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Hartley GA, Okhovat M, Hoyt SJ, Fuller E, Pauloski N, Alexandre N, Alexandrov I, Drennan R, Dubocanin D, Gilbert DM, Mao Y, McCann C, Neph S, Ryabov F, Sasaki T, Storer JM, Svendsen D, Troy W, Wells J, Core L, Stergachis A, Carbone L, O'Neill RJ. Centromeric transposable elements and epigenetic status drive karyotypic variation in the eastern hoolock gibbon. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.08.29.610280. [PMID: 39257810 PMCID: PMC11384015 DOI: 10.1101/2024.08.29.610280] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/12/2024]
Abstract
Great apes have maintained a stable karyotype with few large-scale rearrangements; in contrast, gibbons have undergone a high rate of chromosomal rearrangements coincident with rapid centromere turnover. Here we characterize assembled centromeres in the Eastern hoolock gibbon, Hoolock leuconedys (HLE), finding a diverse group of transposable elements (TEs) that differ from the canonical alpha satellites found across centromeres of other apes. We find that HLE centromeres contain a CpG methylation centromere dip region, providing evidence this epigenetic feature is conserved in the absence of satellite arrays; nevertheless, we report a variety of atypical centromeric features, including protein-coding genes and mismatched replication timing. Further, large structural variations define HLE centromeres and distinguish them from other gibbons. Combined with differentially methylated TEs, topologically associated domain boundaries, and segmental duplications at chromosomal breakpoints, we propose that a "perfect storm" of multiple genomic attributes with propensities for chromosome instability shaped gibbon centromere evolution.
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Affiliation(s)
- Gabrielle A Hartley
- Institute for Systems Genomics, University of Connecticut, Storrs, CT, USA
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT, USA
| | - Mariam Okhovat
- Department of Medicine, Knight Cardiovascular Institute, Oregon Health and Science University, Portland, OR, USA
| | - Savannah J Hoyt
- Institute for Systems Genomics, University of Connecticut, Storrs, CT, USA
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT, USA
| | - Emily Fuller
- Institute for Systems Genomics, University of Connecticut, Storrs, CT, USA
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT, USA
| | - Nicole Pauloski
- Institute for Systems Genomics, University of Connecticut, Storrs, CT, USA
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT, USA
| | - Nicolas Alexandre
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, CA, USA
| | - Ivan Alexandrov
- Department of Anatomy and Anthropology and Department of Human Molecular Genetics and Biochemistry, Faculty of Medicine, Tel Aviv University, Israel
| | - Ryan Drennan
- Institute for Systems Genomics, University of Connecticut, Storrs, CT, USA
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT, USA
| | - Danilo Dubocanin
- Division of Medical Genetics, Department of Medicine, University of Washington, Seattle, WA, USA
| | - David M Gilbert
- San Diego Biomedical Research Institute, San Diego, CA 92121, USA
| | - Yizi Mao
- Division of Medical Genetics, Department of Medicine, University of Washington, Seattle, WA, USA
| | - Christine McCann
- Institute for Systems Genomics, University of Connecticut, Storrs, CT, USA
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT, USA
| | - Shane Neph
- Division of Medical Genetics, Department of Medicine, University of Washington, Seattle, WA, USA
| | - Fedor Ryabov
- UC Santa Cruz Genomics Institute, University of California Santa Cruz, Santa Cruz, CA, USA
- Department of Biomolecular Engineering, University of California Santa Cruz, CA, USA
| | - Takayo Sasaki
- San Diego Biomedical Research Institute, San Diego, CA 92121, USA
| | - Jessica M Storer
- Institute for Systems Genomics, University of Connecticut, Storrs, CT, USA
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT, USA
| | - Derek Svendsen
- Institute for Systems Genomics, University of Connecticut, Storrs, CT, USA
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT, USA
| | | | - Jackson Wells
- Department of Medicine, Knight Cardiovascular Institute, Oregon Health and Science University, Portland, OR, USA
| | - Leighton Core
- Institute for Systems Genomics, University of Connecticut, Storrs, CT, USA
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT, USA
| | - Andrew Stergachis
- Division of Medical Genetics, Department of Medicine, University of Washington, Seattle, WA, USA
| | - Lucia Carbone
- Department of Medicine, Knight Cardiovascular Institute, Oregon Health and Science University, Portland, OR, USA
- Department of Molecular and Medical Genetics, Oregon Health and Science University, Portland, OR, USA
- Department of Medical Informatics and Clinical Epidemiology, Oregon Health and Science University, Portland, OR, USA
- Division of Genetics, Oregon National Primate Research Center, Portland, OR, USA
| | - Rachel J O'Neill
- Institute for Systems Genomics, University of Connecticut, Storrs, CT, USA
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT, USA
- Department of Genetics and Genome Sciences, UConn Health, Farmington, CT, USA
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Matsudaira K, Reichard UH, Ishida T, Malaivijitnond S. Introgression and mating patterns between white-handed gibbons (Hylobates lar) and pileated gibbons (Hylobates pileatus) in a natural hybrid zone. PLoS One 2022; 17:e0264519. [PMID: 35358199 PMCID: PMC8970389 DOI: 10.1371/journal.pone.0264519] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Accepted: 02/14/2022] [Indexed: 12/03/2022] Open
Abstract
Gibbons (Family Hylobatidae) are a suitable model for exploring hybridization in pair-living primates as several species form hybrid zones. In Khao Yai National Park, Thailand, white-handed gibbons (Hylobates lar) and pileated gibbons (Hylobates pileatus) are distributed parapatrically and hybridize in a narrow zone. Their phenotypic characteristics suggest limited inter-species gene flow, although this has never been assessed. To uncover the history and degree of gene flow between the two species, we studied the genetic structure of gibbons in the hybrid zone by analyzing fecal DNA samples, phenotypic characteristics, vocalizations and individuals’ social status. We determined eight autosomal single nucleotide variant (SNV) loci, and mitochondrial DNA (mtDNA) and Y-chromosomal haplotypes of 72 gibbons. We compared these markers with reference types of wild pureblood white-handed gibbons (n = 12) in Kaeng Krachan National Park and pureblood pileated gibbons (n = 4) in Khao Soi Dao Wildlife Sanctuary. Autosomal genotypic analyses confirmed the various levels of mixed ancestry for several adult gibbons with or without atypical phenotypic traits in Khao Yai National Park. In some other adult gibbons, the mixed ancestry was not detected in either autosomal SNVs or their phenotypic traits but the mtDNA. Both male and female adult hybrids formed reproductive units mainly with a phenotypic pureblood partner and many of them produced offspring. Taken together, our results suggest that once hybridization occurs, white-handed-pileated-gibbon hybrids can reproduce with either parental species and that the backcrossing and thus introgression may occur in successive generations, with no drastic changes in phenotypic appearance.
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Affiliation(s)
- Kazunari Matsudaira
- Department of Biology, Faculty of Science, Chulalongkorn University, Bangkok, Thailand
- * E-mail:
| | - Ulrich H. Reichard
- Department of Anthropology and Center for Ecology, Southern Illinois University Carbondale, Carbondale, Illinois, United States of America
| | - Takafumi Ishida
- Department of Biological Sciences, School of Science, The University of Tokyo, Tokyo, Japan
| | - Suchinda Malaivijitnond
- Department of Biology, Faculty of Science, Chulalongkorn University, Bangkok, Thailand
- National Primate Research Center of Thailand, Chulalongkorn University, Saraburi, Thailand
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3
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Fan X, Pinthong K, de Oliveira EHC, Tanomtong A, Chen H, Weise A, Liehr T. First Comprehensive Characterization of Phayre’s Leaf-Monkey (Trachypithecus phayrei) Karyotype. Front Genet 2022; 13:841681. [PMID: 35360869 PMCID: PMC8961670 DOI: 10.3389/fgene.2022.841681] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Accepted: 01/31/2022] [Indexed: 11/24/2022] Open
Abstract
The chromosomal homologies of human (Homo sapiens—HSA) and Trachypithecus phayrei (TPH—Phayre’s leaf-monkey, family Cercopithecidae) have previously been studied by using classical chromosome staining/banding and fluorescence in situ hybridization (FISH) from the 1970s to 1990s. In this study, we carried out molecular cytogenetics applying human multicolor banding (MCB), locus-specific, and human heterochromatin-specific probes to establish the first detailed chromosomal map of TPH, which was not available until now. Accordingly, it was possible to precisely determine evolutionary-conserved breakpoints (ECBs) and the orientation of evolutionary-conserved segments compared to HSA. It could be shown that five chromosomes remained completely unchanged between these two species, and 16 chromosomes underwent only intrachromosomal changes. In addition, 50 ECBs that failed to be resolved in previous reports were exactly identified and characterized in this study. It could also be shown that 43.5% of TPH centromere positions were conserved and 56.5% were altered compared to HSA. Interestingly, 82% ECBs in TPH corresponded to human fragile sites. Overall, this study is an essential contribution to future studies and reviews on chromosomal evolution in Cercopithecidae.
