1
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Logsdon GA, Rozanski AN, Ryabov F, Potapova T, Shepelev VA, Catacchio CR, Porubsky D, Mao Y, Yoo D, Rautiainen M, Koren S, Nurk S, Lucas JK, Hoekzema K, Munson KM, Gerton JL, Phillippy AM, Ventura M, Alexandrov IA, Eichler EE. The variation and evolution of complete human centromeres. Nature 2024; 629:136-145. [PMID: 38570684 PMCID: PMC11062924 DOI: 10.1038/s41586-024-07278-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2023] [Accepted: 03/07/2024] [Indexed: 04/05/2024]
Abstract
Human centromeres have been traditionally very difficult to sequence and assemble owing to their repetitive nature and large size1. As a result, patterns of human centromeric variation and models for their evolution and function remain incomplete, despite centromeres being among the most rapidly mutating regions2,3. Here, using long-read sequencing, we completely sequenced and assembled all centromeres from a second human genome and compared it to the finished reference genome4,5. We find that the two sets of centromeres show at least a 4.1-fold increase in single-nucleotide variation when compared with their unique flanks and vary up to 3-fold in size. Moreover, we find that 45.8% of centromeric sequence cannot be reliably aligned using standard methods owing to the emergence of new α-satellite higher-order repeats (HORs). DNA methylation and CENP-A chromatin immunoprecipitation experiments show that 26% of the centromeres differ in their kinetochore position by >500 kb. To understand evolutionary change, we selected six chromosomes and sequenced and assembled 31 orthologous centromeres from the common chimpanzee, orangutan and macaque genomes. Comparative analyses reveal a nearly complete turnover of α-satellite HORs, with characteristic idiosyncratic changes in α-satellite HORs for each species. Phylogenetic reconstruction of human haplotypes supports limited to no recombination between the short (p) and long (q) arms across centromeres and reveals that novel α-satellite HORs share a monophyletic origin, providing a strategy to estimate the rate of saltatory amplification and mutation of human centromeric DNA.
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Affiliation(s)
- Glennis A Logsdon
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
- Department of Genetics, Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Allison N Rozanski
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - Fedor Ryabov
- Masters Program in National Research University Higher School of Economics, Moscow, Russia
| | - Tamara Potapova
- Stowers Institute for Medical Research, Kansas City, MO, USA
| | | | - Claudia R Catacchio
- Department of Biosciences, Biotechnology and Environment, University of Bari Aldo Moro, Bari, Italy
| | - David Porubsky
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - Yafei Mao
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Ministry of Education, Shanghai Jiao Tong University, Shanghai, China
| | - DongAhn Yoo
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - Mikko Rautiainen
- Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
- Institute for Molecular Medicine Finland (FIMM), Helsinki Institute of Life Science (HiLIFE), University of Helsinki, Helsinki, Finland
| | - Sergey Koren
- Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Sergey Nurk
- Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
- Oxford Nanopore Technologies, Oxford, United Kingdom
| | - Julian K Lucas
- Department of Biomolecular Engineering, University of California, Santa Cruz, Santa Cruz, CA, USA
- UC Santa Cruz Genomics Institute, University of California, Santa Cruz, Santa Cruz, CA, USA
| | - Kendra Hoekzema
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - Katherine M Munson
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | | | - Adam M Phillippy
- Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Mario Ventura
- Department of Biosciences, Biotechnology and Environment, University of Bari Aldo Moro, Bari, Italy
| | - Ivan A Alexandrov
- Department of Human Molecular Genetics and Biochemistry, Tel Aviv University, Tel Aviv, Israel
- Department of Anatomy and Anthropology, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
- Dan David Center for Human Evolution and Biohistory Research, Tel Aviv University, Tel Aviv, Israel
| | - Evan E Eichler
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA.
- Howard Hughes Medical Institute, University of Washington, Seattle, WA, USA.
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2
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Zhou Y, Tian J, Jiang H, Han M, Wang Y, Lu J. Phylogeography and demographic history of macaques, fascicularis species group, in East Asia: Inferred from multiple genomic markers. Mol Phylogenet Evol 2024; 194:108042. [PMID: 38401812 DOI: 10.1016/j.ympev.2024.108042] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2023] [Revised: 02/06/2024] [Accepted: 02/18/2024] [Indexed: 02/26/2024]
Abstract
Climate changes at larger scales have influenced dispersal and range shifts of many taxa in East Asia. The fascicularis species group of macaques is composed of four species and is widely distributed in Southeast and East Asia. However, its phylogeography and demographic histories are currently poorly understood. Herein, we assembled autosomal, mitogenome, and Y-chromosome data for 106 individuals, and combined them with 174 mtDNA dloop haplotypes of this species group, with particular focus on the demographic histories and dispersal routes of Macaca fuscata, M. cyclopis, and M. mulatta. The results showed: (1) three monophyletic clades for M. fuscata, M. cyclopis, and M. mulatta based on the multiple genomics analyses; (2) the disparate demographic trajectories of the three species after their split ∼1.0 Ma revealed that M. cyclopis and M. fuscata were derived from an ancestral M. mulatta population; (3) the speciation time of M. cyclopis was later than that of M. fuscata, and their divergence time occurred at the beginning of "Ryukyu Coral Sea Stage" (1.0-0.2 Ma) when the East China Sea land bridge was completely submerged by the sea level rose; and (4) the three parallel rivers (Nujiang, Lancangjiang, and Jinshajiang) of Southwestern China divided M. mulatta into Indian and Chinese genetic populations ∼200 kya. These results shed light on understanding not only the evolutionary history of the fascicularis species group but also the formation mechanism of faunal diversity in East Asia during the Pleistocene.
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Affiliation(s)
- Yanyan Zhou
- School of Life Sciences, Zhengzhou University, Zhengzhou 450001, China; Institute of Biodiversity and Ecology, Zhengzhou University, Zhengzhou 450001, China
| | - Jundong Tian
- School of Life Sciences, Zhengzhou University, Zhengzhou 450001, China; Institute of Biodiversity and Ecology, Zhengzhou University, Zhengzhou 450001, China
| | - Haijun Jiang
- School of Life Sciences, Zhengzhou University, Zhengzhou 450001, China; Institute of Biodiversity and Ecology, Zhengzhou University, Zhengzhou 450001, China
| | - Mengya Han
- School of Life Sciences, Zhengzhou University, Zhengzhou 450001, China; Institute of Biodiversity and Ecology, Zhengzhou University, Zhengzhou 450001, China
| | - Yuwei Wang
- School of Life Sciences, Zhengzhou University, Zhengzhou 450001, China; Institute of Biodiversity and Ecology, Zhengzhou University, Zhengzhou 450001, China
| | - Jiqi Lu
- School of Life Sciences, Zhengzhou University, Zhengzhou 450001, China; Institute of Biodiversity and Ecology, Zhengzhou University, Zhengzhou 450001, China.
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3
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Kistner A, Chichester JA, Wang L, Calcedo R, Greig JA, Cardwell LN, Wright MC, Couthouis J, Sethi S, McIntosh BE, McKeever K, Wadsworth S, Wilson JM, Kakkis E, Sullivan BA. Prednisolone and rapamycin reduce the plasma cell gene signature and may improve AAV gene therapy in cynomolgus macaques. Gene Ther 2024; 31:128-143. [PMID: 37833563 PMCID: PMC10940161 DOI: 10.1038/s41434-023-00423-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Revised: 09/07/2023] [Accepted: 09/28/2023] [Indexed: 10/15/2023]
Abstract
Adeno-associated virus (AAV) vector gene therapy is a promising approach to treat rare genetic diseases; however, an ongoing challenge is how to best modulate host immunity to improve transduction efficiency and therapeutic outcomes. This report presents two studies characterizing multiple prophylactic immunosuppression regimens in male cynomolgus macaques receiving an AAVrh10 gene therapy vector expressing human coagulation factor VIII (hFVIII). In study 1, no immunosuppression was compared with prednisolone, rapamycin (or sirolimus), rapamycin and cyclosporin A in combination, and cyclosporin A and azathioprine in combination. Prednisolone alone demonstrated higher mean peripheral blood hFVIII expression; however, this was not sustained upon taper. Anti-capsid and anti-hFVIII antibody responses were robust, and vector genomes and transgene mRNA levels were similar to no immunosuppression at necropsy. Study 2 compared no immunosuppression with prednisolone alone or in combination with rapamycin or methotrexate. The prednisolone/rapamycin group demonstrated an increase in mean hFVIII expression and a mean delay in anti-capsid IgG development until after rapamycin taper. Additionally, a significant reduction in the plasma cell gene signature was observed with prednisolone/rapamycin, suggesting that rapamycin's tolerogenic effects may include plasma cell differentiation blockade. Immunosuppression with prednisolone and rapamycin in combination could improve therapeutic outcomes in AAV vector gene therapy.
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Affiliation(s)
| | - Jessica A Chichester
- Gene Therapy Program, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Lili Wang
- Gene Therapy Program, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Roberto Calcedo
- Gene Therapy Program, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Affinia Therapeutics, Waltham, MA, USA
| | - Jenny A Greig
- Gene Therapy Program, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Leah N Cardwell
- Ultragenyx Gene Therapy, Ultragenyx Pharmaceutical Inc., Cambridge, MA, USA
| | | | | | | | | | | | - Samuel Wadsworth
- Ultragenyx Gene Therapy, Ultragenyx Pharmaceutical Inc., Cambridge, MA, USA
| | - James M Wilson
- Gene Therapy Program, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Emil Kakkis
- Ultragenyx Pharmaceutical Inc., Novato, CA, USA
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4
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Ito T, Kimura R, Wakamori H, Tanaka M, Tezuka A, Nagano AJ, Hamada Y, Kawamoto Y. Hybridization and its impact on the ontogenetic allometry of skulls in macaques. Evolution 2024; 78:284-299. [PMID: 37952211 DOI: 10.1093/evolut/qpad206] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Revised: 10/25/2023] [Accepted: 11/09/2023] [Indexed: 11/14/2023]
Abstract
The role of hybridization in morphological diversification is a fundamental topic in evolutionary biology. However, despite the accumulated knowledge on adult hybrid variation, how hybridization affects ontogenetic allometry is less well understood. Here, we investigated the effects of hybridization on postnatal ontogenetic allometry in the skulls of a putative hybrid population of introduced Taiwanese macaques (Macaca cyclopis) and native Japanese macaques (Macaca fuscata). Genomic analyses indicated that the population consisted of individuals with varying degrees of admixture, formed by male migration from Japanese to Taiwanese macaques. For overall skull shape, ontogenetic trajectories were shifted by hybridization in a nearly additive manner, with moderate transgressive variation observed throughout development. In contrast, for the maxillary sinus (hollow space in the face), hybrids grew as fast as Taiwanese macaques, diverging from Japanese macaques, which showed slow growth. Consequently, adult hybrids showed a mosaic pattern, that is, the maxillary sinus is as large as that of Taiwanese macaques, while the overall skull shape is intermediate. Our findings suggest that the transgressive variation can be caused by prenatal shape modification and nonadditive inheritance on regional growth rates, highlighting the complex genetic and ontogenetic bases underlying hybridization-induced morphological diversification.
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Affiliation(s)
- Tsuyoshi Ito
- The Kyoto University Museum, Kyoto University, Sakyo, Kyoto, Japan
- Department of Evolution and Phylogeny, Primate Research Institute, Kyoto University, Inuyama, Aichi, Japan
| | - Ryosuke Kimura
- Department of Human Biology and Anatomy, Graduate School of Medicine, University of the Ryukyus, Nishihara, Okinawa, Japan
| | - Hikaru Wakamori
- Department of Evolution and Phylogeny, Primate Research Institute, Kyoto University, Inuyama, Aichi, Japan
| | - Mikiko Tanaka
- Department of Evolution and Phylogeny, Primate Research Institute, Kyoto University, Inuyama, Aichi, Japan
| | - Ayumi Tezuka
- Department of Life Sciences, Faculty of Agriculture, Ryukoku University, Otsu, Shiga, Japan
| | - Atsushi J Nagano
- Department of Life Sciences, Faculty of Agriculture, Ryukoku University, Otsu, Shiga, Japan
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Yamagata, Japan
| | - Yuzuru Hamada
- Department of Evolution and Phylogeny, Primate Research Institute, Kyoto University, Inuyama, Aichi, Japan
| | - Yoshi Kawamoto
- School of Veterinary Medicine, Nippon Veterinary and Life Science University, Musashino, Tokyo, Japan
- Center for Human Evolution Modeling Research, Primate Research Institute, Kyoto University, Inuyama, Aichi, Japan
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5
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Lee W, Hayakawa T, Kiyono M, Yamabata N, Enari H, Enari HS, Fujita S, Kawazoe T, Asai T, Oi T, Kondo T, Uno T, Seki K, Shimada M, Tsuji Y, Langgeng A, MacIntosh A, Suzuki K, Yamada K, Onishi K, Ueno M, Kubo K, Hanya G. Diet-related factors strongly shaped the gut microbiota of Japanese macaques. Am J Primatol 2023; 85:e23555. [PMID: 37766673 DOI: 10.1002/ajp.23555] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Revised: 08/08/2023] [Accepted: 09/17/2023] [Indexed: 09/29/2023]
Abstract
Although knowledge of the functions of the gut microbiome has increased greatly over the past few decades, our understanding of the mechanisms governing its ecology and evolution remains obscure. While host genetic distance is a strong predictor of the gut microbiome in large-scale studies and captive settings, its influence has not always been evident at finer taxonomic scales, especially when considering among the recently diverged animals in natural settings. Comparing the gut microbiome of 19 populations of Japanese macaques Macaca fuscata across the Japanese archipelago, we assessed the relative roles of host genetic distance, geographic distance and dietary factors in influencing the macaque gut microbiome. Our results suggested that the macaques may maintain a core gut microbiome, while each population may have acquired some microbes from its specific habitat/diet. Diet-related factors such as season, forest, and reliance on anthropogenic foods played a stronger role in shaping the macaque gut microbiome. Among closely related mammalian hosts, host genetics may have limited effects on the gut microbiome since the hosts generally have smaller physiological differences. This study contributes to our understanding of the relative roles of host phylogeography and dietary factors in shaping the gut microbiome of closely related mammalian hosts.
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Affiliation(s)
- Wanyi Lee
- Center for Ecological Research, Kyoto University, Inuyama, Japan
- Japan Society for the Promotion of Science, Tokyo, Japan
- Primate Research Institute, Kyoto University, Inuyama, Japan
| | - Takashi Hayakawa
- Faculty of Environmental Earth Science, Hokkaido University, Sapporo, Hokkaido, Japan
| | - Mieko Kiyono
- Graduate School of Human Development and Environment, Kobe University, Kobe, Hyogo, Japan
| | - Naoto Yamabata
- Institute of Natural and Environmental Sciences, University of Hyogo, Sanda, Hyogo, Japan
| | - Hiroto Enari
- Faculty of Agriculture, Yamagata University, Wakabamachi, Tsuruoka, Yamagata, Japan
| | - Haruka S Enari
- Faculty of Agriculture, Yamagata University, Wakabamachi, Tsuruoka, Yamagata, Japan
| | - Shiho Fujita
- Department of Behavioral Physiology and Ecology, Joint Faculty of Veterinary Medicine, Kagoshima University, Kagoshima, Japan
| | - Tatsuro Kawazoe
- Research Institute for Languages and Cultures of Asia and Africa, Tokyo University of Foreign Studies, Tokyo, Japan
| | - Takayuki Asai
- South Kyushu Wildlife Management Center, Kagoshima, Japan
| | - Toru Oi
- Faculty of Bioresources and Environmental Science, Ishikawa Prefectural University, Nonoichi, Ishikawa, Japan
| | | | - Takeharu Uno
- Tohoku Monkey and Mammal Management Center, Sendai, Miyagi, Japan
| | - Kentaro Seki
- Tohoku Monkey and Mammal Management Center, Sendai, Miyagi, Japan
| | - Masaki Shimada
- Department of Animal Sciences, Teikyo University of Science, Uenohara, Yamanashi, Japan
| | - Yamato Tsuji
- Department of Science and Engineering, Ishinomaki Senshu University, Ishinomaki, Miyagi, Japan
| | - Abdullah Langgeng
- Primate Research Institute, Kyoto University, Inuyama, Japan
- Wildlife Research Center, Kyoto University, Kanrin, Inuyama, Japan
| | - Andrew MacIntosh
- Primate Research Institute, Kyoto University, Inuyama, Japan
- Wildlife Research Center, Kyoto University, Kanrin, Inuyama, Japan
| | | | - Kazunori Yamada
- Graduate School of Human Sciences, Osaka University, Suita, Osaka, Japan
| | - Kenji Onishi
- Department of Early Childhood Education, Nara University of Education, Nara, Japan
| | - Masataka Ueno
- Faculty of Applied Sociology, Kindai University, Higashiosaka, Osaka, Japan
| | - Kentaro Kubo
- Cultural Asset Management Division, Board of Education, Oita-City, Japan
| | - Goro Hanya
- Center for Ecological Research, Kyoto University, Inuyama, Japan
- Primate Research Institute, Kyoto University, Inuyama, Japan
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6
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Bembry-Colegrove B, Giarmarco M, Barborek R, Rowlan J, Kuchenbecker J, Rezeanu D, Neitz J, Neitz M. Poster Session II: Intravitreal gene therapy in primate reaches extrafoveal cones. J Vis 2023; 23:66. [PMID: 38109582 DOI: 10.1167/jov.23.15.66] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2023] Open
Abstract
Intravitreal delivery of gene therapy vectors to the retina carries lower risk of adverse events versus subretinal injections, but efficiently targeting cones is a challenge. We used a new adeno-associated vector (AAV) to deliver genes to primate cone photoreceptors. The vector carries a cassette directing expression of an engineered 493 nm opsin to long- and middle-wavelength (L/M) cones, and was injected into the vitreous of the left eye of an adult macaque. An identical AAV carrying a fusion of the engineered opsin to green fluorescent protein (GFP) was injected into the right eye. Electroretinograms were performed on the left eye before and after injection to measure isolated 493 nm light responses; 5 weeks post-injection, response increased modestly. A central strip of the right eye was prepared for histology with cryosections; we found ~30% of cones in the fovea had been transduced, with a preference toward L/M cones (see https://iovs.arvojournals.org/article.aspx?articleid=2782955). Upon close examination of GFP in the peripheral retina, we were surprised to find extensive expression in cones across the retina. Here, we report patches of expression from the perifovea to the retinal margin which reaches ~10% of cones. Expression patches appeared stochastically, or in regions containing blood vessels or disrupted Muller cells. This demonstrates that extrafoveal expression is attainable using intravitreal injection of gene therapy vectors in an adult primate.
