NOM1, had undergone a substitution (ATG→GTA) at the start codon, giving rise to a 36 bp shorter N-terminal sequence compared with the human sequence. Our comparative analysis of the false killer whale LMBR1 genomic locus provides important clues regarding the genetic regions that may play crucial roles in limb development and patterning. Article in Journal/Newspaper Killer Whale Canadian Science Publishing Genome 53 9 658 666 |
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Open Polar |
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Canadian Science Publishing |
op_collection_id |
crcansciencepubl |
language |
English |
topic |
Genetics Molecular Biology General Medicine Biotechnology |
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Genetics Molecular Biology General Medicine Biotechnology Kim, Dae-Won Choi, Sang-Haeng Kim, Ryong Nam Kim, Sun-Hong Paik, Sang-Gi Nam, Seong-Hyeuk Kim, Dong-Wook Kim, Aeri Kang, Aram Park, Hong-Seog Comparative genomic analysis of the false killer whale ( Pseudorca crassidens ) LMBR1 locus |
topic_facet |
Genetics Molecular Biology General Medicine Biotechnology |
description |
The sequencing and comparative genomic analysis of LMBR1 loci in mammals or other species, including human, would be very important in understanding evolutionary genetic changes underlying the evolution of limb development. In this regard, comparative genomic annotation of the false killer whale LMBR1 locus could shed new light on the evolution of limb development. We sequenced two false killer whale BAC clones, corresponding to 156 kb and 144 kb, respectively, harboring the tightly linked RNF32, LMBR1, and NOM1 genes. Our annotation of the false killer whale LMBR1 gene showed that it consists of 17 exons (1473 bp), in contrast to 18 exons (1596 bp) in human, and it displays 93.1% and 95.6% nucleotide and amino acid sequence similarity, respectively, compared with the human gene. In particular, we discovered that exon 10, deleted in the false killer whale LMBR1 gene, is present only in primates, and this fact strongly implies that exon 10 might be crucial in determining primate-specific limb development. ZRS and TFBS sequences have been well conserved across 11 species, suggesting that these regions could be involved in an important function of limb development and limb patterning. The neighboring gene RNF32 showed several lineage-conserved exons, such as exons 2 through 9 conserved in eutherian mammals, exons 3 through 9 conserved in mammals, and exons 5 through 9 conserved in vertebrates. The other neighboring gene, NOM1, had undergone a substitution (ATG→GTA) at the start codon, giving rise to a 36 bp shorter N-terminal sequence compared with the human sequence. Our comparative analysis of the false killer whale LMBR1 genomic locus provides important clues regarding the genetic regions that may play crucial roles in limb development and patterning. |
author2 |
Danzmann, Roy |
format |
Article in Journal/Newspaper |
author |
Kim, Dae-Won Choi, Sang-Haeng Kim, Ryong Nam Kim, Sun-Hong Paik, Sang-Gi Nam, Seong-Hyeuk Kim, Dong-Wook Kim, Aeri Kang, Aram Park, Hong-Seog |
author_facet |
Kim, Dae-Won Choi, Sang-Haeng Kim, Ryong Nam Kim, Sun-Hong Paik, Sang-Gi Nam, Seong-Hyeuk Kim, Dong-Wook Kim, Aeri Kang, Aram Park, Hong-Seog |
author_sort |
Kim, Dae-Won |
title |
Comparative genomic analysis of the false killer whale ( Pseudorca crassidens ) LMBR1 locus |
title_short |
Comparative genomic analysis of the false killer whale ( Pseudorca crassidens ) LMBR1 locus |
title_full |
Comparative genomic analysis of the false killer whale ( Pseudorca crassidens ) LMBR1 locus |
title_fullStr |
Comparative genomic analysis of the false killer whale ( Pseudorca crassidens ) LMBR1 locus |
title_full_unstemmed |
Comparative genomic analysis of the false killer whale ( Pseudorca crassidens ) LMBR1 locus |
title_sort |
comparative genomic analysis of the false killer whale ( pseudorca crassidens ) lmbr1 locus |
publisher |
Canadian Science Publishing |
publishDate |
2010 |
url |
http://dx.doi.org/10.1139/g10-043 http://www.nrcresearchpress.com/doi/full-xml/10.1139/G10-043 http://www.nrcresearchpress.com/doi/pdf/10.1139/G10-043 |
genre |
Killer Whale |
genre_facet |
Killer Whale |
op_source |
Genome volume 53, issue 9, page 658-666 ISSN 0831-2796 1480-3321 |
op_rights |
http://www.nrcresearchpress.com/page/about/CorporateTextAndDataMining |
op_doi |
https://doi.org/10.1139/g10-043 |
container_title |
Genome |
container_volume |
53 |
container_issue |
9 |
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658 |
op_container_end_page |
666 |
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1795669937284448256 |