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Affiliation(s)
- Xiaobo Fan
- Bioengineering School, Xuzhou University of Technology, Xuzhou, China
- Jena University Hospital, Friedrich Schiller University, Institute of Human Genetics, Jena, Germany
| | - Krit Pinthong
- Department of Biology Faculty of Science, Khon Kaen University, Khon Kaen, Thailand
| | - Edivaldo H. C. de Oliveira
- Faculdade de Ciências Naturais, ICEN, Universidade Federal do Pará, Campus Universitário do Guamá, Belém, Brazil
| | - Alongklod Tanomtong
- Department of Biology Faculty of Science, Khon Kaen University, Khon Kaen, Thailand
| | - Hongwei Chen
- Jena University Hospital, Friedrich Schiller University, Institute of Human Genetics, Jena, Germany
| | - Anja Weise
- Jena University Hospital, Friedrich Schiller University, Institute of Human Genetics, Jena, Germany
| | - Thomas Liehr
- Jena University Hospital, Friedrich Schiller University, Institute of Human Genetics, Jena, Germany
- *Correspondence: Thomas Liehr,
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Eyun S. Accelerated pseudogenization of trace amine-associated receptor genes in primates. GENES, BRAIN, AND BEHAVIOR 2019; 18:e12543. [PMID: 30536583 PMCID: PMC6849804 DOI: 10.1111/gbb.12543] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/25/2018] [Revised: 12/03/2018] [Accepted: 12/05/2018] [Indexed: 01/03/2023]
Abstract
Trace amines (TAs) in the mammalian brain have been investigated for four decades. Trace amine-associated receptors (TAARs) were discovered during the search for receptors activated by TAs. TAARs are considered a second class of vertebrate olfactory receptors and successfully proliferated in conjunction with adaptation to living on the ground to detect carnivore odors. Thus, therian mammals have a high number of TAAR genes due to rapid species-specific gene duplications. In primate lineages, however, their genomes have significantly smaller numbers of TAAR genes than do other mammals. To elucidate the evolutionary force driving these patterns, exhaustive data mining of TAAR genes was performed for 13 primate genomes (covering all four infraorders) and two nonprimate euarchontan genomes. This study identified a large number of pseudogenes in many of these primate genomes and thus investigated the pseudogenization event process for the TAAR repertoires. The degeneration of TAARs is likely associated with arboreal inhabitants reducing their exposure to carnivores, and this was accelerated by the change in the nose shape of haplorhines after their divergence from strepsirrhines. Arboreal life may have decreased the reliance on the chemosensing of predators, suggestive of leading to the depauperation of TAAR subfamilies. The evolutionary deterioration of TAARs in primates has been reestablished in recently derived primates due to high selection pressure and probably functional diversity.
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Affiliation(s)
- Seong‐il Eyun
- Department of Life ScienceChung‐Ang UniversitySeoulKorea
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Nie WH, Wang JH, Su WT, Hu Y, He SW, Jiang XL, He K. Species identification of crested gibbons ( Nomascus) in captivity in China using karyotyping- and PCR-based approaches. Zool Res 2018; 39:356-363. [PMID: 29616678 PMCID: PMC6102682 DOI: 10.24272/j.issn.2095-8137.2018.036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
Abstract
Gibbons and siamangs (Hylobatidae) are well-known for their rapid chromosomal evolution, which has resulted in high speciation rate within the family. On the other hand, distinct karyotypes do not prevent speciation, allowing interbreeding between individuals in captivity, and the unwanted hybrids are ethically problematic as all gibbon species are endangered or critically endangered. Thus, accurate species identification is crucial for captive breeding, particularly in China where studbooks are unavailable. Identification based on external morphology is difficult, especially for hybrids, because species are usually similar in appearance. In this study, we employed G-banding karyotyping and fluorescence in situ hybridization (FISH) as well as a PCR-based approach to examine karyotypic characteristics and identify crested gibbons of the genus Nomascus from zoos and nature reserves in China. We characterized and identified five karyotypes from 21 individuals of Nomascus. Using karyotypes and mitochondrial and nuclear genes, we identified three purebred species and three hybrids, including one F2 hybrid between N. gabriellae and N. siki. Our results also supported that N. leucogenys and N. siki shared the same inversion on chromosome 7, which resolves arguments from previous studies. Our results demonstrated that both karyotyping and DNA-based approaches were suitable for identifying purebred species, though neither was ideal for hybrid identification. The advantages and disadvantages of both approaches are discussed. Our results further highlight the importance of animal ethics and welfare, which are critical for endangered species in captivity.
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Affiliation(s)
- Wen-Hui Nie
- Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming Yunnan 650223, China; E-mail:
| | - Jin-Huan Wang
- Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming Yunnan 650223, China
| | - Wei-Ting Su
- Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming Yunnan 650223, China
| | - Yu Hu
- Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming Yunnan 650223, China
| | - Shui-Wang He
- Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming Yunnan 650223, China
| | - Xue-Long Jiang
- Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming Yunnan 650223, China; E-mail:
| | - Kai He
- Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming Yunnan 650223, China; E-mail:.,Kyoto University Museum, Kyoto University, Kyoto 606-8417, Japan
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Robicheau BM, Susko E, Harrigan AM, Snyder M. Ribosomal RNA Genes Contribute to the Formation of Pseudogenes and Junk DNA in the Human Genome. Genome Biol Evol 2018; 9:380-397. [PMID: 28204512 PMCID: PMC5381670 DOI: 10.1093/gbe/evw307] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/30/2016] [Indexed: 12/20/2022] Open
Abstract
Approximately 35% of the human genome can be identified as sequence devoid of a selected-effect function, and not derived from transposable elements or repeated sequences. We provide evidence supporting a known origin for a fraction of this sequence. We show that: 1) highly degraded, but near full length, ribosomal DNA (rDNA) units, including both 45S and Intergenic Spacer (IGS), can be found at multiple sites in the human genome on chromosomes without rDNA arrays, 2) that these rDNA sequences have a propensity for being centromere proximal, and 3) that sequence at all human functional rDNA array ends is divergent from canonical rDNA to the point that it is pseudogenic. We also show that small sequence strings of rDNA (from 45S + IGS) can be found distributed throughout the genome and are identifiable as an “rDNA-like signal”, representing 0.26% of the q-arm of HSA21 and ∼2% of the total sequence of other regions tested. The size of sequence strings found in the rDNA-like signal intergrade into the size of sequence strings that make up the full-length degrading rDNA units found scattered throughout the genome. We conclude that the displaced and degrading rDNA sequences are likely of a similar origin but represent different stages in their evolution towards random sequence. Collectively, our data suggests that over vast evolutionary time, rDNA arrays contribute to the production of junk DNA. The concept that the production of rDNA pseudogenes is a by-product of concerted evolution represents a previously under-appreciated process; we demonstrate here its importance.
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Affiliation(s)
- Brent M Robicheau
- Department of Biology, Acadia University, Wolfville, Nova Scotia, Canada
| | - Edward Susko
- Center for Comparative Genomics and Evolutionary Bioinformatics, Department of Mathematics and Statistics, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Amye M Harrigan
- Department of Biology, Acadia University, Wolfville, Nova Scotia, Canada
| | - Marlene Snyder
- Department of Biology, Acadia University, Wolfville, Nova Scotia, Canada
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Muangkram Y, Wajjwalku W, Amano A, Sukmak M. The novel primers for mammal species identification-based mitochondrial cytochrome b sequence: implication for reserved wild animals in Thailand and endangered mammal species in Southeast Asia. Mitochondrial DNA A DNA Mapp Seq Anal 2016; 29:62-72. [PMID: 27758125 DOI: 10.1080/24701394.2016.1238902] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
We presented the powerful techniques for species identification using the short amplicon of mitochondrial cytochrome b gene sequence. Two faecal samples and one single hair sample of the Asian tapir were tested using the new cytochrome b primers. The results showed a high sequence similarity with the mainland Asian tapir group. The comparative sequence analysis of the reserved wild mammals in Thailand and the other endangered mammal species from Southeast Asia comprehensibly verified the potential of our novel primers. The forward and reverse primers were 94.2 and 93.2%, respectively, by the average value of the sequence identity among 77 species sequences, and the overall mean distance was 35.9%. This development technique could provide rapid, simple, and reliable tools for species confirmation. Especially, it could recognize the problematic biological specimens contained less DNA material from illegal products and assist with wildlife crime investigation of threatened species and related forensic casework.