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Affiliation(s)
| | | | | | | | | | | | - Jay Neitz
- University of Washington Department of Ophthalmology
| | - Maureen Neitz
- University of Washington Department of Ophthalmology
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7
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Zemke NR, Armand EJ, Wang W, Lee S, Zhou J, Li YE, Liu H, Tian W, Nery JR, Castanon RG, Bartlett A, Osteen JK, Li D, Zhuo X, Xu V, Chang L, Dong K, Indralingam HS, Rink JA, Xie Y, Miller M, Krienen FM, Zhang Q, Taskin N, Ting J, Feng G, McCarroll SA, Callaway EM, Wang T, Lein ES, Behrens MM, Ecker JR, Ren B. Conserved and divergent gene regulatory programs of the mammalian neocortex. Nature 2023; 624:390-402. [PMID: 38092918 PMCID: PMC10719095 DOI: 10.1038/s41586-023-06819-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2023] [Accepted: 11/01/2023] [Indexed: 12/17/2023]
Abstract
Divergence of cis-regulatory elements drives species-specific traits1, but how this manifests in the evolution of the neocortex at the molecular and cellular level remains unclear. Here we investigated the gene regulatory programs in the primary motor cortex of human, macaque, marmoset and mouse using single-cell multiomics assays, generating gene expression, chromatin accessibility, DNA methylome and chromosomal conformation profiles from a total of over 200,000 cells. From these data, we show evidence that divergence of transcription factor expression corresponds to species-specific epigenome landscapes. We find that conserved and divergent gene regulatory features are reflected in the evolution of the three-dimensional genome. Transposable elements contribute to nearly 80% of the human-specific candidate cis-regulatory elements in cortical cells. Through machine learning, we develop sequence-based predictors of candidate cis-regulatory elements in different species and demonstrate that the genomic regulatory syntax is highly preserved from rodents to primates. Finally, we show that epigenetic conservation combined with sequence similarity helps to uncover functional cis-regulatory elements and enhances our ability to interpret genetic variants contributing to neurological disease and traits.
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Affiliation(s)
- Nathan R Zemke
- Department of Cellular and Molecular Medicine, University of California, San Diego School of Medicine, La Jolla, CA, USA
- Center for Epigenomics, University of California, San Diego School of Medicine, La Jolla, CA, USA
| | - Ethan J Armand
- Department of Cellular and Molecular Medicine, University of California, San Diego School of Medicine, La Jolla, CA, USA
- Bioinformatics and Systems Biology Program, University of California, San Diego, La Jolla, CA, USA
| | - Wenliang Wang
- Genomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Seoyeon Lee
- Department of Cellular and Molecular Medicine, University of California, San Diego School of Medicine, La Jolla, CA, USA
| | - Jingtian Zhou
- Bioinformatics and Systems Biology Program, University of California, San Diego, La Jolla, CA, USA
- Genomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Yang Eric Li
- Department of Cellular and Molecular Medicine, University of California, San Diego School of Medicine, La Jolla, CA, USA
| | - Hanqing Liu
- Genomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, CA, USA
- Division of Biological Sciences, University of California, San Diego, La Jolla, CA, USA
| | - Wei Tian
- Genomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Joseph R Nery
- Genomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Rosa G Castanon
- Genomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Anna Bartlett
- Genomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Julia K Osteen
- Computational Neurobiology Laboratory, The Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Daofeng Li
- Department of Genetics, The Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine, St Louis, MO, USA
| | - Xiaoyu Zhuo
- Department of Genetics, The Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine, St Louis, MO, USA
| | - Vincent Xu
- Department of Genetics, The Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine, St Louis, MO, USA
| | - Lei Chang
- Department of Cellular and Molecular Medicine, University of California, San Diego School of Medicine, La Jolla, CA, USA
| | - Keyi Dong
- Department of Cellular and Molecular Medicine, University of California, San Diego School of Medicine, La Jolla, CA, USA
- Center for Epigenomics, University of California, San Diego School of Medicine, La Jolla, CA, USA
| | - Hannah S Indralingam
- Department of Cellular and Molecular Medicine, University of California, San Diego School of Medicine, La Jolla, CA, USA
- Center for Epigenomics, University of California, San Diego School of Medicine, La Jolla, CA, USA
| | - Jonathan A Rink
- Computational Neurobiology Laboratory, The Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Yang Xie
- Department of Cellular and Molecular Medicine, University of California, San Diego School of Medicine, La Jolla, CA, USA
| | - Michael Miller
- Department of Cellular and Molecular Medicine, University of California, San Diego School of Medicine, La Jolla, CA, USA
- Center for Epigenomics, University of California, San Diego School of Medicine, La Jolla, CA, USA
| | - Fenna M Krienen
- Princeton Neuroscience Institute, Princeton University, Princeton, NJ, USA
- Department of Genetics, Harvard Medical School, Boston, USA
| | - Qiangge Zhang
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- McGovern Institute for Brain Research, Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Naz Taskin
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | - Guoping Feng
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- McGovern Institute for Brain Research, Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Steven A McCarroll
- Department of Genetics, Harvard Medical School, Boston, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Edward M Callaway
- Systems Neurobiology Laboratories, The Salk Institute for Biological Studies, La Jolla, CA, USA
- Department of Neurosciences, University of California San Diego, La Jolla, CA, USA
| | - Ting Wang
- Department of Genetics, The Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine, St Louis, MO, USA
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO, USA
| | - Ed S Lein
- Allen Institute for Brain Science, Seattle, WA, USA
- Department of Neurological Surgery, University of Washington, Seattle, WA, USA
| | - M Margarita Behrens
- Computational Neurobiology Laboratory, The Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Joseph R Ecker
- Genomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, CA, USA.
- Howard Hughes Medical Institute, The Salk Institute for Biological Studies, La Jolla, CA, USA.
| | - Bing Ren
- Department of Cellular and Molecular Medicine, University of California, San Diego School of Medicine, La Jolla, CA, USA.
- Center for Epigenomics, University of California, San Diego School of Medicine, La Jolla, CA, USA.
- Institute of Genomic Medicine, Moores Cancer Center, School of Medicine, University of California San Diego, La Jolla, CA, USA.
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8
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Tan X, Qi J, Liu Z, Fan P, Liu G, Zhang L, Shen Y, Li J, Roos C, Zhou X, Li M. Phylogenomics Reveals High Levels of Incomplete Lineage Sorting at the Ancestral Nodes of the Macaque Radiation. Mol Biol Evol 2023; 40:msad229. [PMID: 37823401 PMCID: PMC10638670 DOI: 10.1093/molbev/msad229] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Revised: 09/06/2023] [Accepted: 10/08/2023] [Indexed: 10/13/2023] Open
Abstract
The genus Macaca includes 23 species assigned into 4 to 7 groups. It exhibits the largest geographic range and represents the most successful example of adaptive radiation of nonhuman primates. However, intrageneric phylogenetic relationships among species remain controversial and have not been resolved so far. In this study, we conducted a phylogenomic analysis on 16 newly generated and 8 published macaque genomes. We found strong evidence supporting the division of this genus into 7 species groups. Incomplete lineage sorting (ILS) was the primary factor contributing to the discordance observed among gene trees; however, we also found evidence of hybridization events, specifically between the ancestral arctoides/sinica and silenus/nigra lineages that resulted in the hybrid formation of the fascicularis/mulatta group. Combined with fossil data, our phylogenomic data were used to establish a scenario for macaque radiation. These findings provide insights into ILS and potential ancient introgression events that were involved in the radiation of macaques, which will lead to a better understanding of the rapid speciation occurring in nonhuman primates.
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Affiliation(s)
- Xinxin Tan
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- Geneplus-Beijing Institute, Beijing 102206, China
| | - Jiwei Qi
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Zhijin Liu
- College of Life Sciences, Capital Normal University, Beijing 100049, China
| | - Pengfei Fan
- School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, China
| | - Gaoming Liu
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Liye Zhang
- Primate Genetics Laboratory, German Primate Center, Leibniz Institute for Primate Research, Göttingen 37077, Germany
| | - Ying Shen
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Jing Li
- Key Laboratory of Bio-resources and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610064, China
| | - Christian Roos
- Primate Genetics Laboratory, German Primate Center, Leibniz Institute for Primate Research, Göttingen 37077, Germany
- Gene Bank of Primates, German Primate Center, Leibniz Institute for Primate Research, Göttingen 37077, Germany
| | - Xuming Zhou
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Ming Li
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
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9
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Martins KM, Breton C, Zheng Q, Zhang Z, Latshaw C, Greig JA, Wilson JM. Prevalent and Disseminated Recombinant and Wild-Type Adeno-Associated Virus Integration in Macaques and Humans. Hum Gene Ther 2023; 34:1081-1094. [PMID: 37930949 PMCID: PMC10659022 DOI: 10.1089/hum.2023.134] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2023] [Accepted: 08/25/2023] [Indexed: 11/08/2023] Open
Abstract
Integration of naturally occurring adeno-associated viruses (AAV; wild-type AAV [wtAAV]) and those used in gene therapy (recombinant AAV [rAAV]) into host genomic DNA has been documented for over two decades. Results from mouse and dog studies have raised concerns of insertional mutagenesis and clonal expansion following AAV exposure, particularly in the context of gene therapy. This study aimed to characterize the genomic location, abundance, and expansion of wtAAV and rAAV integrations in macaque and human genomes. Using an unbiased, next-generation sequencing-based approach, we identified the genome-wide integration loci in tissue samples (primarily liver) in 168 nonhuman primates (NHPs) and 85 humans naïve to rAAV exposure and 86 NHPs treated with rAAV in preclinical studies. Our results suggest that rAAV and wtAAV integrations exhibit similar, broad distribution patterns across species, with a higher frequency in genomic regions highly vulnerable to DNA damage or close to highly transcribed genes. rAAV exhibited a higher abundance of unique integration loci, whereas wtAAV integration loci were associated with greater clonal expansion. This expansive and detailed characterization of AAV integration in NHPs and humans provides key translational insights, with important implications for the safety of rAAV as a gene therapy vector.
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Affiliation(s)
- Kelly M. Martins
- Gene Therapy Program, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Camilo Breton
- Gene Therapy Program, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Qi Zheng
- Gene Therapy Program, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Zhe Zhang
- Gene Therapy Program, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Caitlin Latshaw
- Gene Therapy Program, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Jenny A. Greig
- Gene Therapy Program, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - James M. Wilson
- Gene Therapy Program, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
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10
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Lan W, Quan L, Li Y, Ou J, Duan B, Mei T, Tan X, Chen W, Feng L, Wan C, Zhao W, Chodosh J, Seto D, Zhang Q. Isolation of novel simian adenoviruses from macaques for development of a vector for human gene therapy and vaccines. J Virol 2023; 97:e0101423. [PMID: 37712705 PMCID: PMC10617444 DOI: 10.1128/jvi.01014-23] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Accepted: 07/16/2023] [Indexed: 09/16/2023] Open
Abstract
IMPORTANCE Adenoviruses are widely used in gene therapy and vaccine delivery. Due to the high prevalence of human adenoviruses (HAdVs), the pre-existing immunity against HAdVs in humans is common, which limits the wide and repetitive use of HAdV vectors. In contrast, the pre-existing immunity against simian adenoviruses (SAdVs) is low in humans. Therefore, we performed epidemiological investigations of SAdVs in simians and found that the SAdV prevalence was as high as 33.9%. The whole-genome sequencing and sequence analysis showed SAdV diversity and possible cross species transmission. One isolate with low level of pre-existing neutralizing antibodies in humans was used to construct replication-deficient SAdV vectors with E4orf6 substitution and E1/E3 deletion. Interestingly, we found that the E3 region plays a critical role in its replication in human cells, but the absence of this region could be compensated for by the E4orf6 from HAdV-5 and the E1 expression intrinsic to HEK293 cells.
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Affiliation(s)
- Wendong Lan
- BSL-3 Laboratory (Guangdong), Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University, Guangzhou, Guangdong, China
| | - Lulu Quan
- BSL-3 Laboratory (Guangdong), Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University, Guangzhou, Guangdong, China
| | - Yiqiang Li
- Institute of Medical Microbiology, Jinan University, Guangzhou, Guangdong, China
| | - Junxian Ou
- Institute of Medical Microbiology, Jinan University, Guangzhou, Guangdong, China
| | - Biyan Duan
- Institute of Medical Microbiology, Jinan University, Guangzhou, Guangdong, China
| | - Ting Mei
- Institute of Medical Microbiology, Jinan University, Guangzhou, Guangdong, China
| | - Xiao Tan
- Institute of Medical Microbiology, Jinan University, Guangzhou, Guangdong, China
| | - Weiwei Chen
- The Fifth Medical Center, Chinese PLA General Hospital, Beijing, China
| | - Liqiang Feng
- State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, Guangdong, China
| | - Chengsong Wan
- BSL-3 Laboratory (Guangdong), Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University, Guangzhou, Guangdong, China
| | - Wei Zhao
- BSL-3 Laboratory (Guangdong), Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University, Guangzhou, Guangdong, China
| | - James Chodosh
- Department of Ophthalmology and Visual Sciences, University of New Mexico School of Medicine, Albuquerque, New Mexico, USA
| | - Donald Seto
- Bioinformatics and Computational Biology Program, School of Systems Biology, George Mason University, Manassas, Virginia, USA
| | - Qiwei Zhang
- BSL-3 Laboratory (Guangdong), Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University, Guangzhou, Guangdong, China
- Institute of Medical Microbiology, Jinan University, Guangzhou, Guangdong, China
- Key Laboratory of Viral Pathogenesis & Infection Prevention and Control (Jinan University), Ministry of Education, Guangzhou, Guangdong, China
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11
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Zhang BL, Chen W, Wang Z, Pang W, Luo MT, Wang S, Shao Y, He WQ, Deng Y, Zhou L, Chen J, Yang MM, Wu Y, Wang L, Fernández-Bellon H, Molloy S, Meunier H, Wanert F, Kuderna L, Marques-Bonet T, Roos C, Qi XG, Li M, Liu Z, Schierup MH, Cooper DN, Liu J, Zheng YT, Zhang G, Wu DD. Comparative genomics reveals the hybrid origin of a macaque group. Sci Adv 2023; 9:eadd3580. [PMID: 37262187 PMCID: PMC10413639 DOI: 10.1126/sciadv.add3580] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Accepted: 01/25/2023] [Indexed: 06/03/2023]
Abstract
Although species can arise through hybridization, compelling evidence for hybrid speciation has been reported only rarely in animals. Here, we present phylogenomic analyses on genomes from 12 macaque species and show that the fascicularis group originated from an ancient hybridization between the sinica and silenus groups ~3.45 to 3.56 million years ago. The X chromosomes and low-recombination regions exhibited equal contributions from each parental lineage, suggesting that they were less affected by subsequent backcrossing and hence could have played an important role in maintaining hybrid integrity. We identified many reproduction-associated genes that could have contributed to the development of the mixed sexual phenotypes characteristic of the fascicularis group. The phylogeny within the silenus group was also resolved, and functional experimentation confirmed that all extant Western silenus species are susceptible to HIV-1 infection. Our study provides novel insights into macaque evolution and reveals a hybrid speciation event that has occurred only very rarely in primates.
