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Kitano T, Kim CG, Blancher A, Saitou N. No Distinction of Orthology/Paralogy between Human and Chimpanzee Rh Blood Group Genes. Genome Biol Evol 2016; 8:519-27. [PMID: 26872772 PMCID: PMC4824203 DOI: 10.1093/gbe/evw022] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
On human (Homo sapiens) chromosome 1, there is a tandem duplication encompassing Rh blood group genes (Hosa_RHD and Hosa_RHCE). This duplication occurred in the common ancestor of humans, chimpanzees (Pan troglodytes), and gorillas, after splitting from their common ancestor with orangutans. Although several studies have been conducted on ape Rh blood group genes, the clear genome structures of the gene clusters remain unknown. Here, we determined the genome structure of the gene cluster of chimpanzee Rh genes by sequencing five BAC (Bacterial Artificial Chromosome) clones derived from chimpanzees. We characterized three complete loci (Patr_RHα, Patr_RHβ, and Patr_RHγ). In the Patr_RHβ locus, a short version of the gene, which lacked the middle part containing exons 4-8, was observed. The Patr_RHα and Patr_RHβ genes were located on the locations corresponding to Hosa_RHD and Hosa_RHCE, respectively, and Patr_RHγ was in the immediate vicinity of Patr_RHβ. Sequence comparisons revealed high sequence similarity between Patr_RHβ and Hosa_RHCE, while the chimpanzee Rh gene closest to Hosa_RHD was not Patr_RHα but rather Patr_RHγ. The results suggest that rearrangements and gene conversions frequently occurred between these genes and that the classic orthology/paralogy dichotomy no longer holds between human and chimpanzee Rh blood group genes.
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Affiliation(s)
- Takashi Kitano
- Division of Population Genetics, National Institute of Genetics, Mishima, Japan Present address: Department of Biomolecular Functional Engineering, College of Engineering, Ibaraki University, Hitachi, Japan
| | - Choong-Gon Kim
- Division of Population Genetics, National Institute of Genetics, Mishima, Japan Present address: Marine Ecosystem Research Division, Korea Institute of Ocean Science and Technology, Ansan, Korea
| | - Antoine Blancher
- Laboratoire d'Immunogénétique Moléculaire (LIMT, EA3034), Faculté de Médecine Purpan, Université Paul Sabatier, Toulouse III, France
| | - Naruya Saitou
- Division of Population Genetics, National Institute of Genetics, Mishima, Japan
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Perry GH, Tchinda J, McGrath SD, Zhang J, Picker SR, Cáceres AM, Iafrate AJ, Tyler-Smith C, Scherer SW, Eichler EE, Stone AC, Lee C. Hotspots for copy number variation in chimpanzees and humans. Proc Natl Acad Sci U S A 2006; 103:8006-11. [PMID: 16702545 PMCID: PMC1472420 DOI: 10.1073/pnas.0602318103] [Citation(s) in RCA: 191] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
Copy number variation is surprisingly common among humans and can be involved in phenotypic diversity and variable susceptibility to complex diseases, but little is known of the extent of copy number variation in nonhuman primates. We have used two array-based comparative genomic hybridization platforms to identify a total of 355 copy number variants (CNVs) in the genomes of 20 wild-born chimpanzees (Pan troglodytes) and have compared the identified chimpanzee CNVs to known human CNVs from previous studies. Many CNVs were observed in the corresponding regions in both chimpanzees and humans; especially those CNVs of higher frequency. Strikingly, these loci are enriched 20-fold for ancestral segmental duplications, which may facilitate CNV formation through nonallelic homologous recombination mechanisms. Therefore, some of these regions may be unstable "hotspots" for the genesis of copy number variation, with recurrent duplications and deletions occurring across and within species.
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Affiliation(s)
- George H. Perry
- *School of Human Evolution and Social Change, Arizona State University, Tempe, AZ 85287
- Department of Pathology, Brigham and Women’s Hospital, Boston, MA 02115
| | - Joelle Tchinda
- Department of Pathology, Brigham and Women’s Hospital, Boston, MA 02115
| | - Sean D. McGrath
- Department of Genome Sciences, University of Washington School of Medicine and the
| | - Junjun Zhang
- The Centre for Applied Genomics, Department of Genetics and Genomic Biology, The Hospital for Sick Children, Toronto, ON, Canada M5G 1X8
| | - Simon R. Picker
- Department of Pathology, Brigham and Women’s Hospital, Boston, MA 02115
| | - Angela M. Cáceres
- *School of Human Evolution and Social Change, Arizona State University, Tempe, AZ 85287
| | - A. John Iafrate
- Department of Pathology, Massachusetts General Hospital, Boston, MA 02114
- Harvard Medical School, Boston, MA 02115
| | - Chris Tyler-Smith
- **The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SA, United Kingdom; and
| | - Stephen W. Scherer
- The Centre for Applied Genomics, Department of Genetics and Genomic Biology, The Hospital for Sick Children, Toronto, ON, Canada M5G 1X8
- Department of Molecular and Medical Genetics, University of Toronto, ON, Canada M5S 1A8
| | - Evan E. Eichler
- Department of Genome Sciences, University of Washington School of Medicine and the
- Howard Hughes Medical Institute, Seattle, WA 98195
| | - Anne C. Stone
- *School of Human Evolution and Social Change, Arizona State University, Tempe, AZ 85287
| | - Charles Lee
- Department of Pathology, Brigham and Women’s Hospital, Boston, MA 02115
- Harvard Medical School, Boston, MA 02115
- To whom correspondence should be addressed at:
Department of Pathology, Brigham and Women’s Hospital, 20 Shattuck Street, Thorn Building, Room 6-12A, Boston, MA 02115. E-mail:
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