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Affiliation(s)
- Yuttamol Muangkram
- a Graduate School of Life Sciences , Ritsumeikan University , Kusatsu , Shiga , Japan.,b Faculty of Veterinary Medicine , Kasetsart University , Kamphaeng Saen , Nakhon Pathom , Thailand
| | - Worawidh Wajjwalku
- b Faculty of Veterinary Medicine , Kasetsart University , Kamphaeng Saen , Nakhon Pathom , Thailand
| | - Akira Amano
- a Graduate School of Life Sciences , Ritsumeikan University , Kusatsu , Shiga , Japan
| | - Manakorn Sukmak
- b Faculty of Veterinary Medicine , Kasetsart University , Kamphaeng Saen , Nakhon Pathom , Thailand
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9
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Sangpakdee W, Tanomtong A, Fan X, Pinthong K, Weise A, Liehr T. Application of multicolor banding combined with heterochromatic and locus-specific probes identify evolutionary conserved breakpoints in Hylobates pileatus. Mol Cytogenet 2016; 9:17. [PMID: 26893612 PMCID: PMC4758170 DOI: 10.1186/s13039-016-0228-x] [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] [Received: 01/11/2016] [Accepted: 02/10/2016] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The question what makes Homo sapiens sapiens (HSA) special among other species is one of the basic questions of mankind. A small contribution to answer this question is to study the chromosomal constitution of HSA compared to other, closely related species. In order to check the types and extent of evolutionary conserved breakpoints we studied here for the first time the chromosomes of Hylobates pileatus (HPI) compared to HSA and Hylobates lar (HLA) by means of molecular cytogenetics. RESULTS Overall, 68 new evolutionary conserved breakpoints compared to HSA could be characterized in this study. Interestingly, only seven of those were different compared to HLA. However, application of heterochromatic human DNA-probes provided evidence that observed high chromosomal rearrangement rates of gibbons in HPI happened rather in these repetitive elements than in euchromatin, even though most centromeric positions were preserved in HPI compared to HSA. CONCLUSION Understanding genomes of other species and comparing them to HSA needs full karyotypic and high resolution genomic data to approach both: euchromatic and heterochromatic regions of the studied chromosome-content. This study provides full karyotypic data and previously not available data on heterochromatin-syntenies of HPI and HSA.
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Affiliation(s)
- Wiwat Sangpakdee
- Jena University Hospital, Friedrich Schiller University, Institute of Human Genetics, Kollegiengasse 10, D-07743 Jena, Germany ; Department of Biology Faculty of Science, Khon Kaen University, 123 Moo 16 Mittapap Rd., Muang District, Khon Kaen, 40002 Thailand
| | - Alongklod Tanomtong
- Department of Biology Faculty of Science, Khon Kaen University, 123 Moo 16 Mittapap Rd., Muang District, Khon Kaen, 40002 Thailand
| | - Xiaobo Fan
- Jena University Hospital, Friedrich Schiller University, Institute of Human Genetics, Kollegiengasse 10, D-07743 Jena, Germany
| | - Krit Pinthong
- Faculty of Science and Technology, Surindra Rajabhat University, 186 Moo 1, Maung District, Surin, 32000 Thailand
| | - Anja Weise
- Jena University Hospital, Friedrich Schiller University, Institute of Human Genetics, Kollegiengasse 10, D-07743 Jena, Germany
| | - Thomas Liehr
- Jena University Hospital, Friedrich Schiller University, Institute of Human Genetics, Kollegiengasse 10, D-07743 Jena, Germany
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Roos C. Phylogeny and Classification of Gibbons (Hylobatidae). DEVELOPMENTS IN PRIMATOLOGY: PROGRESS AND PROSPECTS 2016. [DOI: 10.1007/978-1-4939-5614-2_7] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
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Fan X, Supiwong W, Weise A, Mrasek K, Kosyakova N, Tanomtong A, Pinthong K, Trifonov VA, Cioffi MDB, Grothmann P, Liehr T, Oliveira EH. Comprehensive characterization of evolutionary conserved breakpoints in four New World Monkey karyotypes compared to Chlorocebus aethiops and Homo sapiens. Heliyon 2015; 1:e00042. [PMID: 27441227 PMCID: PMC4945616 DOI: 10.1016/j.heliyon.2015.e00042] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2015] [Revised: 10/20/2015] [Accepted: 10/23/2015] [Indexed: 11/21/2022] Open
Abstract
Comparative cytogenetic analysis in New World Monkeys (NWMs) using human multicolor banding (MCB) probe sets were not previously done. Here we report on an MCB based FISH-banding study complemented with selected locus-specific and heterochromatin specific probes in four NWMs and one Old World Monkey (OWM) species, i.e. in Alouatta caraya (ACA), Callithrix jacchus (CJA), Cebus apella (CAP), Saimiri sciureus (SSC), and Chlorocebus aethiops (CAE), respectively. 107 individual evolutionary conserved breakpoints (ECBs) among those species were identified and compared with those of other species in previous reports. Especially for chromosomal regions being syntenic to human chromosomes 6, 8, 9, 10, 11, 12 and 16 previously cryptic rearrangements could be observed. 50.4% (54/107) NWM-ECBs were colocalized with those of OWMs, 62.6% (62/99) NWM-ECBs were related with those of Hylobates lar (HLA) and 66.3% (71/107) NWM-ECBs corresponded with those known from other mammalians. Furthermore, human fragile sites were aligned with the ECBs found in the five studied species and interestingly 66.3% ECBs colocalized with those fragile sites (FS). Overall, this study presents detailed chromosomal maps of one OWM and four NWM species. This data will be helpful to further investigation on chromosome evolution in NWM and hominoids in general and is prerequisite for correct interpretation of future sequencing based genomic studies in those species.
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Key Words
- ACA, Alouatta caraya
- Atelidae
- BACs, bacterial artificial chromosomes
- CAE, Chlorocebus aethiops
- CAP, Cebus apella
- CJA, Callithrix jacchus
- Cebidae
- EC, evolutionary conserved
- ECBs, evolutionary conserved breakpoints
- Evolutionary conserved breakpoints
- Evolutionary genetics
- FISH, fluorescence in situ hybridization
- FS, fragile site
- Fragile sites
- Genetics
- HCM, heterochromatin mix
- HLA, Hylobates lar
- HSA, Homo sapiens
- HSBs, homologous syntenic blocks
- MCB, multicolor banding
- Multicolor banding
- NGS, Next-generation sequencing
- NOR, nucleolus organizer region
- NWMs, New World Monkeys
- New World Monkeys
- OWMs, Old World Monkeys
- Old World Monkeys
- SSC, Saimiri sciureus
- subCTM, sub-centromere/subtelomere-specific multicolor (FISH)
- wcp, whole human chromosome painting
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Affiliation(s)
- Xiaobo Fan
- Jena University Hospital, Friedrich Schiller University, Institute of Human Genetics, Kollegiengasse 10, D-07743 Jena, Germany
| | - Weerayuth Supiwong
- Department of Biology Faculty of Science, KhonKaen University, 123 Moo 16 Mittapap Rd., Muang District, KhonKaen 40002, Thailand
| | - Anja Weise
- Jena University Hospital, Friedrich Schiller University, Institute of Human Genetics, Kollegiengasse 10, D-07743 Jena, Germany
| | - Kristin Mrasek
- Jena University Hospital, Friedrich Schiller University, Institute of Human Genetics, Kollegiengasse 10, D-07743 Jena, Germany
| | - Nadezda Kosyakova
- Jena University Hospital, Friedrich Schiller University, Institute of Human Genetics, Kollegiengasse 10, D-07743 Jena, Germany
| | - Alongkoad Tanomtong
- Department of Biology Faculty of Science, KhonKaen University, 123 Moo 16 Mittapap Rd., Muang District, KhonKaen 40002, Thailand
| | - Krit Pinthong
- Department of Biology Faculty of Science, KhonKaen University, 123 Moo 16 Mittapap Rd., Muang District, KhonKaen 40002, Thailand
| | | | - Marcelo de Bello Cioffi
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, SP, Brazil
| | - Pierre Grothmann
- Serengeti-Park Hodenhagen GmbH, Am Safaripark 1, 29693, Hodenhagen, Germany
| | - Thomas Liehr
- Jena University Hospital, Friedrich Schiller University, Institute of Human Genetics, Kollegiengasse 10, D-07743 Jena, Germany
| | - Edivaldo H.C.de Oliveira
- Faculdade de Ciências Naturais, ICEN, Universidade Federal do Pará, Campus Universitário do Guamá, 66075-110 Belém-PA, Brazil
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Choi Y, Jung YD, Ayarpadikannan S, Koga A, Imai H, Hirai H, Roos C, Kim HS. Novel variable number of tandem repeats of gibbon MAOA gene and its evolutionary significance. Genome 2015; 57:427-32. [PMID: 25360715 DOI: 10.1139/gen-2014-0065] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Variable number of tandem repeats (VNTRs) are scattered throughout the primate genome, and genetic variation of these VNTRs have been accumulated during primate radiation. Here, we analyzed VNTRs upstream of the monoamine oxidase A (MAOA) gene in 11 different gibbon species. An abundance of truncated VNTR sequences and copy number differences were observed compared to those of human VNTR sequences. To better understand the biological role of these VNTRs, a luciferase activity assay was conducted and results indicated that selected VNTR sequences of the MAOA gene from human and three different gibbon species (Hylobates klossii, Hylobates lar, and Nomascus concolor) showed silencing ability. Together, these data could be useful for understanding the evolutionary history and functional significance of MAOA VNTR sequences in gibbon species.