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Affiliation(s)
- Bao-Lin Zhang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
| | - Wu Chen
- Guangzhou Zoo and Guangzhou Wildlife Research Center, Guangzhou 510070, China
| | - Zefu Wang
- Key Laboratory for Bio-resource and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Biology and the Environment, Nanjing Forestry University, Nanjing 210037, China
| | - Wei Pang
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences, KIZ-CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
| | - Meng-Ting Luo
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences, KIZ-CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
| | - Sheng Wang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
| | - Yong Shao
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
| | - Wen-Qiang He
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences, KIZ-CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
| | - Yuan Deng
- BGI-Shenzhen, Shenzhen 518083, China
- Section for Ecology and Evolution, Department of Biology, University of Copenhagen, Copenhagen DK-2100, Denmark
| | - Long Zhou
- Center for Evolutionary and Organismal Biology and Women’s Hospital at Zhejiang University School of Medicine, Hangzhou 310058, China
| | | | - Min-Min Yang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
| | - Yajiang Wu
- Guangzhou Zoo and Guangzhou Wildlife Research Center, Guangzhou 510070, China
| | - Lu Wang
- Shaanxi Key Laboratory for Animal Conservation, College of Life Sciences, Northwest University, Xi’an, China
| | | | | | - Hélène Meunier
- Centre de Primatologie, de l'Université de Strasbourg, Niederhausbergen, France
- Laboratoire de Neurosciences Cognitives et Adaptatives, UMR 7364, Université de Strasbourg, Strasbourg, France
| | - Fanélie Wanert
- Plateforme SILABE, Université de Strasbourg, Niederhausbergen, France
| | - Lukas Kuderna
- Genome Interpretation Department, Illumina Inc., Foster City, CA, USA
| | - Tomas Marques-Bonet
- Institute of Evolutionary Biology (UPF-CSIC), PRBB, Dr. Aiguader 88, Barcelona 08003, Spain
- Catalan Institution of Research and Advanced Studies (ICREA), Passeig de Lluís Companys, 23, Barcelona 08010, Spain
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Baldiri i Reixac 4, Barcelona 08028, Spain
- Institut Català de Paleontologia Miquel Crusafont, Universitat Autònoma de Barcelona, Edifici ICTA-ICP, c/Columnes s/n, 08193 Cerdanyola del Vallès, Barcelona, Spain
| | - Christian Roos
- Primate Genetics Laboratory, German Primate Center, Göttingen, Germany
- Gene Bank of Primates, German Primate Center, Göttingen, Germany
| | - Xiao-Guang Qi
- Shaanxi Key Laboratory for Animal Conservation, College of Life Sciences, Northwest University, Xi’an, China
| | - Ming Li
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Zhijin Liu
- College of Life Sciences, Capital Normal University, Beijing 100048, China
| | | | - David N. Cooper
- Institute of Medical Genetics, School of Medicine, Cardiff University, Cardiff CF14 4XN, UK
| | - Jianquan Liu
- Key Laboratory for Bio-resource and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China
- State Key Laboratory of Grassland Agro-ecosystem, Institute of Innovation Ecology and College of Life Sciences, Lanzhou University, Lanzhou 730000, China
| | - Yong-Tang Zheng
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences, KIZ-CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
- National Resource Center for Non-Human Primates, Kunming Primate Research Center and National Research Facility for Phenotypic and Genetic Analysis of Model Animals (Primate Facility), Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650107, China
| | - Guojie Zhang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
- Center for Evolutionary and Organismal Biology and Women’s Hospital at Zhejiang University School of Medicine, Hangzhou 310058, China
- Liangzhu Laboratory, Zhejiang University Medical Center, 1369 West Wenyi Road, Hangzhou 311121, China
- Villum Center for Biodiversity Genomics, Section for Ecology and Evolution, Department of Biology, University of Copenhagen, Copenhagen 2100, Denmark
| | - Dong-Dong Wu
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
- National Resource Center for Non-Human Primates, Kunming Primate Research Center and National Research Facility for Phenotypic and Genetic Analysis of Model Animals (Primate Facility), Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650107, China
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming 650223, China
- Kunming Natural History Museum of Zoology, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China
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12
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Li Z, Sun Y, Ding L, Yang J, Huang J, Cheng M, Wu L, Zhuang Z, Chen C, Huang Y, Zhu Z, Jiang S, Huang F, Wang C, Liu S, Liu L, Lei Y. Deciphering the distinct transcriptomic and gene regulatory map in adult macaque basal ganglia cells. Gigascience 2022; 12:giad095. [PMID: 38091510 PMCID: PMC10716911 DOI: 10.1093/gigascience/giad095] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2023] [Revised: 08/09/2023] [Accepted: 10/10/2023] [Indexed: 12/18/2023] Open
Abstract
BACKGROUND The basal ganglia are a complex of interconnected subcortical structures located beneath the mammalian cerebral cortex. The degeneration of dopaminergic neurons in the basal ganglia is the primary pathological feature of Parkinson's disease. Due to a lack of integrated analysis of multiomics datasets across multiple basal ganglia brain regions, very little is known about the regulatory mechanisms of this area. FINDINGS We utilized high-throughput transcriptomic and epigenomic analysis to profile over 270,000 single-nucleus cells to create a cellular atlas of the basal ganglia, characterizing the cellular composition of 4 regions of basal ganglia in adult macaque brain, including the striatum, substantia nigra (SN), globus pallidum, and amygdala. We found a distinct epigenetic regulation on gene expression of neuronal and nonneuronal cells across regions in basal ganglia. We identified a cluster of SN-specific astrocytes associated with neurodegenerative diseases and further explored the conserved and primate-specific transcriptomics in SN cell types across human, macaque, and mouse. Finally, we integrated our epigenetic landscape of basal ganglia cells with human disease heritability and identified a regulatory module consisting of candidate cis-regulatory elements that are specific to medium spiny neurons and associated with schizophrenia. CONCLUSIONS In general, our macaque basal ganglia atlas provides valuable insights into the comprehensive transcriptome and epigenome of the most important and populous cell populations in the macaque basal ganglia. We have identified 49 cell types based on transcriptomic profiles and 47 cell types based on epigenomic profiles, some of which exhibit region specificity, and characterized the molecular relationships underlying these brain regions.
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Affiliation(s)
- Zihao Li
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
- BGI Research, Hangzhou 310030, China
| | - Yunong Sun
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
- BGI Research, Hangzhou 310030, China
| | | | - Jing Yang
- BGI Research, Hangzhou 310030, China
| | | | | | - Liang Wu
- BGI Research, Shenzhen 518083, China
| | | | - Cheng Chen
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
- BGI Research, Hangzhou 310030, China
| | - Yunqi Huang
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
- BGI Research, Hangzhou 310030, China
| | - Zhiyong Zhu
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
- BGI Research, Hangzhou 310030, China
| | - Siyuan Jiang
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
- BGI Research, Hangzhou 310030, China
| | - Fubaoqian Huang
- BGI Research, Hangzhou 310030, China
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, China
| | - Chunqing Wang
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
- BGI Research, Shenzhen 518083, China
| | - Shiping Liu
- BGI Research, Hangzhou 310030, China
- BGI Research, Shenzhen 518083, China
| | - Longqi Liu
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
- BGI Research, Hangzhou 310030, China
- BGI Research, Shenzhen 518083, China
| | - Ying Lei
- BGI Research, Shenzhen 518083, China
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13
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Gonzalez TJ, Simon KE, Blondel LO, Fanous MM, Roger AL, Maysonet MS, Devlin GW, Smith TJ, Oh DK, Havlik LP, Castellanos Rivera RM, Piedrahita JA, ElMallah MK, Gersbach CA, Asokan A. Cross-species evolution of a highly potent AAV variant for therapeutic gene transfer and genome editing. Nat Commun 2022; 13:5947. [PMID: 36210364 PMCID: PMC9548504 DOI: 10.1038/s41467-022-33745-4] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Accepted: 09/26/2022] [Indexed: 11/08/2022] Open
Abstract
Recombinant adeno-associated viral (AAV) vectors are a promising gene delivery platform, but ongoing clinical trials continue to highlight a relatively narrow therapeutic window. Effective clinical translation is confounded, at least in part, by differences in AAV biology across animal species. Here, we tackle this challenge by sequentially evolving AAV capsid libraries in mice, pigs and macaques. We discover a highly potent, cross-species compatible variant (AAV.cc47) that shows improved attributes benchmarked against AAV serotype 9 as evidenced by robust reporter and therapeutic gene expression, Cre recombination and CRISPR genome editing in normal and diseased mouse models. Enhanced transduction efficiency of AAV.cc47 vectors is further corroborated in macaques and pigs, providing a strong rationale for potential clinical translation into human gene therapies. We envision that ccAAV vectors may not only improve predictive modeling in preclinical studies, but also clinical translatability by broadening the therapeutic window of AAV based gene therapies.
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Affiliation(s)
- Trevor J Gonzalez
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC, USA
| | - Katherine E Simon
- Department of Surgery, Duke University School of Medicine, Durham, NC, USA
- North Carolina State University College of Veterinary Medicine, Raleigh, NC, USA
| | - Leo O Blondel
- Department of Surgery, Duke University School of Medicine, Durham, NC, USA
| | - Marco M Fanous
- Department of Surgery, Duke University School of Medicine, Durham, NC, USA
| | - Angela L Roger
- Department of Pediatrics, Duke University School of Medicine, Durham, NC, USA
| | | | - Garth W Devlin
- Department of Surgery, Duke University School of Medicine, Durham, NC, USA
| | - Timothy J Smith
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC, USA
| | - Daniel K Oh
- Department of Surgery, Duke University School of Medicine, Durham, NC, USA
| | - L Patrick Havlik
- Department of Surgery, Duke University School of Medicine, Durham, NC, USA
| | | | - Jorge A Piedrahita
- North Carolina State University College of Veterinary Medicine, Raleigh, NC, USA
| | - Mai K ElMallah
- Department of Pediatrics, Duke University School of Medicine, Durham, NC, USA
| | - Charles A Gersbach
- Duke Regeneration Center, Duke University School of Medicine, Durham, NC, USA
- Department of Biomedical Engineering, Duke University, Durham, NC, USA
| | - Aravind Asokan
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC, USA.
- Department of Surgery, Duke University School of Medicine, Durham, NC, USA.
- Duke Regeneration Center, Duke University School of Medicine, Durham, NC, USA.
- Department of Biomedical Engineering, Duke University, Durham, NC, USA.
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14
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Sadoughi B, Schneider D, Daniel R, Schülke O, Ostner J. Aging gut microbiota of wild macaques are equally diverse, less stable, but progressively personalized. Microbiome 2022; 10:95. [PMID: 35718778 PMCID: PMC9206754 DOI: 10.1186/s40168-022-01283-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Accepted: 04/21/2022] [Indexed: 06/15/2023]
Abstract
BACKGROUND Pronounced heterogeneity of age trajectories has been identified as a hallmark of the gut microbiota in humans and has been explained by marked changes in lifestyle and health condition. Comparatively, age-related personalization of microbiota is understudied in natural systems limiting our comprehension of patterns observed in humans from ecological and evolutionary perspectives. RESULTS Here, we tested age-related changes in the diversity, stability, and composition of the gut bacterial community using 16S rRNA gene sequencing with dense repeated sampling over three seasons in a cross-sectional age sample of adult female Assamese macaques (Macaca assamensis) living in their natural forest habitat. Gut bacterial composition exhibited a personal signature which became less stable as individuals aged. This lack of stability was not explained by differences in microbiota diversity but rather linked to an increase in the relative abundance of rare bacterial taxa. The lack of age-related changes in core taxa or convergence with age to a common state of the community hampered predicting gut bacterial composition of aged individuals. On the contrary, we found increasing personalization of the gut bacterial composition with age, indicating that composition in older individuals was increasingly divergent from the rest of the population. Reduced direct transmission of bacteria resulting from decreasing social activity may contribute to, but not be sufficient to explain, increasing personalization with age. CONCLUSIONS Together, our results challenge the assumption of a constant microbiota through adult life in a wild primate. Within the limits of this study, the fact that increasing personalization of the aging microbiota is not restricted to humans suggests the underlying process to be evolved instead of provoked only by modern lifestyle of and health care for the elderly. Video abstract.
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Affiliation(s)
- Baptiste Sadoughi
- Department of Behavioral Ecology, Johann-Friedrich-Blumenbach Institute for Zoology and Anthropology, Georg-August-University Göttingen, Kellnerweg 6, D-37077, Göttingen, Germany.
- Research Group Primate Social Evolution, German Primate Center, Leibniz Institute for Primate Research, Göttingen, Germany.
- Genomic and Applied Microbiology and Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, Georg-August-University Göttingen, Göttingen, Germany.
- Leibniz ScienceCampus Primate Cognition, German Primate Center, Leibniz Institute for Primate Research, Göttingen, Germany.
| | - Dominik Schneider
- Genomic and Applied Microbiology and Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, Georg-August-University Göttingen, Göttingen, Germany
| | - Rolf Daniel
- Genomic and Applied Microbiology and Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, Georg-August-University Göttingen, Göttingen, Germany
| | - Oliver Schülke
- Department of Behavioral Ecology, Johann-Friedrich-Blumenbach Institute for Zoology and Anthropology, Georg-August-University Göttingen, Kellnerweg 6, D-37077, Göttingen, Germany
- Research Group Primate Social Evolution, German Primate Center, Leibniz Institute for Primate Research, Göttingen, Germany
- Leibniz ScienceCampus Primate Cognition, German Primate Center, Leibniz Institute for Primate Research, Göttingen, Germany
| | - Julia Ostner
- Department of Behavioral Ecology, Johann-Friedrich-Blumenbach Institute for Zoology and Anthropology, Georg-August-University Göttingen, Kellnerweg 6, D-37077, Göttingen, Germany
- Research Group Primate Social Evolution, German Primate Center, Leibniz Institute for Primate Research, Göttingen, Germany
- Leibniz ScienceCampus Primate Cognition, German Primate Center, Leibniz Institute for Primate Research, Göttingen, Germany
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15
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Evans BJ, Peter BM, Melnick DJ, Andayani N, Supriatna J, Zhu J, Tosi AJ. Mitonuclear interactions and introgression genomics of macaque monkeys ( Macaca) highlight the influence of behaviour on genome evolution. Proc Biol Sci 2021; 288:20211756. [PMID: 34610767 PMCID: PMC8493204 DOI: 10.1098/rspb.2021.1756] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Accepted: 09/14/2021] [Indexed: 12/24/2022] Open
Abstract
In most macaques, females are philopatric and males migrate from their natal ranges, which results in pronounced divergence of mitochondrial genomes within and among species. We therefore predicted that some nuclear genes would have to acquire compensatory mutations to preserve compatibility with diverged interaction partners from the mitochondria. We additionally expected that these sex-differences would have distinctive effects on gene flow in the X and autosomes. Using new genomic data from 29 individuals from eight species of Southeast Asian macaque, we identified evidence of natural selection associated with mitonuclear interactions, including extreme outliers of interspecies differentiation and metrics of positive selection, low intraspecies polymorphism and atypically long runs of homozygosity associated with nuclear-encoded genes that interact with mitochondria-encoded genes. In one individual with introgressed mitochondria, we detected a small but significant enrichment of autosomal introgression blocks from the source species of her mitochondria that contained genes which interact with mitochondria-encoded loci. Our analyses also demonstrate that sex-specific demography sculpts genetic exchange across multiple species boundaries. These findings show that behaviour can have profound but indirect effects on genome evolution by influencing how interacting components of different genomic compartments (mitochondria, the autosomes and the sex chromosomes) move through time and space.
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Affiliation(s)
- Ben J. Evans
- Biology Department, Life Sciences Building Room 328, McMaster University, 1280 Main Street West, Hamilton, Ontario, Canada L8S 4K1
| | - Benjamin M. Peter
- Department of Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig Germany
| | - Don J. Melnick
- Department of Ecology, Evolution, and Environmental Biology, Columbia University, 10th floor Schermerhorn Extension, 119th Street and Amsterdam Avenue, New York, NY 10027 USA
| | - Noviar Andayani
- Department of Biology, Universitas Indonesia, Gedung E, Kampus UI Depok, Depok 16424, Indonesia
| | - Jatna Supriatna
- Department of Biology, Universitas Indonesia, Gedung E, Kampus UI Depok, Depok 16424, Indonesia
- Institute for Sustainable Earth and Resources (I-SER), Gedung Laboratorium Multidisiplin, Universitas Indonesia, Gedung E, Kampus UI Depok, Depok 16424, Indonesia
- Research Center for Climate Change (RCCC-UI), Gedung Laboratorium Multidisiplin, Faculty of Mathematics and Natural Sciences, Universitas Indonesia, Gedung E, Kampus UI Depok, Depok 16424, Indonesia
| | - Jianlong Zhu
- Biology Department, Life Sciences Building Room 328, McMaster University, 1280 Main Street West, Hamilton, Ontario, Canada L8S 4K1
| | - Anthony J. Tosi
- Anthropology Department, Kent State University, 238 Lowry Hall, Kent, OH 44242, USA
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16
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Sucunza D, Rico AJ, Roda E, Collantes M, González-Aseguinolaza G, Rodríguez-Pérez AI, Peñuelas I, Vázquez A, Labandeira-García JL, Broccoli V, Lanciego JL. Glucocerebrosidase Gene Therapy Induces Alpha-Synuclein Clearance and Neuroprotection of Midbrain Dopaminergic Neurons in Mice and Macaques. Int J Mol Sci 2021; 22:4825. [PMID: 34062940 PMCID: PMC8125775 DOI: 10.3390/ijms22094825&set/a 996529505+983673223] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/16/2023] Open
Abstract
Mutations in the GBA1 gene coding for glucocerebrosidase (GCase) are the main genetic risk factor for Parkinson's disease (PD). Indeed, identifying reduced GCase activity as a common feature underlying the typical neuropathological signatures of PD-even when considering idiopathic forms of PD-has recently paved the way for designing novel strategies focused on enhancing GCase activity to reduce alpha-synuclein burden and preventing dopaminergic cell death. Here we have performed bilateral injections of a viral vector coding for the mutated form of alpha-synuclein (rAAV9-SynA53T) for disease modeling purposes, both in mice as well as in nonhuman primates (NHPs), further inducing a progressive neuronal death in the substantia nigra pars compacta (SNpc). Next, another vector coding for the GBA1 gene (rAAV9-GBA1) was unilaterally delivered in the SNpc of mice and NHPs one month after the initial insult, together with the contralateral delivery of an empty/null rAAV9 for control purposes. Obtained results showed that GCase enhancement reduced alpha-synuclein burden, leading to improved survival of dopaminergic neurons. Data reported here support using GCase gene therapy as a disease-modifying treatment for PD and related synucleinopathies, including idiopathic forms of these disorders.