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Affiliation(s)
- Yuri Choi
- a Department of Biological Sciences, College of Natural Sciences, Pusan National University, Busan 609-735, Republic of Korea
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13
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Abstract
The world of primate genomics is expanding rapidly in new and exciting ways owing to lowered costs and new technologies in molecular methods and bioinformatics. The primate order is composed of 78 genera and 478 species, including human. Taxonomic inferences are complex and likely a consequence of ongoing hybridization, introgression, and reticulate evolution among closely related taxa. Recently, we applied large-scale sequencing methods and extensive taxon sampling to generate a highly resolved phylogeny that affirms, reforms, and extends previous depictions of primate speciation. The next stage of research uses this phylogeny as a foundation for investigating genome content, structure, and evolution across primates. Ongoing and future applications of a robust primate phylogeny are discussed, highlighting advancements in adaptive evolution of genes and genomes, taxonomy and conservation management of endangered species, next-generation genomic technologies, and biomedicine.
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Affiliation(s)
- Jill Pecon-Slattery
- Laboratory of Genomic Diversity, National Cancer Institute, Frederick, Maryland 21702; Current Affiliation: Smithsonian Conservation Biology Institute, National Zoological Park, Front Royal, Virginia 22630;
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14
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Weise A, Kosyakova N, Voigt M, Aust N, Mrasek K, Löhmer S, Rubtsov N, Karamysheva TV, Trifonov VA, Hardekopf D, Jančušková T, Pekova S, Wilhelm K, Liehr T, Fan X. Comprehensive Analyses of White-Handed Gibbon Chromosomes Enables Access to 92 Evolutionary Conserved Breakpoints Compared to the Human Genome. Cytogenet Genome Res 2015; 145:42-9. [PMID: 25926034 DOI: 10.1159/000381764] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/25/2015] [Indexed: 11/19/2022] Open
Abstract
Gibbon species (Hylobatidae) impress with an unusually high number of numerical and structural chromosomal changes within the family itself as well as compared to other Hominoidea including humans. In former studies applying molecular cytogenetic methods, 86 evolutionary conserved breakpoints (ECBs) were reported in the white-handed gibbon (Hylobates lar, HLA) with respect to the human genome. To analyze those ECBs in more detail and also to achieve a better understanding of the fast karyotype evolution in Hylobatidae, molecular data for these regions are indispensably necessary. In the present study, we obtained whole chromosome-specific probes by microdissection of all 21 HLA autosomes and prepared them for aCGH. Locus-specific DNA probes were also used for further molecular cytogenetic characterization of selected regions. Thus, we could map 6 yet unreported ECBs in HLA with respect to the human genome. Additionally, in 26 of the 86 previously reported ECBs, the present approach enabled a more precise breakpoint mapping. Interestingly, a preferred localization of ECBs within segmental duplications, copy number variant regions, and fragile sites was observed.
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Affiliation(s)
- Anja Weise
- Institute of Human Genetics, Jena University Hospital, Friedrich Schiller University, Jena, Germany
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15
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Baicharoen S, Miyabe-Nishiwaki T, Arsaithamkul V, Hirai Y, Duangsa-ard K, Siriaroonrat B, Domae H, Srikulnath K, Koga A, Hirai H. Locational diversity of alpha satellite DNA and intergeneric hybridization aspects in the Nomascus and Hylobates genera of small apes. PLoS One 2014; 9:e109151. [PMID: 25290445 PMCID: PMC4188616 DOI: 10.1371/journal.pone.0109151] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2014] [Accepted: 08/29/2014] [Indexed: 01/05/2023] Open
Abstract
Recently, we discovered that alpha satellite DNA has unique and genus-specific localizations on the chromosomes of small apes. This study describes the details of alpha satellite localization in the genera Nomascus and Hylobates and explores their usefulness in distinguishing parental genome sets in hybrids between these genera. Fluorescence in situ hybridization was used to establish diagnostic criteria of alpha satellite DNA markers in discriminating small ape genomes. In particular we established the genus specificity of alpha satellite distribution in three species of light-cheeked gibbons (Nomascus leucogenys, N. siki, and N. gabriellae) in comparison to that of Hylobates lar. Then we determined the localization of alpha satellite DNA in a hybrid individual which resulted from a cross between these two genera. In Nomascus the alpha satellite DNA blocks were located at the centromere, telomere, and four interstitial regions. In Hylobates detectable amounts of alpha satellite DNA were seen only at centromeric regions. The differences in alpha satellite DNA locations between Nomascus and Hylobates allowed us to easily distinguish the parental chromosomal sets in the genome of intergeneric hybrid individuals found in Thai and Japanese zoos. Our study illustrates how molecular cytogenetic markers can serve as diagnostic tools to identify the origin of individuals. These molecular tools can aid zoos, captive breeding programs and conservation efforts in managing small apes species. Discovering more information on alpha satellite distribution is also an opportunity to examine phylogenetic and evolutionary questions that are still controversial in small apes.
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Affiliation(s)
- Sudarath Baicharoen
- Bioscience Program, Faculty of Science, Kasetsart University, Bangkok, Thailand
- Center for Advanced Studies in Tropical Natural Resources, National Research University-Kasetsart University, Bangkok, Thailand
- Conservation, Research and Education Division, Zoological Park Organization, Bangkok, Thailand
| | | | - Visit Arsaithamkul
- Conservation, Research and Education Division, Zoological Park Organization, Bangkok, Thailand
| | - Yuriko Hirai
- Primate Research Institute, Kyoto University, Inuyama, Aichi, Japan
| | | | - Boripat Siriaroonrat
- Conservation, Research and Education Division, Zoological Park Organization, Bangkok, Thailand
| | | | - Kornsorn Srikulnath
- Center for Advanced Studies in Tropical Natural Resources, National Research University-Kasetsart University, Bangkok, Thailand
- Department of Genetics, Faculty of Science, Kasetsart University, Bangkok, Thailand
| | - Akihiko Koga
- Primate Research Institute, Kyoto University, Inuyama, Aichi, Japan
| | - Hirohisa Hirai
- Primate Research Institute, Kyoto University, Inuyama, Aichi, Japan
- * E-mail:
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16
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Xiaobo F, Pinthong K, Mkrtchyan H, Siripiyasing P, Kosyakova N, Supiwong W, Tanomtong A, Chaveerach A, Liehr T, de Bello Cioffi M, Weise A. First detailed reconstruction of the karyotype of Trachypithecus cristatus (Mammalia: Cercopithecidae). Mol Cytogenet 2013; 6:58. [PMID: 24341374 PMCID: PMC3914712 DOI: 10.1186/1755-8166-6-58] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2013] [Accepted: 11/21/2013] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND The chromosomal homologies of human (Homo sapiens = HSA) and silvered leaf monkey (Trachypithecus cristatus = TCR) have been previously studied by classical chromosome staining and by fluorescence in situ hybridization (FISH) applying chromosome-specific DNA probes of all human chromosomes in the 1980s and 1990s, respectively. RESULTS However, as the resolution of these techniques is limited we used multicolor banding (MCB) at an ~250-band level, and other selected human DNA probes to establish a detailed chromosomal map of TCR. Therefore it was possible to precisely determine evolutionary conserved breakpoints, orientation of segments and distribution of specific regions in TCR compared to HSA. Overall, 69 evolutionary conserved breakpoints including chromosomal segments, which failed to be resolved in previous reports, were exactly identified and characterized. CONCLUSIONS This work also represents the first molecular cytogenetic one characterizing a multiple sex chromosome system with a male karyotype 44,XY1Y2. The obtained results are compared to other available data for old world monkeys and drawbacks in hominoid evolution are discussed.
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Affiliation(s)
- Fan Xiaobo
- Institute of Human Genetics, Jena University Hospital, Friedrich Schiller University, Kollegiengasse 10, Jena D-07743, Germany
| | - Krit Pinthong
- Faculty of Science and Technology, Surindra Rajabhat University, 186 Moo 1, Surin, Maung District 32000, Thailand
| | - Hasmik Mkrtchyan
- Center of Medical Genetics and Primary Health Care, Abovyan Str 34/3, 001, Yerevan, Armenia
| | - Pornnarong Siripiyasing
- Faculty of Science and Technology, Rajabhat Maha Sarakham University, 80 Nakonsawan Rd, Maha Sarakham, Talad, Maung District 44000, Thailand
| | - Nadezda Kosyakova
- Institute of Human Genetics, Jena University Hospital, Friedrich Schiller University, Kollegiengasse 10, Jena D-07743, Germany
| | - Weerayuth Supiwong
- Department of Biology, Faculty of Science, Khon Kaen University, 123 Moo 16 Mittapap Rd., Khon Kaen, Muang District 40002, Thailand
| | - Alongkoad Tanomtong
- Department of Biology, Faculty of Science, Khon Kaen University, 123 Moo 16 Mittapap Rd., Khon Kaen, Muang District 40002, Thailand
| | - Arunrat Chaveerach
- Department of Biology, Faculty of Science, Khon Kaen University, 123 Moo 16 Mittapap Rd., Khon Kaen, Muang District 40002, Thailand
| | - Thomas Liehr
- Institute of Human Genetics, Jena University Hospital, Friedrich Schiller University, Kollegiengasse 10, Jena D-07743, Germany
| | - Marcelo de Bello Cioffi
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, SP, Brazil
| | - Anja Weise
- Institute of Human Genetics, Jena University Hospital, Friedrich Schiller University, Kollegiengasse 10, Jena D-07743, Germany
- Institut für Humangenetik, Postfach, Jena D-07740, Germany
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17
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Chan YC, Roos C, Inoue-Murayama M, Inoue E, Shih CC, Pei KJC, Vigilant L. Inferring the evolutionary histories of divergences in Hylobates and Nomascus gibbons through multilocus sequence data. BMC Evol Biol 2013; 13:82. [PMID: 23586586 PMCID: PMC3637282 DOI: 10.1186/1471-2148-13-82] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2013] [Accepted: 04/08/2013] [Indexed: 01/15/2023] Open
Abstract
BACKGROUND Gibbons (Hylobatidae) are the most diverse group of living apes. They exist as geographically-contiguous species which diverged more rapidly than did their close relatives, the great apes (Hominidae). Of the four extant gibbon genera, the evolutionary histories of two polyspecific genera, Hylobates and Nomascus, have been the particular focus of research but the DNA sequence data used was largely derived from the maternally inherited mitochondrial DNA (mtDNA) locus. RESULTS To investigate the evolutionary relationships and divergence processes of gibbon species, particularly those of the Hylobates genus, we produced and analyzed a total of 11.5 kb DNA of sequence at 14 biparentally inherited autosomal loci. We find that on average gibbon genera have a high average sequence diversity but a lower degree of genetic differentiation as compared to great ape genera. Our multilocus species tree features H. pileatus in a basal position and a grouping of the four Sundaic island species (H. agilis, H. klossii, H. moloch and H. muelleri). We conducted pairwise comparisons based on an isolation-with-migration (IM) model and detect signals of asymmetric gene flow between H. lar and H. moloch, between H. agilis and H. muelleri, and between N. leucogenys and N. siki. CONCLUSIONS Our multilocus analyses provide inferences of gibbon evolutionary histories complementary to those based on single gene data. The results of IM analyses suggest that the divergence processes of gibbons may be accompanied by gene flow. Future studies using analyses of multi-population model with samples of known provenance for Hylobates and Nomascus species would expand the understanding of histories of gene flow during divergences for these two gibbon genera.
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Affiliation(s)
- Yi-Chiao Chan
- Department of Primatology, Max-Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, Leipzig 04103, Germany.
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18
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Capozzi O, Carbone L, Stanyon RR, Marra A, Yang F, Whelan CW, de Jong PJ, Rocchi M, Archidiacono N. A comprehensive molecular cytogenetic analysis of chromosome rearrangements in gibbons. Genome Res 2012; 22:2520-8. [PMID: 22892276 PMCID: PMC3514681 DOI: 10.1101/gr.138651.112] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Chromosome rearrangements in small apes are up to 20 times more frequent than in most mammals. Because of their complexity, the full extent of chromosome evolution in these hominoids is not yet fully documented. However, previous work with array painting, BAC-FISH, and selective sequencing in two of the four karyomorphs has shown that high-resolution methods can precisely define chromosome breakpoints and map the complex flow of evolutionary chromosome rearrangements. Here we use these tools to precisely define the rearrangements that have occurred in the remaining two karyomorphs, genera Symphalangus (2n = 50) and Hoolock (2n = 38). This research provides the most comprehensive insight into the evolutionary origins of chromosome rearrangements involved in transforming small apes genome. Bioinformatics analyses of the human–gibbon synteny breakpoints revealed association with transposable elements and segmental duplications, providing some insight into the mechanisms that might have promoted rearrangements in small apes. In the near future, the comparison of gibbon genome sequences will provide novel insights to test hypotheses concerning the mechanisms of chromosome evolution. The precise definition of synteny block boundaries and orientation, chromosomal fusions, and centromere repositioning events presented here will facilitate genome sequence assembly for these close relatives of humans.
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Affiliation(s)
- Oronzo Capozzi
- Department of Genetics and Microbiology, University of Bari, 70126 Bari, Italy
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19
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Stanyon R, Rocchi M, Bigoni F, Archidiacono N. Evolutionary molecular cytogenetics of catarrhine primates: past, present and future. Cytogenet Genome Res 2012; 137:273-84. [PMID: 22710640 DOI: 10.1159/000339381] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
The catarrhine primates were the first group of species studied with comparative molecular cytogenetics. Many of the fundamental techniques and principles of analysis were initially applied to comparisons in these primates, including interspecific chromosome painting, reciprocal chromosome painting and the extensive use of cloned DNA probes for evolutionary analysis. The definition and importance of chromosome syntenies and associations for a correct cladistics analysis of phylogenomic relationships were first applied to catarrhines. These early chromosome painting studies vividly illustrated a striking conservation of the genome between humans and macaques. Contemporarily, it also revealed profound differences between humans and gibbons, a group of species more closely related to humans, making it clear that chromosome evolution did not follow a molecular clock. Chromosome painting has now been applied to more that 60 primate species and the translocation history has been mapped onto the major taxonomic divisions in the tree of primate evolution. In situ hybridization of cloned DNA probes, primarily BAC-FISH, also made it possible to more precisely map breakpoints with spanning and flanking BACs. These studies established marker order and disclosed intrachromosomal rearrangements. When applied comparatively to a range of primate species, they led to the discovery of evolutionary new centromeres as an important new category of chromosome evolution. BAC-FISH studies are intimately connected to genome sequencing, and probes can usually be assigned to a precise location in the genome assembly. This connection ties molecular cytogenetics securely to genome sequencing, assuring that molecular cytogenetics will continue to have a productive future in the multidisciplinary science of phylogenomics.
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Affiliation(s)
- R Stanyon
- Department of Evolutionary Biology, University of Florence, Florence, Italy.
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20
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The evolutionary life cycle of the resilient centromere. Chromosoma 2012; 121:327-40. [PMID: 22527114 DOI: 10.1007/s00412-012-0369-6] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2012] [Revised: 03/20/2012] [Accepted: 03/20/2012] [Indexed: 12/13/2022]
Abstract
The centromere is a chromosomal structure that is essential for the accurate segregation of replicated eukaryotic chromosomes to daughter cells. In most centromeres, the underlying DNA is principally made up of repetitive DNA elements, such as tandemly repeated satellite DNA and retrotransposable elements. Paradoxically, for such an essential genomic region, the DNA is rapidly evolving both within and between species. In this review, we show that the centromere locus is a resilient structure that can undergo evolutionary cycles of birth, growth, maturity, death and resurrection. The birth phase is highlighted by examples in humans and other organisms where centromere DNA deletions or chromosome rearrangements can trigger the epigenetic assembly of neocentromeres onto genomic sites without typical features of centromere DNA. In addition, functional centromeres can be generated in the laboratory using various methodologies. Recent mapping of the foundation centromere mark, the histone H3 variant CENP-A, onto near-complete genomes has uncovered examples of new centromeres which have not accumulated centromere repeat DNA. During the growth period of the centromere, repeat DNA begins to appear at some, but not all, loci. The maturity stage is characterised by centromere repeat accumulation, expansions and contractions and the rapid evolution of the centromere DNA between chromosomes of the same species and between species. This stage provides inherent centromere stability, facilitated by repression of gene activity and meiotic recombination at and around the centromeres. Death to a centromere can result from genomic instability precipitating rearrangements, deletions, accumulation of mutations and the loss of essential centromere binding proteins. Surprisingly, ancestral centromeres can undergo resurrection either in the field or in the laboratory, via as yet poorly understood mechanisms. The underlying principle for the preservation of a centromeric evolutionary life cycle is to provide resilience and perpetuity for the all-important structure and function of the centromere.