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Affiliation(s)
- Diego Sucunza
- Centro de Investigación Médica Aplicada (CIMA), Department of Neurosciences, Universidad de Navarra, 31008 Pamplona, Spain; (D.S.); (E.R.)
- Centro de Investigación Biomédica en Red de Enfermedades Neurodegenerativas (CiberNed), 28031 Madrid, Spain; (G.G.-A.); (A.I.R.-P.); (J.L.L.-G.)
- Instituto de Investigación Sanitaria de Navarra (IdiSNA), 31008 Pamplona, Spain; (M.C.); (I.P.); (A.V.)
| | - Alberto J. Rico
- Centro de Investigación Médica Aplicada (CIMA), Department of Neurosciences, Universidad de Navarra, 31008 Pamplona, Spain; (D.S.); (E.R.)
- Centro de Investigación Biomédica en Red de Enfermedades Neurodegenerativas (CiberNed), 28031 Madrid, Spain; (G.G.-A.); (A.I.R.-P.); (J.L.L.-G.)
- Instituto de Investigación Sanitaria de Navarra (IdiSNA), 31008 Pamplona, Spain; (M.C.); (I.P.); (A.V.)
- Correspondence: (A.J.R.); (J.L.L.)
| | - Elvira Roda
- Centro de Investigación Médica Aplicada (CIMA), Department of Neurosciences, Universidad de Navarra, 31008 Pamplona, Spain; (D.S.); (E.R.)
- Centro de Investigación Biomédica en Red de Enfermedades Neurodegenerativas (CiberNed), 28031 Madrid, Spain; (G.G.-A.); (A.I.R.-P.); (J.L.L.-G.)
- Instituto de Investigación Sanitaria de Navarra (IdiSNA), 31008 Pamplona, Spain; (M.C.); (I.P.); (A.V.)
| | - María Collantes
- Instituto de Investigación Sanitaria de Navarra (IdiSNA), 31008 Pamplona, Spain; (M.C.); (I.P.); (A.V.)
- Department of Nuclear Medicine, Clínica Universidad de Navarra, 31008 Pamplona, Spain
| | - Gloria González-Aseguinolaza
- Centro de Investigación Biomédica en Red de Enfermedades Neurodegenerativas (CiberNed), 28031 Madrid, Spain; (G.G.-A.); (A.I.R.-P.); (J.L.L.-G.)
- Instituto de Investigación Sanitaria de Navarra (IdiSNA), 31008 Pamplona, Spain; (M.C.); (I.P.); (A.V.)
- Centro de Investigación Médica Aplicada (CIMA), Department of Gene Therapy, Universidad de Navarra, 31008 Pamplona, Spain
| | - Ana I. Rodríguez-Pérez
- Centro de Investigación Biomédica en Red de Enfermedades Neurodegenerativas (CiberNed), 28031 Madrid, Spain; (G.G.-A.); (A.I.R.-P.); (J.L.L.-G.)
- Research Center for Molecular Medicine and Chronic Diseases (CIMUS), Universidad de Santiago de Compostela, 15782 Santiago de Compostela, Spain
| | - Iván Peñuelas
- Instituto de Investigación Sanitaria de Navarra (IdiSNA), 31008 Pamplona, Spain; (M.C.); (I.P.); (A.V.)
- Department of Nuclear Medicine, Clínica Universidad de Navarra, 31008 Pamplona, Spain
| | - Alfonso Vázquez
- Instituto de Investigación Sanitaria de Navarra (IdiSNA), 31008 Pamplona, Spain; (M.C.); (I.P.); (A.V.)
- Complejo Hospitalario de Navarra, Department of Neurosurgery, Servicio Navarro de Salud, 31008 Pamplona, Spain
| | - José L. Labandeira-García
- Centro de Investigación Biomédica en Red de Enfermedades Neurodegenerativas (CiberNed), 28031 Madrid, Spain; (G.G.-A.); (A.I.R.-P.); (J.L.L.-G.)
- Research Center for Molecular Medicine and Chronic Diseases (CIMUS), Universidad de Santiago de Compostela, 15782 Santiago de Compostela, Spain
| | - Vania Broccoli
- San Raffaele Scientific Institute, Stem Cell and Neurogenesis Unit, Division of Neuroscience, 20132 Milano, Italy;
| | - José L. Lanciego
- Centro de Investigación Médica Aplicada (CIMA), Department of Neurosciences, Universidad de Navarra, 31008 Pamplona, Spain; (D.S.); (E.R.)
- Centro de Investigación Biomédica en Red de Enfermedades Neurodegenerativas (CiberNed), 28031 Madrid, Spain; (G.G.-A.); (A.I.R.-P.); (J.L.L.-G.)
- Instituto de Investigación Sanitaria de Navarra (IdiSNA), 31008 Pamplona, Spain; (M.C.); (I.P.); (A.V.)
- Correspondence: (A.J.R.); (J.L.L.)
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17
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Khanal L, Chalise MK, Fan PF, Kyes RC, Jiang XL. Multilocus phylogeny suggests a distinct species status for the Nepal population of Assam macaques ( Macaca assamensis): implications for evolution and conservation. Zool Res 2021; 42:3-13. [PMID: 33410309 PMCID: PMC7840459 DOI: 10.24272/j.issn.2095-8137.2020.279] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2020] [Accepted: 01/05/2021] [Indexed: 11/23/2022] Open
Abstract
Phylogenetic relationships within the sinica-group of macaques based on morphological, behavioral, and molecular characteristics have remained controversial. The Nepal population of Assam macaques ( Macaca assamensis) (NPAM), the westernmost population of the species, is morphologically distinct but has never been used in phylogenetic analyses. Here, the phylogenetic relationship of NPAM with other congeners was tested using multiple mitochondrial and Y-chromosomal loci. The divergence times and evolutionary genetic distances among macaques were also estimated. Results revealed two major mitochondrial DNA clades of macaques under the sinica-group: the first clade included M. thibetana, M. sinica, and eastern subspecies of Assam macaque ( M. assamensis assamensis); the second clade included M. radiata together with species from the eastern and central Himalaya, namely, M. leucogenys, M. munzala, and NPAM. Among the second-clade species, NPAM was the first to diverge from the other members of the clade around 1.9 million years ago. Our results revealed that NPAM is phylogenetically distinct from the eastern Assam macaques and closer to other species and hence may represent a separate species. Because of its phylogenetic distinctiveness, isolated distribution, and small population size, the Nepal population of sinica-group macaques warrants detailed taxonomic revision and high conservation priority.
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Affiliation(s)
- Laxman Khanal
- Central Department of Zoology, Institute of Science and Technology, Tribhuvan University, Kathmandu 44613, Nepal
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650203, China. E-mail:
| | - Mukesh Kumar Chalise
- Central Department of Zoology, Institute of Science and Technology, Tribhuvan University, Kathmandu 44613, Nepal
- Nepal Biodiversity Research Society (NEBORS), Lalitpur 23513, Nepal
| | - Peng-Fei Fan
- School of Life Sciences, Sun Yat-sen University, Guangzhou, Guangdong 510275, China
| | - Randall C Kyes
- Department of Psychology, Global Health, and Anthropology, Center for Global Field Study, and Washington National Primate Research Center, University of Washington, Seattle 98195, USA
| | - Xue-Long Jiang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650203, China. E-mail:
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18
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Osada N, Matsudaira K, Hamada Y, Malaivijitnond S. Testing Sex-Biased Admixture Origin of Macaque Species Using Autosomal and X-Chromosomal Genomic Sequences. Genome Biol Evol 2021; 13:evaa209. [PMID: 33045051 PMCID: PMC8631084 DOI: 10.1093/gbe/evaa209] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/29/2020] [Indexed: 11/22/2022] Open
Abstract
The role of sex-specific demography in hybridization and admixture of genetically diverged species and populations is essential to understand the origins of the genomic diversity of sexually reproducing organisms. In order to infer how sex-linked loci have been differentiated undergoing frequent hybridization and admixture, we examined 17 whole-genome sequences of seven species representing the genus Macaca, which shows frequent inter-specific hybridization and predominantly female philopatry. We found that hybridization and admixture were prevalent within these species. For three cases of suggested hybrid origin of species/subspecies, Macaca arctoides, Macaca fascicularis ssp. aurea, and Chinese Macaca mulatta, we examined the level of admixture of X chromosomes, which is less affected by male-biased migration than that of autosomes. In one case, we found that Macaca cyclopis and Macaca fuscata was genetically closer to Chinese M. mulatta than to the Indian M. mulatta, and the admixture level of Chinese M. mulatta and M. fuscata/cyclopis was more pronounced on the X chromosome than on autosomes. Since the mitochondrial genomes of Chinese M. mulatta, M. cyclopis, and M. fuscata were found to cluster together, and the mitochondrial genome of Indian M. mulatta is more distantly related, the observed pattern of genetic differentiation on X-chromosomal loci is consistent with the nuclear swamping hypothesis, in which strong, continuous male-biased introgression from the ancestral Chinese M. mulatta population to a population related to M. fuscata and M. cyclopis generated incongruencies between the genealogies of the mitochondrial and nuclear genomes.
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Affiliation(s)
- Naoki Osada
- Faculty of Information Science and Technology, Hokkaido University, Sapporo, Hokkaido, Japan
- Global Station for Big Data and Cybersecurity, GI-CoRE, Hokkaido University, Sapporo, Hokkaido, Japan
| | - Kazunari Matsudaira
- Department of Biology, Faculty of Science, Chulalongkorn University, Pathumwan, Bangkok, Thailand
- Unit of Human Biology and Genetics, Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Bunkyo-ku, Tokyo, Japan
| | - Yuzuru Hamada
- Evolutionary Morphology Section, Department of Evolution and Phylogeny, Primate Research Institute, Kyoto University, Inuyama, Aichi, Japan
| | - Suchinda Malaivijitnond
- Department of Biology, Faculty of Science, Chulalongkorn University, Pathumwan, Bangkok, Thailand
- National Primate Research Center of Thailand, Chulalongkorn University, Saraburi Province, Thailand
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19
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Li J, Fan Z, Shen F, Pendleton AL, Song Y, Xing J, Yue B, Kidd JM, Li J. Genomic Copy Number Variation Study of Nine Macaca Species Provides New Insights into Their Genetic Divergence, Adaptation, and Biomedical Application. Genome Biol Evol 2020; 12:2211-2230. [PMID: 32970804 PMCID: PMC7846157 DOI: 10.1093/gbe/evaa200] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/19/2020] [Indexed: 02/06/2023] Open
Abstract
Copy number variation (CNV) can promote phenotypic diversification and adaptive evolution. However, the genomic architecture of CNVs among Macaca species remains scarcely reported, and the roles of CNVs in adaptation and evolution of macaques have not been well addressed. Here, we identified and characterized 1,479 genome-wide hetero-specific CNVs across nine Macaca species with bioinformatic methods, along with 26 CNV-dense regions and dozens of lineage-specific CNVs. The genes intersecting CNVs were overrepresented in nutritional metabolism, xenobiotics/drug metabolism, and immune-related pathways. Population-level transcriptome data showed that nearly 46% of CNV genes were differentially expressed across populations and also mainly consisted of metabolic and immune-related genes, which implied the role of CNVs in environmental adaptation of Macaca. Several CNVs overlapping drug metabolism genes were verified with genomic quantitative polymerase chain reaction, suggesting that these macaques may have different drug metabolism features. The CNV-dense regions, including 15 first reported here, represent unstable genomic segments in macaques where biological innovation may evolve. Twelve gains and 40 losses specific to the Barbary macaque contain genes with essential roles in energy homeostasis and immunity defense, inferring the genetic basis of its unique distribution in North Africa. Our study not only elucidated the genetic diversity across Macaca species from the perspective of structural variation but also provided suggestive evidence for the role of CNVs in adaptation and genome evolution. Additionally, our findings provide new insights into the application of diverse macaques to drug study.
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Affiliation(s)
- Jing Li
- Key Laboratory of Bio-Resources and Eco-Environment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu, Sichuan, China
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Zhenxin Fan
- Key Laboratory of Bio-Resources and Eco-Environment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu, Sichuan, China
- Sichuan Key Laboratory of Conservation Biology on Endangered Wildlife, College of Life Sciences, Sichuan University, Chengdu, Sichuan, China
| | - Feichen Shen
- Department of Human Genetics, Medical School, University of Michigan
| | | | - Yang Song
- Key Laboratory of Bio-Resources and Eco-Environment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu, Sichuan, China
| | - Jinchuan Xing
- Department of Genetics and the Human Genetics Institute of New Jersey, Rutgers, The State University of New Jersey, Piscataway
| | - Bisong Yue
- Key Laboratory of Bio-Resources and Eco-Environment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu, Sichuan, China
| | - Jeffrey M Kidd
- Department of Human Genetics, Medical School, University of Michigan
| | - Jing Li
- Key Laboratory of Bio-Resources and Eco-Environment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu, Sichuan, China
- Sichuan Key Laboratory of Conservation Biology on Endangered Wildlife, College of Life Sciences, Sichuan University, Chengdu, Sichuan, China
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20
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Shami AN, Zheng X, Munyoki SK, Ma Q, Manske GL, Green CD, Sukhwani M, Orwig KE, Li JZ, Hammoud SS. Single-Cell RNA Sequencing of Human, Macaque, and Mouse Testes Uncovers Conserved and Divergent Features of Mammalian Spermatogenesis. Dev Cell 2020; 54:529-547.e12. [PMID: 32504559 DOI: 10.1016/j.devcel.2020.05.010] [Citation(s) in RCA: 122] [Impact Index Per Article: 30.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2019] [Revised: 03/10/2020] [Accepted: 05/11/2020] [Indexed: 12/21/2022]
Abstract
Spermatogenesis is a highly regulated process that produces sperm to transmit genetic information to the next generation. Although extensively studied in mice, our current understanding of primate spermatogenesis is limited to populations defined by state-specific markers from rodent data. As between-species differences have been reported in the duration and differentiation hierarchy of this process, it remains unclear how molecular markers and cell states are conserved or have diverged from mice to man. To address this challenge, we employ single-cell RNA sequencing to identify transcriptional signatures of major germ and somatic cell types of the testes in human, macaque, and mice. This approach reveals similarities and differences in expression throughout spermatogenesis, including the stem/progenitor pool of spermatogonia, markers of differentiation, potential regulators of meiosis, RNA turnover during spermatid differentiation, and germ cell-soma communication. These datasets provide a rich foundation for future targeted mechanistic studies of primate germ cell development and in vitro gametogenesis.
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Affiliation(s)
| | - Xianing Zheng
- Department of Human Genetics, University of Michigan, Ann Arbor, MI, USA
| | - Sarah K Munyoki
- Department of Obstetrics, Gynecology, and Reproductive Sciences, Integrative Systems Biology Graduate Program, Magee-Womens Research Institute, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Qianyi Ma
- Department of Human Genetics, University of Michigan, Ann Arbor, MI, USA
| | - Gabriel L Manske
- Cellular and Molecular Biology Program, University of Michigan, Ann Arbor, MI, USA
| | | | - Meena Sukhwani
- Department of Obstetrics, Gynecology, and Reproductive Sciences, Integrative Systems Biology Graduate Program, Magee-Womens Research Institute, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Kyle E Orwig
- Department of Obstetrics, Gynecology, and Reproductive Sciences, Integrative Systems Biology Graduate Program, Magee-Womens Research Institute, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA.
| | - Jun Z Li
- Department of Human Genetics, University of Michigan, Ann Arbor, MI, USA; Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA.
| | - Saher Sue Hammoud
- Department of Human Genetics, University of Michigan, Ann Arbor, MI, USA; Cellular and Molecular Biology Program, University of Michigan, Ann Arbor, MI, USA; Department of Obstetrics and Gynecology, University of Michigan, Ann Arbor, MI, USA; Department of Urology, University of Michigan, Ann Arbor, MI, USA.