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21
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Abstract
The evolutionary history of chromosomes can be tracked by the comparative hybridization of large panels of bacterial artificial chromosome clones. This approach has disclosed an unprecedented phenomenon: 'centromere repositioning', that is, the movement of the centromere along the chromosome without marker order variation. The occurrence of evolutionary new centromeres (ENCs) is relatively frequent. In macaque, for instance, 9 out of 20 autosomal centromeres are evolutionarily new; in donkey at least 5 such neocentromeres originated after divergence from the zebra, in less than 1 million years. Recently, orangutan chromosome 9, considered to be heterozygous for a complex rearrangement, was discovered to be an ENC. In humans, in addition to neocentromeres that arise in acentric fragments and result in clinical phenotypes, 8 centromere-repositioning events have been reported. These 'real-time' repositioned centromere-seeding events provide clues to ENC birth and progression. In the present paper, we provide a review of the centromere repositioning. We add new data on the population genetics of the ENC of the orangutan, and describe for the first time an ENC on the X chromosome of squirrel monkeys. Next-generation sequencing technologies have started an unprecedented, flourishing period of rapid whole-genome sequencing. In this context, it is worth noting that these technologies, uncoupled from cytogenetics, would miss all the biological data on evolutionary centromere repositioning. Therefore, we can anticipate that classical and molecular cytogenetics will continue to have a crucial role in the identification of centromere movements. Indeed, all ENCs and human neocentromeres were found following classical and molecular cytogenetic investigations.
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22
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Graphodatsky AS, Trifonov VA, Stanyon R. The genome diversity and karyotype evolution of mammals. Mol Cytogenet 2011; 4:22. [PMID: 21992653 PMCID: PMC3204295 DOI: 10.1186/1755-8166-4-22] [Citation(s) in RCA: 84] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2011] [Accepted: 10/12/2011] [Indexed: 01/30/2023] Open
Abstract
The past decade has witnessed an explosion of genome sequencing and mapping in evolutionary diverse species. While full genome sequencing of mammals is rapidly progressing, the ability to assemble and align orthologous whole chromosome regions from more than a few species is still not possible. The intense focus on building of comparative maps for companion (dog and cat), laboratory (mice and rat) and agricultural (cattle, pig, and horse) animals has traditionally been used as a means to understand the underlying basis of disease-related or economically important phenotypes. However, these maps also provide an unprecedented opportunity to use multispecies analysis as a tool for inferring karyotype evolution. Comparative chromosome painting and related techniques are now considered to be the most powerful approaches in comparative genome studies. Homologies can be identified with high accuracy using molecularly defined DNA probes for fluorescence in situ hybridization (FISH) on chromosomes of different species. Chromosome painting data are now available for members of nearly all mammalian orders. In most orders, there are species with rates of chromosome evolution that can be considered as 'default' rates. The number of rearrangements that have become fixed in evolutionary history seems comparatively low, bearing in mind the 180 million years of the mammalian radiation. Comparative chromosome maps record the history of karyotype changes that have occurred during evolution. The aim of this review is to provide an overview of these recent advances in our endeavor to decipher the karyotype evolution of mammals by integrating the published results together with some of our latest unpublished results.
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Vallender EJ. Expanding whole exome resequencing into non-human primates. Genome Biol 2011; 12:R87. [PMID: 21917143 PMCID: PMC3308050 DOI: 10.1186/gb-2011-12-9-r87] [Citation(s) in RCA: 63] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2011] [Revised: 08/03/2011] [Accepted: 09/02/2011] [Indexed: 01/03/2023] Open
Abstract
Background Complete exome resequencing has the power to greatly expand our understanding of non-human primate genomes. This includes both a better appreciation of the variation that exists in non-human primate model species, but also an improved annotation of their genomes. By developing an understanding of the variation between individuals, non-human primate models of human disease can be better developed. This effort is hindered largely by the lack of comprehensive information on specific non-human primate genetic variation and the costs of generating these data. If the tools that have been developed in humans for complete exome resequencing can be applied to closely related non-human primate species, then these difficulties can be circumvented. Results Using a human whole exome enrichment technique, chimpanzee and rhesus macaque samples were captured alongside a human sample and sequenced using standard next-generation methodologies. The results from the three species were then compared for efficacy. The chimpanzee sample showed similar coverage levels and distributions following exome capture based on the human genome as the human sample. The rhesus macaque sample showed significant coverage in protein-coding sequence but significantly less in untranslated regions. Both chimpanzee and rhesus macaque showed significant numbers of frameshift mutations compared to self-genomes and suggest a need for further annotation. Conclusions Current whole exome resequencing technologies can successfully be used to identify coding-region variation in non-human primates extending into old world monkeys. In addition to identifying variation, whole exome resequencing can aid in better annotation of non-human primate genomes.
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Affiliation(s)
- Eric J Vallender
- New England Primate Research Center, Harvard Medical School, One Pine Hill Drive, Southborough, MA 01772, USA.
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24
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Perelman P, Johnson WE, Roos C, Seuánez HN, Horvath JE, Moreira MAM, Kessing B, Pontius J, Roelke M, Rumpler Y, Schneider MPC, Silva A, O'Brien SJ, Pecon-Slattery J. A molecular phylogeny of living primates. PLoS Genet 2011; 7:e1001342. [PMID: 21436896 PMCID: PMC3060065 DOI: 10.1371/journal.pgen.1001342] [Citation(s) in RCA: 874] [Impact Index Per Article: 67.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2010] [Accepted: 02/16/2011] [Indexed: 12/13/2022] Open
Abstract
Comparative genomic analyses of primates offer considerable potential to define and understand the processes that mold, shape, and transform the human genome. However, primate taxonomy is both complex and controversial, with marginal unifying consensus of the evolutionary hierarchy of extant primate species. Here we provide new genomic sequence (∼8 Mb) from 186 primates representing 61 (∼90%) of the described genera, and we include outgroup species from Dermoptera, Scandentia, and Lagomorpha. The resultant phylogeny is exceptionally robust and illuminates events in primate evolution from ancient to recent, clarifying numerous taxonomic controversies and providing new data on human evolution. Ongoing speciation, reticulate evolution, ancient relic lineages, unequal rates of evolution, and disparate distributions of insertions/deletions among the reconstructed primate lineages are uncovered. Our resolution of the primate phylogeny provides an essential evolutionary framework with far-reaching applications including: human selection and adaptation, global emergence of zoonotic diseases, mammalian comparative genomics, primate taxonomy, and conservation of endangered species. Advances in human biomedicine, including those focused on changes in genes triggered or disrupted in development, resistance/susceptibility to infectious disease, cancers, mechanisms of recombination, and genome plasticity, cannot be adequately interpreted in the absence of a precise evolutionary context or hierarchy. However, little is known about the genomes of other primate species, a situation exacerbated by a paucity of nuclear molecular sequence data necessary to resolve the complexities of primate divergence over time. We overcome this deficiency by sequencing 54 nuclear gene regions from DNA samples representing ∼90% of the diversity present in living primates. We conduct a phylogenetic analysis to determine the origin, evolution, patterns of speciation, and unique features in genome divergence among primate lineages. The resultant phylogenetic tree is remarkably robust and unambiguously resolves many long-standing issues in primate taxonomy. Our data provide a strong foundation for illuminating those genomic differences that are uniquely human and provide new insights on the breadth and richness of gene evolution across all primate lineages.
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Affiliation(s)
- Polina Perelman
- Laboratory of Genomic Diversity, National Cancer Institute–Frederick, Frederick, Maryland, United States of America
| | - Warren E. Johnson
- Laboratory of Genomic Diversity, National Cancer Institute–Frederick, Frederick, Maryland, United States of America
| | - Christian Roos
- Gene Bank of Primates and Primate Genetics Laboratory, German Primate Center, Göttingen, Germany
| | - Hector N. Seuánez
- Division of Genetics, Instituto Nacional de Câncer and Department of Genetics, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Julie E. Horvath
- Department of Evolutionary Anthropology and Institute for Genome Sciences and Policy, Duke University, Durham, North Carolina, United States of America
| | - Miguel A. M. Moreira
- Division of Genetics, Instituto Nacional de Câncer and Department of Genetics, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Bailey Kessing
- SAIC–Frederick, Laboratory of Genomic Diversity, National Cancer Institute–Frederick, Frederick, Maryland, United States of America
| | - Joan Pontius
- SAIC–Frederick, Laboratory of Genomic Diversity, National Cancer Institute–Frederick, Frederick, Maryland, United States of America
| | - Melody Roelke
- SAIC–Frederick, Laboratory of Genomic Diversity, National Cancer Institute–Frederick, Frederick, Maryland, United States of America
| | - Yves Rumpler
- Physiopathologie et Médecine Translationnelle, Faculté de Médecine, Université Louis Pasteur, Strasbourg, France
| | | | | | - Stephen J. O'Brien
- Laboratory of Genomic Diversity, National Cancer Institute–Frederick, Frederick, Maryland, United States of America
| | - Jill Pecon-Slattery
- Laboratory of Genomic Diversity, National Cancer Institute–Frederick, Frederick, Maryland, United States of America
- * E-mail:
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25
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Kim SK, Carbone L, Becquet C, Mootnick AR, Li DJ, de Jong PJ, Wall JD. Patterns of genetic variation within and between Gibbon species. Mol Biol Evol 2011; 28:2211-8. [PMID: 21368318 PMCID: PMC3144381 DOI: 10.1093/molbev/msr033] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
Gibbons are small, arboreal, highly endangered apes that are understudied compared with other hominoids. At present, there are four recognized genera and approximately 17 species, all likely to have diverged from each other within the last 5-6 My. Although the gibbon phylogeny has been investigated using various approaches (i.e., vocalization, morphology, mitochondrial DNA, karyotype, etc.), the precise taxonomic relationships are still highly debated. Here, we present the first survey of nuclear sequence variation within and between gibbon species with the goal of estimating basic population genetic parameters. We gathered ~60 kb of sequence data from a panel of 19 gibbons representing nine species and all four genera. We observe high levels of nucleotide diversity within species, indicative of large historical population sizes. In addition, we find low levels of genetic differentiation between species within a genus comparable to what has been estimated for human populations. This is likely due to ongoing or episodic gene flow between species, and we estimate a migration rate between Nomascus leucogenys and N. gabriellae of roughly one migrant every two generations. Together, our findings suggest that gibbons have had a complex demographic history involving hybridization or mixing between diverged populations.
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Affiliation(s)
- Sung K Kim
- Institute for Human Genetics, University of California San Francisco, CA, USA
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Alekseyev MA, Pevzner PA. Comparative genomics reveals birth and death of fragile regions in mammalian evolution. Genome Biol 2010; 11:R117. [PMID: 21118492 PMCID: PMC3156956 DOI: 10.1186/gb-2010-11-11-r117] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2010] [Revised: 10/05/2010] [Accepted: 11/30/2010] [Indexed: 12/15/2022] Open
Abstract
Background An important question in genome evolution is whether there exist fragile regions (rearrangement hotspots) where chromosomal rearrangements are happening over and over again. Although nearly all recent studies supported the existence of fragile regions in mammalian genomes, the most comprehensive phylogenomic study of mammals raised some doubts about their existence. Results Here we demonstrate that fragile regions are subject to a birth and death process, implying that fragility has a limited evolutionary lifespan. Conclusions This finding implies that fragile regions migrate to different locations in different mammals, explaining why there exist only a few chromosomal breakpoints shared between different lineages. The birth and death of fragile regions as a phenomenon reinforces the hypothesis that rearrangements are promoted by matching segmental duplications and suggests putative locations of the currently active fragile regions in the human genome.
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Affiliation(s)
- Max A Alekseyev
- Department of Computer Science & Engineering, University of South Carolina, 301 Main St, Columbia, SC 29208, USA.
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Thinh VN, Mootnick AR, Geissmann T, Li M, Ziegler T, Agil M, Moisson P, Nadler T, Walter L, Roos C. Mitochondrial evidence for multiple radiations in the evolutionary history of small apes. BMC Evol Biol 2010; 10:74. [PMID: 20226039 PMCID: PMC2841658 DOI: 10.1186/1471-2148-10-74] [Citation(s) in RCA: 94] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2009] [Accepted: 03/12/2010] [Indexed: 12/01/2022] Open
Abstract
BACKGROUND Gibbons or small apes inhabit tropical and subtropical rain forests in Southeast Asia and adjacent regions, and are, next to great apes, our closest living relatives. With up to 16 species, gibbons form the most diverse group of living hominoids, but the number of taxa, their phylogenetic relationships and their phylogeography is controversial. To further the discussion of these issues we analyzed the complete mitochondrial cytochrome b gene from 85 individuals representing all gibbon species, including most subspecies. RESULTS Based on phylogenetic tree reconstructions, several monophyletic clades were detected, corresponding to genera, species and subspecies. A significantly supported branching pattern was obtained for members of the genus Nomascus but not for the genus Hylobates. The phylogenetic relationships among the four genera were also not well resolved. Nevertheless, the new data permitted the estimation of divergence ages for all taxa for the first time and showed that most lineages emerged during four short time periods. In the first, between approximately 6.7 and approximately 8.3 mya, the four gibbon genera diverged from each other. In the second (approximately 3.0 - approximately 3.9 mya) and in the third period (approximately 1.3 - approximately 1.8 mya), Hylobates and Hoolock differentiated. Finally, between approximately 0.5 and approximately 1.1 mya, Hylobates lar diverged into subspecies. In contrast, differentiation of Nomascus into species and subspecies was a continuous and prolonged process lasting from approximately 4.2 until approximately 0.4 mya. CONCLUSIONS Although relationships among gibbon taxa on various levels remain unresolved, the present study provides a more complete view of the evolutionary and biogeographic history of the hylobatid family, and a more solid genetic basis for the taxonomic classification of the surviving taxa. We also show that mtDNA constitutes a useful marker for the accurate identification of individual gibbons, a tool which is urgently required to locate hunting hotspots and select individuals for captive breeding programs. Further studies including nuclear sequence data are necessary to completely understand the phylogeny and phylogeography of gibbons.
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Affiliation(s)
- Van Ngoc Thinh
- Primate Genetics Laboratory, German Primate Center, Kellnerweg 4, 37077 Göttingen, Germany
| | - Alan R Mootnick
- Gibbon Conservation Center, PO Box 800249, Santa Clarita, CA 91380, USA
| | - Thomas Geissmann
- Anthropological Institute, University Zurich-Irchel, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Ming Li
- Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, 1 Beichen West Road, Chaoyang District, Beijing 100101, PR China
| | - Thomas Ziegler
- Siberut Conservation Programme, Reproductive Biology Unit, German Primate Center, Kellnerweg 4, 37077 Göttingen, Germany
| | - Muhammad Agil
- Department of Clinic, Reproduction and Pathology, Faculty of Veterinary Medicine, Bogor Agricultural University, Jl. Agatis, Kampus IPB Darmaga, 16680 Bogor, Indonesia
| | - Pierre Moisson
- Parc Zoologique et Botanique de Mulhouse, 51, rue du Jardin Zoologique, 68100 Mulhouse, France
| | - Tilo Nadler
- Frankfurt Zoological Society, Endangered Primate Rescue Center, Cuc Phuong National Park, Nho Quan District, Ninh Binh Province, Vietnam
| | - Lutz Walter
- Primate Genetics Laboratory, German Primate Center, Kellnerweg 4, 37077 Göttingen, Germany
- Gene Bank of Primates, German Primate Center, Kellnerweg 4, 37077 Göttingen, Germany
| | - Christian Roos
- Primate Genetics Laboratory, German Primate Center, Kellnerweg 4, 37077 Göttingen, Germany
- Gene Bank of Primates, German Primate Center, Kellnerweg 4, 37077 Göttingen, Germany
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28
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Abi-Rached L, Kuhl H, Roos C, ten Hallers B, Zhu B, Carbone L, de Jong PJ, Mootnick AR, Knaust F, Reinhardt R, Parham P, Walter L. A small, variable, and irregular killer cell Ig-like receptor locus accompanies the absence of MHC-C and MHC-G in gibbons. THE JOURNAL OF IMMUNOLOGY 2009; 184:1379-91. [PMID: 20026738 DOI: 10.4049/jimmunol.0903016] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
The killer cell Ig-like receptors (KIRs) of NK cells recognize MHC class I ligands and function in placental reproduction and immune defense against pathogens. During the evolution of monkeys, great apes, and humans, an ancestral KIR3DL gene expanded to become a diverse and rapidly evolving gene family of four KIR lineages. Characterizing the KIR locus are three framework regions, defining two intervals of variable gene content. By analysis of four KIR haplotypes from two species of gibbon, we find that the smaller apes do not conform to these rules. Although diverse and irregular in structure, the gibbon haplotypes are unusually small, containing only two to five functional genes. Comparison with the predicted ancestral hominoid KIR haplotype indicates that modern gibbon KIR haplotypes were formed by a series of deletion events, which created new hybrid genes as well as eliminating ancestral genes. Of the three framework regions, only KIR3DL3 (lineage V), defining the 5' end of the KIR locus, is present and intact on all gibbon KIR haplotypes. KIR2DL4 (lineage I) defining the central framework region has been a major target for elimination or inactivation, correlating with the absence of its putative ligand, MHC-G, in gibbons. Similarly, the MHC-C-driven expansion of lineage III KIR genes in great apes has not occurred in gibbons because they lack MHC-C. Our results indicate that the selective forces shaping the size and organization of the gibbon KIR locus differed from those acting upon the KIR of other hominoid species.