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21
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Zhang XL, Luo MT, Song JH, Pang W, Zheng YT. An Alu Element Insertion in Intron 1 Results in Aberrant Alternative Splicing of APOBEC3G Pre-mRNA in Northern Pig-Tailed Macaques ( Macaca leonina) That May Reduce APOBEC3G-Mediated Hypermutation Pressure on HIV-1. J Virol 2020; 94:e01722-19. [PMID: 31776266 PMCID: PMC6997765 DOI: 10.1128/jvi.01722-19] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2019] [Accepted: 11/14/2019] [Indexed: 11/20/2022] Open
Abstract
APOBEC3 family members, particularly APOBEC3F and APOBEC3G, inhibit the replication and spread of various retroviruses by inducing hypermutation in newly synthesized viral DNA. Viral hypermutation by APOBEC3 is associated with viral evolution, viral transmission, and disease progression. In recent years, increasing attention has been paid to targeting APOBEC3G for AIDS therapy. Thus, a controllable model system using species such as macaques, which provide a relatively ideal in vivo system, is needed for the study of APOBEC3-related issues. To appropriately utilize this animal model for biomedical research, important differences between human and macaque APOBEC3s must be considered. In this study, we found that the ratio of APOBEC3G-mediated/APOBEC3-mediated HIV-1 hypermutation footprints was much lower in peripheral blood mononuclear cells (PBMCs) from northern pig-tailed macaques than in PBMCs from humans. Next, we identified a novel and conserved APOBEC3G pre-mRNA alternative splicing pattern in macaques, which differed from that in humans and resulted from an Alu element insertion into macaque APOBEC3G gene intron 1. This alternative splicing pattern generating an aberrant APOBEC3G mRNA isoform may significantly dilute full-length APOBEC3G and reduce APOBEC3G-mediated hypermutation pressure on HIV-1 in northern pig-tailed macaques, which was supported by the elimination of other possibilities accounting for this hypermutation difference between the two hosts.IMPORTANCE APOBEC3 family members, particularly APOBEC3F and APOBEC3G, are important cellular antiviral factors. Recently, more attention has been paid to targeting APOBEC3G for AIDS therapy. To appropriately utilize macaque animal models for the study of APOBEC3-related issues, it is important that the differences between human and macaque APOBEC3s are clarified. In this study, we identified a novel and conserved APOBEC3G pre-mRNA alternative splicing pattern in macaques, which differed from that in humans and which may reduce the APOBEC3G-mediated hypermutation pressure on HIV-1 in northern pig-tailed macaques (NPMs). Our work provides important information for the proper application of macaque animal models for APOBEC3-related issues in AIDS research and a better understanding of the biological functions of APOBEC3 proteins.
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Affiliation(s)
- Xiao-Liang Zhang
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences/Key Laboratory of Bioactive Peptides of Yunnan Province, KIZ-CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Center for Biosafety Mega-Science, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, Yunnan, China
| | - Meng-Ting Luo
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences/Key Laboratory of Bioactive Peptides of Yunnan Province, KIZ-CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Center for Biosafety Mega-Science, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China
- Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Jia-Hao Song
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences/Key Laboratory of Bioactive Peptides of Yunnan Province, KIZ-CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Center for Biosafety Mega-Science, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China
- Institute of Health Sciences, Anhui University, Hefei, Anhui, China
| | - Wei Pang
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences/Key Laboratory of Bioactive Peptides of Yunnan Province, KIZ-CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Center for Biosafety Mega-Science, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Yong-Tang Zheng
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences/Key Laboratory of Bioactive Peptides of Yunnan Province, KIZ-CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Center for Biosafety Mega-Science, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China
- Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, Yunnan, China
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22
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Wei Y, de Lange SC, Scholtens LH, Watanabe K, Ardesch DJ, Jansen PR, Savage JE, Li L, Preuss TM, Rilling JK, Posthuma D, van den Heuvel MP. Genetic mapping and evolutionary analysis of human-expanded cognitive networks. Nat Commun 2019; 10:4839. [PMID: 31649260 PMCID: PMC6813316 DOI: 10.1038/s41467-019-12764-8] [Citation(s) in RCA: 69] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2019] [Accepted: 09/24/2019] [Indexed: 01/04/2023] Open
Abstract
Cognitive brain networks such as the default-mode network (DMN), frontoparietal network, and salience network, are key functional networks of the human brain. Here we show that the rapid evolutionary cortical expansion of cognitive networks in the human brain, and most pronounced the DMN, runs parallel with high expression of human-accelerated genes (HAR genes). Using comparative transcriptomics analysis, we present that HAR genes are differentially more expressed in higher-order cognitive networks in humans compared to chimpanzees and macaques and that genes with high expression in the DMN are involved in synapse and dendrite formation. Moreover, HAR and DMN genes show significant associations with individual variations in DMN functional activity, intelligence, sociability, and mental conditions such as schizophrenia and autism. Our results suggest that the expansion of higher-order functional networks subserving increasing cognitive properties has been an important locus of genetic changes in recent human brain evolution.
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Affiliation(s)
- Yongbin Wei
- Connectome Lab, Department of Complex Trait Genetics, Center for Neurogenomics and Cognitive Research, Amsterdam Neuroscience, Vrije Universiteit Amsterdam, 1081 HV, Amsterdam, The Netherlands
| | - Siemon C de Lange
- Connectome Lab, Department of Complex Trait Genetics, Center for Neurogenomics and Cognitive Research, Amsterdam Neuroscience, Vrije Universiteit Amsterdam, 1081 HV, Amsterdam, The Netherlands
| | - Lianne H Scholtens
- Connectome Lab, Department of Complex Trait Genetics, Center for Neurogenomics and Cognitive Research, Amsterdam Neuroscience, Vrije Universiteit Amsterdam, 1081 HV, Amsterdam, The Netherlands
| | - Kyoko Watanabe
- Department of Complex Trait Genetics, Center for Neurogenomics and Cognitive Research, Amsterdam Neuroscience, Vrije Universiteit Amsterdam, 1081 HV, Amsterdam, The Netherlands
| | - Dirk Jan Ardesch
- Connectome Lab, Department of Complex Trait Genetics, Center for Neurogenomics and Cognitive Research, Amsterdam Neuroscience, Vrije Universiteit Amsterdam, 1081 HV, Amsterdam, The Netherlands
| | - Philip R Jansen
- Department of Complex Trait Genetics, Center for Neurogenomics and Cognitive Research, Amsterdam Neuroscience, Vrije Universiteit Amsterdam, 1081 HV, Amsterdam, The Netherlands
- Department of Child and Adolescent Psychiatry, Erasmus Medical Center, 3015 GD, Rotterdam, The Netherlands
| | - Jeanne E Savage
- Department of Complex Trait Genetics, Center for Neurogenomics and Cognitive Research, Amsterdam Neuroscience, Vrije Universiteit Amsterdam, 1081 HV, Amsterdam, The Netherlands
| | - Longchuan Li
- Marcus Autism Center, Children's Healthcare of Atlanta, Emory University School of Medicine, Atlanta, GA, 30322, USA
| | - Todd M Preuss
- Division of Neuropharmacology and Neurologic Diseases, Emory University, Atlanta, GA, 30322, USA
- Center for Translational Social Neuroscience, Emory University, Atlanta, GA, 30322, USA
- Yerkes National Primate Research Center, Emory University, Atlanta, GA, 30322, USA
| | - James K Rilling
- Center for Translational Social Neuroscience, Emory University, Atlanta, GA, 30322, USA
- Yerkes National Primate Research Center, Emory University, Atlanta, GA, 30322, USA
- Department of Anthropology, Emory University, Atlanta, GA, 30322, USA
- Center for Behavioral Neuroscience, Emory University, Atlanta, GA, 30322, USA
- Department of Psychiatry and Behavioral Sciences, Emory University, Atlanta, GA, 30322, USA
| | - Danielle Posthuma
- Department of Complex Trait Genetics, Center for Neurogenomics and Cognitive Research, Amsterdam Neuroscience, Vrije Universiteit Amsterdam, 1081 HV, Amsterdam, The Netherlands
- Department of Clinical Genetics, Amsterdam Neuroscience, Amsterdam UMC, 1081 HV, Amsterdam, The Netherlands
| | - Martijn P van den Heuvel
- Connectome Lab, Department of Complex Trait Genetics, Center for Neurogenomics and Cognitive Research, Amsterdam Neuroscience, Vrije Universiteit Amsterdam, 1081 HV, Amsterdam, The Netherlands.
- Department of Clinical Genetics, Amsterdam Neuroscience, Amsterdam UMC, 1081 HV, Amsterdam, The Netherlands.
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Weinberg-Wolf H, Chang SWC. Differences in how macaques monitor others: Does serotonin play a central role? Wiley Interdiscip Rev Cogn Sci 2019; 10:e1494. [PMID: 30775852 PMCID: PMC6570566 DOI: 10.1002/wcs.1494] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2018] [Revised: 01/11/2019] [Accepted: 01/11/2019] [Indexed: 01/22/2023]
Abstract
Primates must balance the need to monitor other conspecifics to gain social information while not losing other resource opportunities. We consolidate evidence across the fields of primatology, psychology, and neuroscience to examine individual, population, and species differences in how primates, particularly macaques, monitor conspecifics. We particularly consider the role of serotonin in mediating social competency via social attention, aggression, and dominance behaviors. Finally, we consider how the evolution of variation in social tolerance, aggression, and social monitoring might be explained by differences in serotonergic function in macaques. This article is categorized under: Economics > Interactive Decision-Making Psychology > Comparative Psychology Neuroscience > Behavior Cognitive Biology > Evolutionary Roots of Cognition.
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Affiliation(s)
| | - Steve W C Chang
- Department of Psychology, Yale University, New Haven, Connecticut
- Department of Neuroscience, Yale University School of Medicine, New Haven, Connecticut
- Kavli Institute for Neuroscience, Yale University School of Medicine, New Haven, Connecticut
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24
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Nguyen N, Vo A, Sun H, Huang H. Heavy-Tailed Noise Suppression and Derivative Wavelet Scalogram for Detecting DNA Copy Number Aberrations. IEEE/ACM Trans Comput Biol Bioinform 2018; 15:1625-1635. [PMID: 28692986 DOI: 10.1109/tcbb.2017.2723884] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Most existing array comparative genomic hybridization (array CGH) data processing methods and evaluation models assumed that the probability density function (pdf) of noise in array CGH data is a Gaussian distribution. However, in practice, such noise distribution is peaky and heavy-tailed. Therefore, a Gaussian pdf is not adequate to approximate the noise in array CGH data and hence introduces wrong detections of chromosomal aberrations and leads misunderstanding on disease pathogenesis. A more accurate and sufficient model of noise in array CGH data is necessary and beneficial to the detection of DNA copy number variations. We analyze the real array CGH data from different platforms and show that the distribution of noise in array CGH data is fitted very well by generalized Gaussian distribution (GGD). Based on our new noise model, we propose a novel array CGH processing method combining the advantages of both the smoothing and segmentation approaches. The new method uses generalized Gaussian bivariate shrinkage function and one-directional derivative wavelet scalogram in generalized Gaussian noise. In the smoothing step, with the new generalized Gaussian noise model, we derive the heavy-tailed noise suppression algorithm in stationary wavelet domain. In the segmentation step, the 1D Gaussian derivative wavelet scalogram is employed to detect break points. Both real and simulated array CGH data with different noises (such as Gaussian noise, GGD noise, and real noise) are used in our experiments. We demonstrate that our new method outperforms other state-of-the-art methods, in terms of both root mean squared errors and receiver operating characteristic curves.
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25
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Liu SX, Hou W, Zhang XY, Peng CJ, Yue BS, Fan ZX, Li J. Identification and characterization of short tandem repeats in the Tibetan macaque genome based on resequencing data. Zool Res 2018; 39:291-300. [PMID: 29643326 PMCID: PMC5968858 DOI: 10.24272/j.issn.2095-8137.2018.047] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2017] [Accepted: 04/04/2018] [Indexed: 01/17/2023] Open
Abstract
The Tibetan macaque, which is endemic to China, is currently listed as a Near Endangered primate species by the International Union for Conservation of Nature (IUCN). Short tandem repeats (STRs) refer to repetitive elements of genome sequence that range in length from 1-6 bp. They are found in many organisms and are widely applied in population genetic studies. To clarify the distribution characteristics of genome-wide STRs and understand their variation among Tibetan macaques, we conducted a genome-wide survey of STRs with next-generation sequencing of five macaque samples. A total of 1 077 790 perfect STRs were mined from our assembly, with an N50 of 4 966 bp. Mono-nucleotide repeats were the most abundant, followed by tetra- and di-nucleotide repeats. Analysis of GC content and repeats showed consistent results with other macaques. Furthermore, using STR analysis software (lobSTR), we found that the proportion of base pair deletions in the STRs was greater than that of insertions in the five Tibetan macaque individuals (P<0.05, t-test). We also found a greater number of homozygous STRs than heterozygous STRs (P<0.05, t-test), with the Emei and Jianyang Tibetan macaques showing more heterozygous loci than Huangshan Tibetan macaques. The proportion of insertions and mean variation of alleles in the Emei and Jianyang individuals were slightly higher than those in the Huangshan individuals, thus revealing differences in STR allele size between the two populations. The polymorphic STR loci identified based on the reference genome showed good amplification efficiency and could be used to study population genetics in Tibetan macaques. The neighbor-joining tree classified the five macaques into two different branches according to their geographical origin, indicating high genetic differentiation between the Huangshan and Sichuan populations. We elucidated the distribution characteristics of STRs in the Tibetan macaque genome and provided an effective method for screening polymorphic STRs. Our results also lay a foundation for future genetic variation studies of macaques.
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Affiliation(s)
- San-Xu Liu
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu Sichuan 610065, China
| | - Wei Hou
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu Sichuan 610065, China
| | - Xue-Yan Zhang
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu Sichuan 610065, China
| | - Chang-Jun Peng
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu Sichuan 610065, China
| | - Bi-Song Yue
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu Sichuan 610065, China
- Sichuan Key Laboratory of Conservation Biology on Endangered Wildlife, College of Life Sciences, Sichuan University, Chengdu Sichuan 610065, China
| | - Zhen-Xin Fan
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu Sichuan 610065, China
| | - Jing Li
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu Sichuan 610065, China; E-mail:
- Sichuan Key Laboratory of Conservation Biology on Endangered Wildlife, College of Life Sciences, Sichuan University, Chengdu Sichuan 610065, China
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26
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Müller SF, König A, Döring B, Glebe D, Geyer J. Characterisation of the hepatitis B virus cross-species transmission pattern via Na+/taurocholate co-transporting polypeptides from 11 New World and Old World primate species. PLoS One 2018; 13:e0199200. [PMID: 29912972 PMCID: PMC6005513 DOI: 10.1371/journal.pone.0199200] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2018] [Accepted: 06/04/2018] [Indexed: 12/18/2022] Open
Abstract
The hepatic Na+/taurocholate co-transporting polypeptide (NTCP in man, Ntcp in animals) is the high-affinity receptor for the hepatitis B (HBV) and hepatitis D (HDV) viruses. Species barriers for human HBV/HDV within the order Primates were previously attributed to Ntcp sequence variations that disable virus-receptor interaction. However, only a limited number of primate Ntcps have been analysed so far. In the present study, a total of 11 Ntcps from apes, Old and New World monkeys were cloned and expressed in vitro to characterise their interaction with HBV and HDV. All Ntcps showed intact bile salt transport. Human NTCP as well as the Ntcps from the great apes chimpanzee and orangutan showed transport-competing binding of HBV derived myr-preS1-peptides. In contrast, all six Ntcps from the group of Old World monkeys were insensitive to HBV myr-preS1-peptide binding and HBV/HDV infection. This is basically predetermined by the amino acid arginine at position 158 of all studied Old World monkey Ntcps. An exchange from arginine to glycine (as present in humans and great apes) at this position (R158G) alone was sufficient to achieve full transport-competing HBV myr-preS1-peptide binding and susceptibility for HBV/HDV infection. New World monkey Ntcps showed higher sequence heterogeneity, but in two cases with 158G showed transport-competing HBV myr-preS1-peptide binding, and in one case (Saimiri sciureus) even susceptibility for HBV/HDV infection. In conclusion, amino acid position 158 of NTCP/Ntcp is sufficient to discriminate between the HBV/HDV susceptible group of humans and great apes (158G) and the non-susceptible group of Old World monkeys (158R). In the case of the phylogenetically more distant New World monkey Ntcps amino acid 158 plays a significant, but not exclusive role.
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Affiliation(s)
- Simon F. Müller
- Institute of Pharmacology and Toxicology, Biomedical Research Center Seltersberg, Justus Liebig University Giessen, Giessen, Germany
| | - Alexander König
- Institute of Medical Virology, Biomedical Research Center Seltersberg, Justus Liebig University Giessen, Giessen, Germany
| | - Barbara Döring
- Institute of Pharmacology and Toxicology, Biomedical Research Center Seltersberg, Justus Liebig University Giessen, Giessen, Germany
| | - Dieter Glebe
- Institute of Medical Virology, Biomedical Research Center Seltersberg, Justus Liebig University Giessen, Giessen, Germany
| | - Joachim Geyer
- Institute of Pharmacology and Toxicology, Biomedical Research Center Seltersberg, Justus Liebig University Giessen, Giessen, Germany
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27
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Lian XD, Zhang XH, Dai ZX, Zheng YT. Characterization of classical major histocompatibility complex (MHC) class II genes in northern pig-tailed macaques (Macaca leonina). Infect Genet Evol 2017; 56:26-35. [PMID: 29055777 DOI: 10.1016/j.meegid.2017.10.015] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2017] [Revised: 10/03/2017] [Accepted: 10/17/2017] [Indexed: 12/28/2022]
Abstract
The northern pig-tailed macaque (Macaca leonina) has been identified as an independent species from the pig-tailed macaque group. The species is a promising animal model for HIV/AIDS pathogenesis and vaccine studies due to susceptibility to HIV-1. However, the major histocompatibility complex (MHC) genetics in northern pig-tailed macaques remains poorly understood. We have previously studied the MHC class I genes in northern pig-tailed macaques and identified 39 novel alleles. Here, we describe the MHC class II alleles in all six classical loci (DPA, DPB, DQA, DQB, DRA, and DRB) from northern pig-tailed macaques using a sequence-based typing method for the first time. A total of 60 MHC-II alleles were identified of which 27 were shared by other macaque species. Additionally, northern pig-tailed macaques expressed a single DRA and multiple DRB genes similar to the expression in humans and other macaque species. Polymorphism and positive selection were detected, and phylogenetic analysis suggested the presence of a common ancestor in human and northern pig-tailed macaque MHC class II allelic lineages at the DQA, DQB, and DRB loci. The characterization of full-length MHC class II alleles in this study significantly improves understanding of the immunogenetics of northern pig-tailed macaques and provides the groundwork for future animal model studies.
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Affiliation(s)
- Xiao-Dong Lian
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences/Key Laboratory of Bioactive Peptides of Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xi-He Zhang
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences/Key Laboratory of Bioactive Peptides of Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zheng-Xi Dai
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences/Key Laboratory of Bioactive Peptides of Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China
| | - Yong-Tang Zheng
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences/Key Laboratory of Bioactive Peptides of Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China; Kunming Primate Research Center, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China.
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28
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Abstract
Insulin-like growth factor 1 (IGF1) is a multifunctional peptide that is involved in a wide range of physiological and pathophysiological processes in many animal species, ranging from somatic growth in children to metabolism and tissue regeneration and repair in adults. The IGF1 gene is under multifactorial regulation in the few species in which it has been studied, with major control being exerted by growth hormone through a gene expression pathway involving inducible binding of the STAT5b transcription factor to dispersed enhancer elements. In this study, using resources available in public genomic databases, genes encoding IGF1 have been analyzed in a cohort of six nonhuman primate species representing >60 million years of evolutionary diversification from a common ancestor: chimpanzee, gorilla, macaque, olive baboon, marmoset, and mouse lemur. The IGF1 gene has been well conserved among these primates. Similar to human IGF1, each gene appears to be composed of six exons and five introns, and contains recognizable tandem promoters, each with a unique leader exon. Exon and intron lengths are very similar, and DNA sequence conservation is high, not only in orthologous exons and promoter regions, but also in putative growth hormone-activated STAT5b-binding enhancers that are found in analogous locations in IGF1 intron 3 and in 5' distal intergenic DNA. Taken together, the high level of organizational and nucleotide sequence similarity in the IGF1 gene and locus among these seven species supports the contention that common regulatory paradigms had existed prior to the onset of primate speciation >85 million years ago.
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Affiliation(s)
- Peter Rotwein
- Department of Biomedical Sciences, Paul L. Foster School of Medicine, Texas Tech Health University Health Sciences Center, El Paso, Texas 79905
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29
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Purba LHPS, Widayati KA, Tsutsui K, Suzuki-Hashido N, Hayakawa T, Nila S, Suryobroto B, Imai H. Functional characterization of the TAS2R38 bitter taste receptor for phenylthiocarbamide in colobine monkeys. Biol Lett 2017; 13:20160834. [PMID: 28123110 PMCID: PMC5310586 DOI: 10.1098/rsbl.2016.0834] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2016] [Accepted: 01/01/2017] [Indexed: 11/12/2022] Open
Abstract
Bitterness perception in mammals is mostly directed at natural toxins that induce innate avoidance behaviours. Bitter taste is mediated by the G protein-coupled receptor TAS2R, which is located in taste cell membranes. One of the best-studied bitter taste receptors is TAS2R38, which recognizes phenylthiocarbamide (PTC). Here we investigate the sensitivities of TAS2R38 receptors to PTC in four species of leaf-eating monkeys (subfamily Colobinae). Compared with macaque monkeys (subfamily Cercopithecinae), colobines have lower sensitivities to PTC in behavioural and in vitro functional analyses. We identified four non-synonymous mutations in colobine TAS2R38 that are responsible for the decreased sensitivity of the TAS2R38 receptor to PTC observed in colobines compared with macaques. These results suggest that tolerance to bitterness in colobines evolved from an ancestor that was sensitive to bitterness as an adaptation to eating leaves.
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Affiliation(s)
| | - Kanthi Arum Widayati
- Department of Biology, Bogor Agricultural University, West Java 16680, Indonesia
| | - Kei Tsutsui
- Molecular Biology Section, Department of Cellular and Molecular Biology, Primate Research Institute, Kyoto University, Inuyama, Aichi 484-8506, Japan
| | - Nami Suzuki-Hashido
- Molecular Biology Section, Department of Cellular and Molecular Biology, Primate Research Institute, Kyoto University, Inuyama, Aichi 484-8506, Japan
| | - Takashi Hayakawa
- Molecular Biology Section, Department of Cellular and Molecular Biology, Primate Research Institute, Kyoto University, Inuyama, Aichi 484-8506, Japan
| | - Sarah Nila
- Department of Biology, Bogor Agricultural University, West Java 16680, Indonesia
| | - Bambang Suryobroto
- Department of Biology, Bogor Agricultural University, West Java 16680, Indonesia
| | - Hiroo Imai
- Molecular Biology Section, Department of Cellular and Molecular Biology, Primate Research Institute, Kyoto University, Inuyama, Aichi 484-8506, Japan
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30
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Arnaud CM, Suzumura T, Inoue E, Adams MJ, Weiss A, Inoue-Murayama M. Genes, social transmission, but not maternal effects influence responses of wild Japanese macaques (Macaca fuscata) to novel-object and novel-food tests. Primates 2017; 58:103-113. [PMID: 27619670 PMCID: PMC5215262 DOI: 10.1007/s10329-016-0572-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2016] [Accepted: 08/29/2016] [Indexed: 02/07/2023]
Abstract
Using long-term maternal pedigree data, microsatellite analysis, and behavioral tests, we examined whether personality differences in wild Japanese macaques (Macaca fuscata) are associated with additive genetic effects, maternal influences, or belonging to a particular social group. Behaviors elicited by novel-object tests were defined by a component related to caution around novel-objects (Ob-PC1) and behaviors elicited by novel food-tests were defined by correlated components related to consummatory responses (Fo-PC1) and caution around novel foods (Fo-PC2). The repeatability of Ob-PC1 was modest and not significant; the repeatabilities of Fo-PC1 and Fo-PC2 were moderate and significant. Linear mixed effects models found that sex, age, sex × age, provisioning, trial number, date, time of day, season, and distance to the closest monkey were not related to personality. Linear mixed effects models of females older than 2 years found that high rank was associated with greater caution around novel objects. Linear models were used to determine whether sex, age, group membership, maternal kinship, or relatedness had independent effects on the personality similarity of dyads. These analyses found that pairs of macaques that lived in the same group were less similar in their caution around novel objects, more closely related pairs of macaques were more similar in their tendency to eat novel food, and that pairs of macaques in the same group were more similar in how cautious they were around novel foods. Together, these findings suggest that personality in this population of wild monkeys was driven by rank, genetic effects, and group effects, the latter possibly including the need to exploit different niches in the environment.
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Affiliation(s)
| | | | - Eiji Inoue
- Faculty of Science, Toho University, Ota, Japan
| | - Mark J Adams
- Department of Psychiatry, The University of Edinburgh, Edinburgh, UK
| | - Alexander Weiss
- Department of Psychology, School of Philosophy, Psychology and Language Sciences, The University of Edinburgh, 7 George Square, Edinburgh, EH8 9JZ, UK.
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31
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Sato S, Kabeya H, Yoshino A, Sekine W, Suzuki K, Tamate HB, Yamazaki S, Chomel BB, Maruyama S. Japanese Macaques (Macaca fuscata) as Natural Reservoir of Bartonella quintana. Emerg Infect Dis 2016; 21:2168-70. [PMID: 26584238 PMCID: PMC4672446 DOI: 10.3201/eid2112.150632] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Bartonella quintana bacteremia was detected in 6 (13.3%) of 45 wild-caught Japanese macaques (Macaca fuscata). Multilocus sequence typing of the isolates revealed that Japanese macaques were infected with a new and specific B. quintana sequence type. Free-ranging Japanese macaques thus represent another natural reservoir of B. quintana.
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32
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Jiang J, Yu J, Li J, Li P, Fan Z, Niu L, Deng J, Yue B, Li J. Mitochondrial Genome and Nuclear Markers Provide New Insight into the Evolutionary History of Macaques. PLoS One 2016; 11:e0154665. [PMID: 27135608 PMCID: PMC4852913 DOI: 10.1371/journal.pone.0154665] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2015] [Accepted: 04/18/2016] [Indexed: 01/20/2023] Open
Abstract
The evolutionary history of macaques, genus Macaca, has been under debate due to the short times of divergence. In this study, maternal, paternal, and biparental genetic systems were applied to infer phylogenetic relationships among macaques and to trace ancient hybridization events in their evolutionary history. Using a PCR display method, 17 newly phylogenetically informative Alu insertions were identified from M. assamensis. We combined presence/absence analysis of 84 Alu elements with mitochondrial genomes as well as nuclear sequences (five autosomal genes, two Y chromosomal genes, and one X chromosomal fragment) to reconstruct a robust macaque phylogeny. Topologies generated from different inherited markers were similar supporting six well defined species groups and a close relationship of M. assamensis and M. thibetana, but differed in the placing of M. arctoides. Both Alu elements and nuclear genes supported that M. arctoides was close to the sinica group, whereas the mitochondrial data clustered it into the fascicularis/mulatta lineage. Our results reveal that a sex-biased hybridization most likely occurred in the evolutionary history of M. arctoides, and suggest an introgressive pattern of male-mediated gene flow from the ancestors of M. arctoides to the M. mulatta population followed by nuclear swamping. According to the estimation of divergence dates, the hybridization occurred around 0.88~1.77 mya (nuclear data) or 1.38~2.56 mya (mitochondrial data). In general, our study indicates that a combination of various molecular markers could help explain complicated evolutionary relationships. Our results have provided new insights into the evolutionary history of macaques and emphasize that hybridization might play an important role in macaque evolution.
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Affiliation(s)
- Juan Jiang
- Key Laboratory of Bioresources and Ecoenvironment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu 610064 Sichuan, China
| | - Jianqiu Yu
- Chengdu Zoo, Institute of Chengdu Wildlife, Chengdu 610081, China
| | - Jing Li
- Sichuan Key Laboratory of Conservation Biology on Endangered Wildlife, College of Life Sciences, Sichuan University, Chengdu 610064, China
| | - Peng Li
- Key Laboratory of Bioresources and Ecoenvironment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu 610064 Sichuan, China
| | - Zhenxin Fan
- Key Laboratory of Bioresources and Ecoenvironment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu 610064 Sichuan, China
| | - Lili Niu
- Chengdu Zoo, Institute of Chengdu Wildlife, Chengdu 610081, China
| | - Jiabo Deng
- Chengdu Zoo, Institute of Chengdu Wildlife, Chengdu 610081, China
| | - Bisong Yue
- Sichuan Key Laboratory of Conservation Biology on Endangered Wildlife, College of Life Sciences, Sichuan University, Chengdu 610064, China
| | - Jing Li
- Key Laboratory of Bioresources and Ecoenvironment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu 610064 Sichuan, China
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33
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Lian XD, Zhang XH, Dai ZX, Zheng YT. Cloning, sequencing, and polymorphism analysis of novel classical MHC class I alleles in northern pig-tailed macaques (Macaca leonina). Immunogenetics 2016; 68:261-74. [PMID: 26782049 DOI: 10.1007/s00251-015-0897-3] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2015] [Accepted: 12/28/2015] [Indexed: 11/25/2022]
Abstract
The northern pig-tailed macaque (Macaca leonina) has been confirmed to be an independent species from the pig-tailed macaque group of Old World monkey. We have previously reported that the northern pig-tailed macaques were also susceptible to HIV-1. Here, to make this animal a potential HIV/AIDS model and to discover the mechanism of virus control, we attempted to assess the role of major histocompatibility complex (MHC) class I-restricted immune responses to HIV-1 infection, which was associated with viral replication and disease progression. As an initial step, we first cloned and characterized the classical MHC class I gene of northern pig-tailed macaques. In this study, we identified 39 MHC class I alleles including 17 MHC-A and 22 MHC-B alleles. Out of these identified alleles, 30 were novel and 9 were identical to alleles previously reported from other macaque species. The MHC-A and MHC-B loci were both duplicates as rhesus macaques and southern pig-tailed macaques. In addition, we also detected the patterns of positive selection in northern pig-tailed macaques and revealed the existence of balance selection with 20 positive selection sites in the peptide binding region. The analysis of B and F peptide binding pockets in northern and southern pig-tailed macaques and rhesus macaques suggested that they were likely to share a few common peptides to present. Thus, this study provides important MHC immunogenetics information and adds values to northern pig-tailed macaques as a promising HIV/AIDS model.
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Affiliation(s)
- Xiao-Dong Lian
- Key Laboratory of Animal Models and Human Disease Mechanisms of Chinese Academy of Sciences and Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xi-He Zhang
- Key Laboratory of Animal Models and Human Disease Mechanisms of Chinese Academy of Sciences and Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Zheng-Xi Dai
- Key Laboratory of Animal Models and Human Disease Mechanisms of Chinese Academy of Sciences and Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China
| | - Yong-Tang Zheng
- Key Laboratory of Animal Models and Human Disease Mechanisms of Chinese Academy of Sciences and Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China.
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Ruiz-Orera J, Hernandez-Rodriguez J, Chiva C, Sabidó E, Kondova I, Bontrop R, Marqués-Bonet T, Albà M. Origins of De Novo Genes in Human and Chimpanzee. PLoS Genet 2015; 11:e1005721. [PMID: 26720152 PMCID: PMC4697840 DOI: 10.1371/journal.pgen.1005721] [Citation(s) in RCA: 89] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2015] [Accepted: 11/11/2015] [Indexed: 11/18/2022] Open
Abstract
The birth of new genes is an important motor of evolutionary innovation. Whereas many new genes arise by gene duplication, others originate at genomic regions that did not contain any genes or gene copies. Some of these newly expressed genes may acquire coding or non-coding functions and be preserved by natural selection. However, it is yet unclear which is the prevalence and underlying mechanisms of de novo gene emergence. In order to obtain a comprehensive view of this process, we have performed in-depth sequencing of the transcriptomes of four mammalian species--human, chimpanzee, macaque, and mouse--and subsequently compared the assembled transcripts and the corresponding syntenic genomic regions. This has resulted in the identification of over five thousand new multiexonic transcriptional events in human and/or chimpanzee that are not observed in the rest of species. Using comparative genomics, we show that the expression of these transcripts is associated with the gain of regulatory motifs upstream of the transcription start site (TSS) and of U1 snRNP sites downstream of the TSS. In general, these transcripts show little evidence of purifying selection, suggesting that many of them are not functional. However, we find signatures of selection in a subset of de novo genes which have evidence of protein translation. Taken together, the data support a model in which frequently-occurring new transcriptional events in the genome provide the raw material for the evolution of new proteins.