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Affiliation(s)
- Laurent Abi-Rached
- Department of Structural Biology, Stanford University, Stanford, CA 94305, USA
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29
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Capozzi O, Purgato S, D'Addabbo P, Archidiacono N, Battaglia P, Baroncini A, Capucci A, Stanyon R, Della Valle G, Rocchi M. Evolutionary descent of a human chromosome 6 neocentromere: a jump back to 17 million years ago. Genome Res 2009; 19:778-84. [PMID: 19411601 DOI: 10.1101/gr.085688.108] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
Molecular cytogenetics provides a visual, pictorial record of the tree of life, and in this respect the fusion origin of human chromosome 2 is a well-known paradigmatic example. Here we report on a variant chromosome 6 in which the centromere jumped to 6p22.1. ChIP-chip experiments with antibodies against the centromeric proteins CENP-A and CENP-C exactly defined the neocentromere as lying at chr6:26,407-26,491 kb. We investigated in detail the evolutionary history of chromosome 6 in primates and found that the primate ancestor had a homologous chromosome with the same marker order, but with the centromere located at 6p22.1. Sometime between 17 and 23 million years ago (Mya), in the common ancestor of humans and apes, the centromere of chromosome 6 moved from 6p22.1 to its current location. The neocentromere we discovered, consequently, has jumped back to the ancestral position, where a latent centromere-forming potentiality persisted for at least 17 Myr. Because all living organisms form a tree of life, as first conceived by Darwin, evolutionary perspectives can provide compelling underlying explicative grounds for contemporary genomic phenomena.
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Affiliation(s)
- Oronzo Capozzi
- Department of Genetics and Microbiology, University of Bari, Bari, Italy
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Carbone L, Harris RA, Vessere GM, Mootnick AR, Humphray S, Rogers J, Kim SK, Wall JD, Martin D, Jurka J, Milosavljevic A, de Jong PJ. Evolutionary breakpoints in the gibbon suggest association between cytosine methylation and karyotype evolution. PLoS Genet 2009; 5:e1000538. [PMID: 19557196 PMCID: PMC2695003 DOI: 10.1371/journal.pgen.1000538] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2009] [Accepted: 05/26/2009] [Indexed: 01/30/2023] Open
Abstract
Gibbon species have accumulated an unusually high number of chromosomal changes since diverging from the common hominoid ancestor 15-18 million years ago. The cause of this increased rate of chromosomal rearrangements is not known, nor is it known if genome architecture has a role. To address this question, we analyzed sequences spanning 57 breaks of synteny between northern white-cheeked gibbons (Nomascus l. leucogenys) and humans. We find that the breakpoint regions are enriched in segmental duplications and repeats, with Alu elements being the most abundant. Alus located near the gibbon breakpoints (<150 bp) have a higher CpG content than other Alus. Bisulphite allelic sequencing reveals that these gibbon Alus have a lower average density of methylated cytosine that their human orthologues. The finding of higher CpG content and lower average CpG methylation suggests that the gibbon Alu elements are epigenetically distinct from their human orthologues. The association between undermethylation and chromosomal rearrangement in gibbons suggests a correlation between epigenetic state and structural genome variation in evolution.
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Affiliation(s)
- Lucia Carbone
- Children's Hospital and Research Center Oakland, Oakland, California, United States of America.
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31
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Carbone L, Mootnick AR, Nadler T, Moisson P, Ryder O, Roos C, de Jong PJ. A chromosomal inversion unique to the northern white-cheeked gibbon. PLoS One 2009; 4:e4999. [PMID: 19319194 PMCID: PMC2656618 DOI: 10.1371/journal.pone.0004999] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2008] [Accepted: 02/16/2009] [Indexed: 01/03/2023] Open
Abstract
The gibbon family belongs to the superfamily Hominoidea and includes 15 species divided into four genera. Each genus possesses a distinct karyotype with chromosome numbers varying from 38 to 52. This diversity is the result of numerous chromosomal changes that have accumulated during the evolution of the gibbon lineage, a quite unique feature in comparison with other hominoids and most of the other primates. Some gibbon species and subspecies rank among the most endangered primates in the world. Breeding programs can be extremely challenging and hybridization plays an important role within the factors responsible for the decline of captive gibbons. With less than 500 individuals left in the wild, the northern white-cheeked gibbon (Nomascus leucogenys leucogenys, NLE) is the most endangered primate in a successful captive breeding program. We present here the analysis of an inversion that we show being specific for the northern white-cheeked gibbon and can be used as one of the criteria to distinguish this subspecies from other gibbon taxa. The availability of the sequence spanning for one of the breakpoints of the inversion allows detecting it by a simple PCR test also on low quality DNA. Our results demonstrate the important role of genomics in providing tools for conservation efforts.
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Affiliation(s)
- Lucia Carbone
- BACPAC Resources, Children's Hospital of Oakland Research Institute, Oakland, California, United States of America.
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32
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Rocchi M, Stanyon R, Archidiacono N. Evolutionary new centromeres in primates. PROGRESS IN MOLECULAR AND SUBCELLULAR BIOLOGY 2009; 48:103-52. [PMID: 19521814 DOI: 10.1007/978-3-642-00182-6_5] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
The centromere has a pivotal role in structuring chromosomal architecture, but remains a poorly understood and seemingly paradoxical "black hole." Centromeres are a very rapidly evolving segment of the genome and it is now known that centromere shifts in evolution are not rare and must be considered on a par with other chromosome rearrangements. Recently, unprecedented findings on neocentromeres and evolutionary new centromeres (ENC) have helped clarify the relationship of the centromere within the genome and shown that these two phenomena are two faces of the same coin. No prominent sequence features are known that promote centromere formation and both types of new centromeres are formed epigenetically, both clinical neocentromeres and ENC cluster at chromosomal "hotspots." The clustering of neocentromeres in 8p is probably the result of the relatively high frequency of noncanonical pairing. Studies on the evolution of the chromosomes 3, 13, and 15 help explain why there are clusters of neocentromeres. These domains often correspond to ancestral inactivated centromeres and some regions can preserve features that trigger neocentromere emergence over tens of millions of years. Neocentromeres may be correlated with the distribution of segmental duplications (SDs) in regions of extreme plasticity that often can be characterized as gene deserts. Further, because centromeres and associated pericentric regions are dynamically complex, centromere shifts may turbocharge genome reorganization by influencing the distribution of heterochromatin. The "reuse" of regions as centromere seeding-points in evolution and in human clinical cases further extends the concept of "reuse" of specific domains for "chromosomal events."
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Affiliation(s)
- Mariano Rocchi
- Dipartimento di Genetica e Microbiologia, Via Amendola, 165/A, 70126 Bari, Italy.
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Girirajan S, Chen L, Graves T, Marques-Bonet T, Ventura M, Fronick C, Fulton L, Rocchi M, Fulton RS, Wilson RK, Mardis ER, Eichler EE. Sequencing human-gibbon breakpoints of synteny reveals mosaic new insertions at rearrangement sites. Genome Res 2008; 19:178-90. [PMID: 19029537 DOI: 10.1101/gr.086041.108] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
The gibbon genome exhibits extensive karyotypic diversity with an increased rate of chromosomal rearrangements during evolution. In an effort to understand the mechanistic origin and implications of these rearrangement events, we sequenced 24 synteny breakpoint regions in the white-cheeked gibbon (Nomascus leucogenys, NLE) in the form of high-quality BAC insert sequences (4.2 Mbp). While there is a significant deficit of breakpoints in genes, we identified seven human gene structures involved in signaling pathways (DEPDC4, GNG10), phospholipid metabolism (ENPP5, PLSCR2), beta-oxidation (ECH1), cellular structure and transport (HEATR4), and transcription (ZNF461), that have been disrupted in the NLE gibbon lineage. Notably, only three of these genes show the expected evolutionary signatures of pseudogenization. Sequence analysis of the breakpoints suggested both nonclassical nonhomologous end-joining (NHEJ) and replication-based mechanisms of rearrangement. A substantial number (11/24) of human-NLE gibbon breakpoints showed new insertions of gibbon-specific repeats and mosaic structures formed from disparate sequences including segmental duplications, LINE, SINE, and LTR elements. Analysis of these sites provides a model for a replication-dependent repair mechanism for double-strand breaks (DSBs) at rearrangement sites and insights into the structure and formation of primate segmental duplications at sites of genomic rearrangements during evolution.
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Affiliation(s)
- Santhosh Girirajan
- Department of Genome Sciences, Howard Hughes Medical Institute, University of Washington School of Medicine, Seattle, Washington 98195, USA
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