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Affiliation(s)
- Jorge Ruiz-Orera
- Evolutionary Genomics Group, Hospital del Mar Research Institute (IMIM), Barcelona, Spain
| | | | - Cristina Chiva
- Proteomics Unit, Universitat Pompeu Fabra (UPF), Barcelona, Spain
- Proteomics Unit, Centre de Regulació Genòmica (CRG), Barcelona, Spain
| | - Eduard Sabidó
- Proteomics Unit, Universitat Pompeu Fabra (UPF), Barcelona, Spain
- Proteomics Unit, Centre de Regulació Genòmica (CRG), Barcelona, Spain
| | - Ivanela Kondova
- Biomedical Primate Research Center (BPRC), Rijswijk, The Netherlands
| | - Ronald Bontrop
- Biomedical Primate Research Center (BPRC), Rijswijk, The Netherlands
| | - Tomàs Marqués-Bonet
- Department of Experimental and Health Sciences, Universitat Pompeu Fabra (UPF), Barcelona, Spain
- Centro Nacional de Análisis Genómico (CNAG), Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
| | - M.Mar Albà
- Evolutionary Genomics Group, Hospital del Mar Research Institute (IMIM), Barcelona, Spain
- Department of Experimental and Health Sciences, Universitat Pompeu Fabra (UPF), Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
- * E-mail:
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Ram MS, Marne M, Gaur A, Kumara HN, Singh M, Kumar A, Umapathy G. Pre-Historic and Recent Vicariance Events Shape Genetic Structure and Diversity in Endangered Lion-Tailed Macaque in the Western Ghats: Implications for Conservation. PLoS One 2015; 10:e0142597. [PMID: 26561307 PMCID: PMC4641736 DOI: 10.1371/journal.pone.0142597] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2015] [Accepted: 10/23/2015] [Indexed: 11/19/2022] Open
Abstract
Genetic isolation of populations is a potent force that helps shape the course of evolution. However, small populations in isolation, especially in fragmented landscapes, are known to lose genetic variability, suffer from inbreeding depression and become genetically differentiated among themselves. In this study, we assessed the genetic diversity of lion-tailed macaques (Macaca silenus) inhabiting the fragmented landscape of Anamalai hills and examined the genetic structure of the species across its distributional range in the Western Ghats. We sequenced around 900 bases of DNA covering two mitochondrial regions-hypervariable region-I and partial mitochondrial cytochrome b-from individuals sampled both from wild and captivity, constructed and dated phylogenetic trees. We found that the lion-tailed macaque troops in the isolated forest patches in Anamalai hills have depleted mitochondrial DNA diversity compared to troops in larger and continuous forests. Our results also revealed an ancient divergence in the lion-tailed macaque into two distinct populations across the Palghat gap, dating to 2.11 million years ago. In light of our findings, we make a few suggestions on the management of wild and captive populations.
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Affiliation(s)
- Muthuvarmadam S. Ram
- Laboratory for the Conservation of Endangered Species, CSIR-Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad, 500007, India
| | - Minal Marne
- Laboratory for the Conservation of Endangered Species, CSIR-Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad, 500007, India
| | - Ajay Gaur
- Laboratory for the Conservation of Endangered Species, CSIR-Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad, 500007, India
| | | | - Mewa Singh
- Biopsychology Laboratory, and Institution of Excellence, University of Mysore, Mysore, 570006, India
| | - Ajith Kumar
- Wildlife Conservation Society-India, Centre for Wildlife Studies, Bangalore, 560070, India
| | - Govindhaswamy Umapathy
- Laboratory for the Conservation of Endangered Species, CSIR-Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad, 500007, India
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Arlet M, Jubin R, Masataka N, Lemasson A. Grooming-at-a-distance by exchanging calls in non-human primates. Biol Lett 2015; 11:20150711. [PMID: 26510675 PMCID: PMC4650185 DOI: 10.1098/rsbl.2015.0711] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2015] [Accepted: 10/01/2015] [Indexed: 11/12/2022] Open
Abstract
The 'social bonding hypothesis' predicts that, in large social groups, functions of gestural grooming should be partially transferred to vocal interactions. Hence, vocal exchanges would have evolved in primates to play the role of grooming-at-a-distance in order to facilitate the maintenance of social cohesion. However, there are few empirical studies testing this hypothesis. To address this point, we compared the rate of contact call exchanges between females in two captive groups of Japanese macaques as a function of female age, dominance rank, genetic relatedness and social affinity measured by spatial proximity and grooming interactions. We found a significant positive relationship between the time spent on grooming by two females and the frequency with which they exchanged calls. Our results conform to the predictions of the social bonding hypothesis, i.e. vocal exchanges can be interpreted as grooming-at-a-distance.
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Affiliation(s)
- Malgorzata Arlet
- Animal and Human Ethology Research Unit-C.N.R.S, Université de Rennes 1, Paimpont, France School of Biology, Indian Institute for Science education and Research, Thiruvananthapuram, India
| | - Ronan Jubin
- Animal and Human Ethology Research Unit-C.N.R.S, Université de Rennes 1, Paimpont, France
| | - Nobuo Masataka
- Cognition and learning section, Primate Research Institute, Kyoto University, Kyoto, Japan
| | - Alban Lemasson
- Animal and Human Ethology Research Unit-C.N.R.S, Université de Rennes 1, Paimpont, France Institut Universitaire de France, Paris, France
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Matsunaga E, Nambu S, Oka M, Tanaka M, Taoka M, Iriki A. Identification of tool use acquisition-associated genes in the primate neocortex. Dev Growth Differ 2015; 57:484-495. [PMID: 26173833 DOI: 10.1111/dgd.12227] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2015] [Revised: 05/05/2015] [Accepted: 05/07/2015] [Indexed: 12/14/2022]
Abstract
Japanese macaques are able to learn how to use rakes to take food after only a few weeks of training. Since tool-use training induced rapid morphological changes in some restricted brain areas, this system will be a good model for studying the neural basis of plasticity in human brains. To examine the mechanisms of tool-use associated brain expansion on the molecular and cellular level, here, we performed comprehensive analysis of gene expressions with microarray. We identified various transcripts showing differential expression between trained and untrained monkeys in the region around the lateral and intraparietal sulci. Among candidates, we focused on genes related to synapse formation and function. Using quantitative reverse transcription-polymerase chain reaction and histochemical analysis, we confirmed at least three genes (ADAM19, SPON2, and WIF1) with statistically different expression levels in neurons and glial cells. Comparative analysis revealed that tool use-associated genes were more obviously expressed in macaque monkeys than marmosets or mice. Thus, our findings suggest that cognitive tasks induce structural changes in the neocortex via gene expression, and that learning-associated genes innately differ with relation to learning ability.
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Affiliation(s)
- Eiji Matsunaga
- Laboratory for Symbolic Cognitive Development, RIKEN Brain Science Institute, Hirosawa 2-1, Wako, 351-0198, Japan
| | - Sanae Nambu
- Laboratory for Symbolic Cognitive Development, RIKEN Brain Science Institute, Hirosawa 2-1, Wako, 351-0198, Japan
| | - Mariko Oka
- Laboratory for Symbolic Cognitive Development, RIKEN Brain Science Institute, Hirosawa 2-1, Wako, 351-0198, Japan
| | - Michio Tanaka
- Laboratory for Symbolic Cognitive Development, RIKEN Brain Science Institute, Hirosawa 2-1, Wako, 351-0198, Japan
| | - Miki Taoka
- Laboratory for Symbolic Cognitive Development, RIKEN Brain Science Institute, Hirosawa 2-1, Wako, 351-0198, Japan
| | - Atsushi Iriki
- Laboratory for Symbolic Cognitive Development, RIKEN Brain Science Institute, Hirosawa 2-1, Wako, 351-0198, Japan
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Suzuki-Hashido N, Hayakawa T, Matsui A, Go Y, Ishimaru Y, Misaka T, Abe K, Hirai H, Satta Y, Imai H. Rapid Expansion of Phenylthiocarbamide Non-Tasters among Japanese Macaques. PLoS One 2015. [PMID: 26201026 PMCID: PMC4511751 DOI: 10.1371/journal.pone.0132016] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Bitter taste receptors (TAS2R proteins) allow mammals to detect and avoid ingestion of toxins in food. Thus, TAS2Rs play an important role in food choice and are subject to complex natural selection pressures. In our previous study, we examined nucleotide variation in TAS2R38, a gene expressing bitter taste receptor for phenylthiocarbamide (PTC), in 333 Japanese macaques (Macaca fuscata) from 9 local populations in Japan. We identified a PTC “non-taster” TAS2R38 allele in Japanese macaques that was caused by a loss of the start codon. This PTC non-taster allele was only found in a limited local population (the Kii area), at a frequency of 29%. In this study, we confirmed that this allele was present in only the Kii population by analyzing an additional 264 individuals from eight new populations. Using cellular and behavioral experiments, we found that this allele lost its receptor function for perceiving PTC. The nucleotide sequences of the allele including flanking regions (of about 10 kb) from 23 chromosomes were identical, suggesting that a non-taster allele arose and expanded in the Kii population during the last 13,000 years. Genetic analyses of non-coding regions in Kii individuals and neighboring populations indicated that the high allele frequency in the Kii population could not be explained by demographic history, suggesting that positive selection resulted in a rapid increase in PTC non-tasters in the Kii population. The loss-of-function that occurred at the TAS2R38 locus presumably provided a fitness advantage to Japanese macaques in the Kii population. Because TAS2R38 ligands are often found in plants, this functional change in fitness is perhaps related to feeding habit specificity. These findings should provide valuable insights for elucidating adaptive evolutionary changes with respect to various environments in wild mammals.
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Affiliation(s)
- Nami Suzuki-Hashido
- Molecular Biology Section, Department of Cellular and Molecular Biology, Primate Research Institute, Kyoto University, Inuyama, Aichi, Japan
- Japan Society for the Promotion of Science, Tokyo, Japan
| | - Takashi Hayakawa
- Molecular Biology Section, Department of Cellular and Molecular Biology, Primate Research Institute, Kyoto University, Inuyama, Aichi, Japan
- Japan Society for the Promotion of Science, Tokyo, Japan
| | - Atsushi Matsui
- Molecular Biology Section, Department of Cellular and Molecular Biology, Primate Research Institute, Kyoto University, Inuyama, Aichi, Japan
| | - Yasuhiro Go
- Molecular Biology Section, Department of Cellular and Molecular Biology, Primate Research Institute, Kyoto University, Inuyama, Aichi, Japan
| | - Yoshiro Ishimaru
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
| | - Takumi Misaka
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
| | - Keiko Abe
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
| | - Hirohisa Hirai
- Molecular Biology Section, Department of Cellular and Molecular Biology, Primate Research Institute, Kyoto University, Inuyama, Aichi, Japan
| | - Yoko Satta
- Department of Evolutionary Studies of Biosystems, The Graduate University for Advanced Studies (Sokendai), Hayama, Kanagawa, Japan
- * E-mail: (YS); (HI)
| | - Hiroo Imai
- Department of Evolutionary Studies of Biosystems, The Graduate University for Advanced Studies (Sokendai), Hayama, Kanagawa, Japan
- * E-mail: (YS); (HI)
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Hu QX, Fan Y, Xu L, Pang W, Wang S, Zheng YT, Lv LB, Yao YG. Analysis of the complete mitochondrial genome and characterization of diverse NUMTs of Macaca leonina. Gene 2015; 571:279-85. [PMID: 26151895 DOI: 10.1016/j.gene.2015.06.085] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2015] [Revised: 06/08/2015] [Accepted: 06/26/2015] [Indexed: 11/19/2022]
Abstract
As a non-human primate, the pig-tailed macaque has received wide attention because it can be infected by HIV-1. In this study, we determined the complete mtDNA sequence of the northern pig-tailed macaque (Macaca leonina). Unexpectedly, during the amplification of the mtDNA control region (D-loop region) we observed several D-loop-like sequences, which were NUMTs (nuclear mitochondrial sequences) and a total of 14 D-loop-like NUMT haplotypes were later identified in five individuals. The neighbor-joining tree and estimated divergence time based on these D-loop-like NUMT sequences of M. leonina provide some insights into the understanding of the evolutionary history of NUMTs. D-loop-like haplotypes G and H, which also exist in the nuclear genome of mulatta, appear to have been translocated into the nuclear genome before the divergence of M. mulatta and M. leonina. The other D-loop-like NUMT haplotypes were translocated into the nuclear genome of M. leonina after the divergence of the two species. Later sequence conversion was predicted to occur among these 14 D-loop-like NUMT haplotypes. The overall structure of the mtDNA of M. leonina was found to be similar to that seen in other mammalian mitochondrial genomes. Phylogenetic analysis based on the maximum likelihood method shows M. leonina clustered with Macaca silenus among the analyzed mammalian species.
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Affiliation(s)
- Qiu-Xiang Hu
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences & Yunnan Province, Kunming Institute of Zoology, Kunming, Yunnan 650223, China; Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, Yunnan 650223, China
| | - Yu Fan
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences & Yunnan Province, Kunming Institute of Zoology, Kunming, Yunnan 650223, China; Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, Yunnan 650223, China
| | - Ling Xu
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences & Yunnan Province, Kunming Institute of Zoology, Kunming, Yunnan 650223, China; Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, Yunnan 650223, China
| | - Wei Pang
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences & Yunnan Province, Kunming Institute of Zoology, Kunming, Yunnan 650223, China
| | - Shuang Wang
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences & Yunnan Province, Kunming Institute of Zoology, Kunming, Yunnan 650223, China
| | - Yong-Tang Zheng
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences & Yunnan Province, Kunming Institute of Zoology, Kunming, Yunnan 650223, China; Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, Yunnan 650223, China; Kunming Primate Research Center, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
| | - Long-Bao Lv
- Kunming Primate Research Center, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
| | - Yong-Gang Yao
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences & Yunnan Province, Kunming Institute of Zoology, Kunming, Yunnan 650223, China; Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, Yunnan 650223, China; Kunming Primate Research Center, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China.
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Huang YF, Midha M, Chen TH, Wang YT, Smith DG, Pei KJC, Chiu KP. Complete Taiwanese Macaque (Macaca cyclopis) Mitochondrial Genome: Reference-Assisted de novo Assembly with Multiple k-mer Strategy. PLoS One 2015; 10:e0130673. [PMID: 26125617 PMCID: PMC4488429 DOI: 10.1371/journal.pone.0130673] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2015] [Accepted: 05/24/2015] [Indexed: 11/18/2022] Open
Abstract
The Taiwanese (Formosan) macaque (Macaca cyclopis) is the only nonhuman primate endemic to Taiwan. This primate species is valuable for evolutionary studies and as subjects in medical research. However, only partial fragments of the mitochondrial genome (mitogenome) of this primate species have been sequenced, not mentioning its nuclear genome. We employed next-generation sequencing to generate 2 x 90 bp paired-end reads, followed by reference-assisted de novo assembly with multiple k-mer strategy to characterize the M. cyclopis mitogenome. We compared the assembled mitogenome with that of other macaque species for phylogenetic analysis. Our results show that, the M. cyclopis mitogenome consists of 16,563 nucleotides encoding for 13 protein-coding genes, 2 ribosomal RNAs and 22 transfer RNAs. Phylogenetic analysis indicates that M. cyclopis is most closely related to M. mulatta lasiota (Chinese rhesus macaque), supporting the notion of Asia-continental origin of M. cyclopis proposed in previous studies based on partial mitochondrial sequences. Our work presents a novel approach for assembling a mitogenome that utilizes the capabilities of de novo genome assembly with assistance of a reference genome. The availability of the complete Taiwanese macaque mitogenome will facilitate the study of primate evolution and the characterization of genetic variations for the potential usage of this species as a non-human primate model for medical research.
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Affiliation(s)
- Yu-Feng Huang
- Genomics Research Center, Academia Sinica, Taipei, Taiwan
- * E-mail:
| | - Mohit Midha
- Genomics Research Center, Academia Sinica, Taipei, Taiwan
- Institute of Biochemistry and Molecular Biology, National Yang-Ming University, Taipei, Taiwan
| | - Tzu-Han Chen
- Genomics Research Center, Academia Sinica, Taipei, Taiwan
| | - Yu-Tai Wang
- National Center for High-Performance Computing, Hsinchu, Taiwan
| | - David Glenn Smith
- Department of Anthropology, University of California Davis, Davis, CA, United States of America
| | - Kurtis Jai-Chyi Pei
- Institute of Wildlife Conservation, College of Veterinary Medicine, National Pingtung University of Science and Technology, Pingtung, Taiwan
| | - Kuo Ping Chiu
- Genomics Research Center, Academia Sinica, Taipei, Taiwan
- Institute of Biochemistry and Molecular Biology, National Yang-Ming University, Taipei, Taiwan
- College of Life Science, National Taiwan University, Taipei, Taiwan
- Institute of Systems Biology and Bioinformatics, National Central University, Jhongli, Taiwan
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Chakraborty D, Sinha A, Ramakrishnan U. Mixed fortunes: ancient expansion and recent decline in population size of a subtropical montane primate, the Arunachal macaque Macaca munzala. PLoS One 2014; 9:e97061. [PMID: 25054863 PMCID: PMC4108313 DOI: 10.1371/journal.pone.0097061] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2013] [Accepted: 04/14/2014] [Indexed: 11/18/2022] Open
Abstract
Quaternary glacial oscillations are known to have caused population size fluctuations in many temperate species. Species from subtropical and tropical regions are, however, considerably less studied, despite representing most of the biodiversity hotspots in the world including many highly threatened by anthropogenic activities such as hunting. These regions, consequently, pose a significant knowledge gap in terms of how their fauna have typically responded to past climatic changes. We studied an endangered primate, the Arunachal macaque Macaca munzala, from the subtropical southern edge of the Tibetan plateau, a part of the Eastern Himalaya biodiversity hotspot, also known to be highly threatened due to rampant hunting. We employed a 534 bp-long mitochondrial DNA sequence and 22 autosomal microsatellite loci to investigate the factors that have potentially shaped the demographic history of the species. Analysing the genetic data with traditional statistical methods and advance Bayesian inferential approaches, we demonstrate a limited effect of past glacial fluctuations on the demographic history of the species before the last glacial maximum, approximately 20,000 years ago. This was, however, immediately followed by a significant population expansion possibly due to warmer climatic conditions, approximately 15,000 years ago. These changes may thus represent an apparent balance between that displayed by the relatively climatically stable tropics and those of the more severe, temperate environments of the past. This study also draws attention to the possibility that a cold-tolerant species like the Arunachal macaque, which could withstand historical climate fluctuations and grow once the climate became conducive, may actually be extremely vulnerable to anthropogenic exploitation, as is perhaps indicated by its Holocene ca. 30-fold population decline, approximately 3,500 years ago. Our study thus provides a quantitative appraisal of these demographically important events, emphasising the ability to potentially infer the occurrence of two separate historical events from contemporary genetic data.
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Affiliation(s)
- Debapriyo Chakraborty
- Nature Conservation Foundation, Gokulam Park, Mysore, India
- National Centre for Biological Sciences, GKVK Campus, Bangalore, India
- * E-mail:
| | - Anindya Sinha
- Nature Conservation Foundation, Gokulam Park, Mysore, India
- National Centre for Biological Sciences, GKVK Campus, Bangalore, India
- National Institute of Advanced Studies, Indian Institute of Science Campus, Bangalore, India
| | - Uma Ramakrishnan
- National Centre for Biological Sciences, GKVK Campus, Bangalore, India
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Abstract
The growing interest of modeling human diseases using genetically modified (transgenic) nonhuman primates (NHPs) is a direct result of NHPs (rhesus macaque, etc.) close relation to humans. NHPs share similar developmental paths with humans in their anatomy, physiology, genetics, and neural functions; and in their cognition, emotion, and social behavior. The NHP model within biomedical research has played an important role in the development of vaccines, assisted reproductive technologies, and new therapies for many diseases. Biomedical research has not been the primary role of NHPs. They have mainly been used for safety evaluation and pharmacokinetics studies, rather than determining therapeutic efficacy. The development of the first transgenic rhesus macaque (2001) revolutionized the role of NHP models in biomedicine. Development of the transgenic NHP model of Huntington's disease (2008), with distinctive clinical features, further suggested the uniqueness of the model system; and the potential role of the NHP model for human genetic disorders. Modeling human genetic diseases using NHPs will continue to thrive because of the latest advances in molecular, genetic, and embryo technologies. NHPs rising role in biomedical research, specifically pre-clinical studies, is foreseeable. The path toward the development of transgenic NHPs and the prospect of transgenic NHPs in their new role in future biomedicine needs to be reviewed. This article will focus on the advancement of transgenic NHPs in the past decade, including transgenic technologies and disease modeling. It will outline new technologies that may have significant impact in future NHP modeling and will conclude with a discussion of the future prospects of the transgenic NHP model.
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He Z, Bammann H, Han D, Xie G, Khaitovich P. Conserved expression of lincRNA during human and macaque prefrontal cortex development and maturation. RNA 2014; 20:1103-11. [PMID: 24847104 PMCID: PMC4074677 DOI: 10.1261/rna.043075.113] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2013] [Accepted: 04/09/2014] [Indexed: 05/20/2023]
Abstract
The current annotation of the human genome includes more than 12,000 long intergenic noncoding RNAs (lincRNA). While a handful of lincRNA have been shown to play important regulatory roles, the functionality of most remains unclear. Here, we examined the expression conservation and putative functionality of lincRNA in human and macaque prefrontal cortex (PFC) development and maturation. We analyzed transcriptome sequence (RNA-seq) data from 38 human and 40 macaque individuals covering the entire postnatal development interval. Using the human data set, we detected the expression of 5835 lincRNA annotated in GENCODE and further identified 1888 novel lincRNA. Most of these lincRNA show low DNA sequence conservation, as well as low expression levels. Remarkably, developmental expression patterns of these lincRNA were as conserved between humans and macaques as those of protein-coding genes. Transfection of development-associated lincRNA into human SH-SY5Y cells affected gene expression, indicating their regulatory potential. In brain, expression of these putative target genes correlated with the expression of the corresponding lincRNA during human and macaque PFC development. These results support the potential functionality of lincRNA in primate PFC development.
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Affiliation(s)
- Zhisong He
- CAS Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai 200031, China
- Graduate School of Chinese Academy of Sciences, 100039 Beijing, China
| | - Hindrike Bammann
- CAS Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai 200031, China
- Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Dingding Han
- CAS Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai 200031, China
| | - Gangcai Xie
- CAS Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai 200031, China
- Graduate School of Chinese Academy of Sciences, 100039 Beijing, China
| | - Philipp Khaitovich
- CAS Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai 200031, China
- Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
- Corresponding authorE-mail
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Brahmachary M, Guilmatre A, Quilez J, Hasson D, Borel C, Warburton P, Sharp AJ. Digital genotyping of macrosatellites and multicopy genes reveals novel biological functions associated with copy number variation of large tandem repeats. PLoS Genet 2014; 10:e1004418. [PMID: 24945355 PMCID: PMC4063668 DOI: 10.1371/journal.pgen.1004418] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2013] [Accepted: 04/22/2014] [Indexed: 11/30/2022] Open
Abstract
Tandem repeats are common in eukaryotic genomes, but due to difficulties in assaying them remain poorly studied. Here, we demonstrate the utility of Nanostring technology as a targeted approach to perform accurate measurement of tandem repeats even at extremely high copy number, and apply this technology to genotype 165 HapMap samples from three different populations and five species of non-human primates. We observed extreme variability in copy number of tandemly repeated genes, with many loci showing 5–10 fold variation in copy number among humans. Many of these loci show hallmarks of genome assembly errors, and the true copy number of many large tandem repeats is significantly under-represented even in the high quality ‘finished’ human reference assembly. Importantly, we demonstrate that most large tandem repeat variations are not tagged by nearby SNPs, and are therefore essentially invisible to SNP-based GWAS approaches. Using association analysis we identify many cis correlations of large tandem repeat variants with nearby gene expression and DNA methylation levels, indicating that variations of tandem repeat length are associated with functional effects on the local genomic environment. This includes an example where expansion of a macrosatellite repeat is associated with increased DNA methylation and suppression of nearby gene expression, suggesting a mechanism termed “repeat induced gene silencing”, which has previously been observed only in transgenic organisms. We also observed multiple signatures consistent with altered selective pressures at tandemly repeated loci, suggesting important biological functions. Our studies show that tandemly repeated loci represent a highly variable fraction of the genome that have been systematically ignored by most previous studies, copy number variation of which can exert functionally significant effects. We suggest that future studies of tandem repeat loci will lead to many novel insights into their role in modulating both genomic and phenotypic diversity. Here we utilize Nanostring digital assays and show their utility for estimating copy number of 186 multicopy genes and tandem repeats. By analyzing patterns of single nucleotide variation around these variants, we show that copy number variation at the vast majority of tandem repeat variations is not effectively tagged by nearby SNPs, and thus standard genome-wide association studies that focus on SNPs provide little or no information about such variants. By comparing patterns of tandem repeat copy number with variation in local gene expression and DNA methylation, we also identify extensive functional effects on local genome function. This includes an example of a non-coding macrosatellite repeat, expansion of which exerts a repressive effect on a nearby gene accompanied by accumulations of local DNA methylation. Finally, comparison of diverse human populations with a number of primate genomes shows that many of these sequences have undergone extreme changes in copy number during recent human and primate evolution, and show signatures that suggest possible selective effects. Overall, we conclude that multicopy genes and macrosatellites represent a highly variable fraction of the genome with important functional effects that has been systematically ignored by previous studies.
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Affiliation(s)
- Manisha Brahmachary
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
| | - Audrey Guilmatre
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
| | - Javier Quilez
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
| | - Dan Hasson
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
| | - Christelle Borel
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
| | - Peter Warburton
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
| | - Andrew J. Sharp
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
- * E-mail:
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Borsetti A, Ferrantelli F, Maggiorella MT, Sernicola L, Bellino S, Gallinaro A, Farcomeni S, Mee ET, Rose NJ, Cafaro A, Titti F, Ensoli B. Effect of MHC haplotype on immune response upon experimental SHIVSF162P4cy infection of Mauritian cynomolgus macaques. PLoS One 2014; 9:e93235. [PMID: 24695530 PMCID: PMC3973703 DOI: 10.1371/journal.pone.0093235] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2013] [Accepted: 03/03/2014] [Indexed: 01/06/2023] Open
Abstract
Little is known about the effects of Major Histocompatibility Complex (MHC) haplotypes on immunity to primate lentiviruses involving both acquired and innate immune responses. We present statistical evidence of the influence of MHC polymorphism on antiviral immunity of Mauritian cynomolgus macaques (MCM) following simian/human immunodeficiency virus SHIVSF162P4cy infection, involving the production of pro- and anti-inflammatory cytokines and α-defensins, which may modulate acquired immune responses. During the acute phase of infection, IL-10 correlated positively with viral load and negatively with CD4+T cell counts. Furthermore, α-defensins production was directly correlated with plasma viral RNA, particularly at peak of viral load. When the effects of the MHC were analyzed, a significant association between lower anti-Env binding and neutralizing antibody levels with class IB M4 haplotype and with class IA, IB M4 haplotype, respectively, was observed in the post-acute phase. Lower antibody responses may have resulted into a poor control of infection thus explaining the previously reported lower CD4 T cell counts in these monkeys. Class II M3 haplotype displayed significantly lower acute and post-acute IL-10 levels. In addition, significantly lower levels of α-defensins were detected in class IA M3 haplotype monkeys than in non-M3 macaques, in the post-acute phase of infection. These data indicate that the MHC could contribute to the delicate balance of pro-inflammatory mechanisms, particularly with regard to the association between IL-10 and α-defensins in lentivirus infection. Our results show that host genetic background, virological and immunological parameters should be considered for the design and interpretation of HIV-1 vaccine efficacy studies.
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Affiliation(s)
| | | | | | | | | | | | | | - Edward T. Mee
- Division of Virology, National Institute for Biological Standards and Control, Medicines and Healthcare products Regulatory Agency, South Mimms, Hertfordshire, United Kingdom
| | - Nicola J. Rose
- Division of Virology, National Institute for Biological Standards and Control, Medicines and Healthcare products Regulatory Agency, South Mimms, Hertfordshire, United Kingdom
| | - Aurelio Cafaro
- National AIDS Center, Istituto Superiore di Sanità, Rome, Italy
| | - Fausto Titti
- National AIDS Center, Istituto Superiore di Sanità, Rome, Italy
| | - Barbara Ensoli
- National AIDS Center, Istituto Superiore di Sanità, Rome, Italy
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Matsen FA, Small CT, Soliven K, Engel GA, Feeroz MM, Wang X, Craig KL, Hasan MK, Emerman M, Linial ML, Jones-Engel L. A novel Bayesian method for detection of APOBEC3-mediated hypermutation and its application to zoonotic transmission of simian foamy viruses. PLoS Comput Biol 2014; 10:e1003493. [PMID: 24586139 PMCID: PMC3937129 DOI: 10.1371/journal.pcbi.1003493] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2013] [Accepted: 01/16/2014] [Indexed: 02/07/2023] Open
Abstract
Simian Foamy Virus (SFV) can be transmitted from non-human primates (NHP) to humans. However, there are no documented cases of human to human transmission, and significant differences exist between infection in NHP and human hosts. The mechanism for these between-host differences is not completely understood. In this paper we develop a new Bayesian approach to the detection of APOBEC3-mediated hypermutation, and use it to compare SFV sequences from human and NHP hosts living in close proximity in Bangladesh. We find that human APOBEC3G can induce genetic changes that may prevent SFV replication in infected humans in vivo.
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Affiliation(s)
- Frederick A. Matsen
- Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Christopher T. Small
- Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Khanh Soliven
- Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Gregory A. Engel
- University of Washington, Seattle, Washington, United States of America
- Swedish Medical Center, Seattle, Washington, United States of America
| | | | - Xiaoxing Wang
- Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Karen L. Craig
- Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | | | - Michael Emerman
- Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Maxine L. Linial
- Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Lisa Jones-Engel
- University of Washington, Seattle, Washington, United States of America
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Sukmak M, Malaivijitnond S, Schülke O, Ostner J, Hamada Y, Wajjwalku W. Preliminary study of the genetic diversity of eastern Assamese macaques (Macaca assamensis assamensis) in Thailand based on mitochondrial DNA and microsatellite markers. Primates 2013; 55:189-97. [PMID: 24142419 DOI: 10.1007/s10329-013-0388-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2013] [Accepted: 10/04/2013] [Indexed: 10/26/2022]
Abstract
Human overpopulation, deforestation, invasion of agricultural areas, and livestock are the primary causes for population fragmentation of wildlife. The distribution range of species of the genus Macaca is constantly decreasing and becoming increasingly fragmented due to forest deterioration. Assamese macaques (M. assamensis) are classified as near threatened in the International Union for Conservation of Nature (IUCN) Red List of Threatened Animals (2008) and have been declared a protected wildlife animal according to Wildlife Preservation and Protection Act, B.E.2535 (1992) of Thailand. As studies of the population history and genetic diversity of Assamese macaques in Thailand are currently lacking, we aimed at a first investigation of their genetic diversity based on mitochondrial DNA [hypervariable regions 1 and 2 (HV1, HV2) and cytochrome B (CYTB) regions], as well as 15 microsatellite markers of five sampling sites distributed across Thailand. Our results indicate that Assamese macaques in Thailand are diverse, with eight maternal haplotypes and a low inbreeding coefficient in the Phu Khieo Wildlife Sanctuary (PKWS) population. Moreover, our phylogenetic and median-joining network analysis based on mitochondrial (mt)DNA suggests a population distribution in accordance with the evolutionary scenario proposed for M. sinica. Today, the population of Assamese macaques is fragmented, and conservation strategies are needed to ensure the maintenance of genetic diversity of this primate species.
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Affiliation(s)
- Manakorn Sukmak
- Center for Agricultural Biotechnology, Kasetsart University, Kamphaeng Saen Campus, Nakhon Pathom, 73140, Thailand
- Center of Excellence on Agricultural Biotechnology: (AG-BIO/PERDO-CHE), Bangkok, 10900, Thailand
| | - Suchinda Malaivijitnond
- Primate Research Unit, Department of Biology, Faculty of Science, Chulalongkorn University, Bangkok, 10330, Thailand
| | - Oliver Schülke
- Courant Research Centre Evolution of Social Behaviour, Georg August University, Göttingen, Germany
| | - Julia Ostner
- Courant Research Centre Evolution of Social Behaviour, Georg August University, Göttingen, Germany
| | - Yuzuru Hamada
- Evolutionary Morphology Section, Primate Research Institute, Kyoto University, Inuyama, Japan
| | - Worawidh Wajjwalku
- Department of Pathology, Faculty of Veterinary Medicine, Kasetsart University, Kamphaeng Saen Campus, Nakhon Pathom, 73140, Thailand.
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Baskaev KK, Kholodenko RV, Malakhova GV, Gaĭfullin NM, Korzeneva EA, Suntsova MV, Buzdin AA. [Experimental analysis of human specific protein coding open reading frame c11orf72]. Bioorg Khim 2013; 39:151-8. [PMID: 23964515 DOI: 10.1134/s1068162013020039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Gene c11orf72 (also known as FLJ90834) included in human gene reference list was previously predicted on the basis oftranscriptome analysis. We show that c11orf72 predicted protein coding open reading frame is specific for human genome and that it is absent from DNAs of other investigated primate species (chimpanzee, macaque). For the first time, we systematically analyzed c11orf72 expression in five normal and two cancerous human tissues (testicles, heart, brain, lung, bladder, bladder tumor and testicular tumor) and found no transcriptional activity there. Promoter of c11orf72, located close to promoter of a housekeeping gene NDUFV1, has shown high methylation level, whereas NDUFV1 promoter was almost free from methylation. The protein product for cllorf72 was analyzed using heterologous expression in human cell lines NT2/D1 (Tera2) and HepG2, in N- and C-terminal fusion constructs with the fluorescent protein TurboGFP. C11orf72 protein showed no cytotoxic or promitotic activity and was distributed diffusely through the cell. Our data confirm the possibility of gain of new protein-coding genes during human evolution due to simple accumulation of point mutations. However, we found no evidence for the functional significance of gene c11orf72.
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Abstract
The evolutionary study of social systems in non-human primates has long been focused on ecological determinants. The predictive value of socio-ecological models remains quite low, however, in particular because such equilibrium models cannot integrate the course of history. The use of phylogenetic methods indicates that many patterns of primate societies have been conserved throughout evolutionary history. For example, the study of social relations in macaques revealed that their social systems are made of sets of correlated behavioural traits. Some macaque species are portrayed by marked social intolerance, a steep dominance gradient and strong nepotism, whereas others display a higher level of social tolerance, relaxed dominance and a weaker influence of kinship. Linkages between behavioural traits occur at different levels of organization, and act as constraints that limit evolutionary responses to external pressures. Whereas these constraints can exert strong stabilizing selection that opposes the potential changes required by the ecological environment, selective mechanisms may have the potential to switch the whole social system from one state to another by acting primarily on some key behavioural traits that could work as pacemakers.
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Affiliation(s)
- Bernard Thierry
- Centre National de la Recherche Scientifique, Département Ecologie, Physiologie et Ethologie, Strasbourg 67000, France.
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