Comparative transcriptome analysis between rhesus macaques ( Macaca mulatta ) and crab-eating macaques ( M. fascicularis )
Understanding gene expression variations between species is pivotal for deciphering the evolutionary diversity in phenotypes. Rhesus macaques ( , MMU) and crab-eating macaques ( , MFA) serve as crucial nonhuman primate biomedical models with different phenotypes. To date, however, large-scale compar...
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| Veröffentlicht in: | Dōngwùxué yánjiū 2024-03, Vol.45 (2), p.299-310 |
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| creator | Mao, Yu-Xiang Li, Yamei Yang, Zikun Xu, Ning Zhang, Shilong Wang, Xuankai Yang, Xiangyu Sun, Qiang Mao, Yafei |
| description | Understanding gene expression variations between species is pivotal for deciphering the evolutionary diversity in phenotypes. Rhesus macaques (
, MMU) and crab-eating macaques (
, MFA) serve as crucial nonhuman primate biomedical models with different phenotypes. To date, however, large-scale comparative transcriptome research between these two species has not yet been fully explored. Here, we conducted systematic comparisons utilizing newly sequenced RNA-seq data from 84 samples (41 MFA samples and 43 MMU samples) encompassing 14 common tissues. Our findings revealed a small fraction of genes (3.7%) with differential expression between the two species, as well as 36.5% of genes with tissue-specific expression in both macaques. Comparison of gene expression between macaques and humans indicated that 22.6% of orthologous genes displayed differential expression in at least two tissues. Moreover, 19.41% of genes that overlapped with macaque-specific structural variants showed differential expression between humans and macaques. Of these, the
gene exhibited elevated expression in humans compared to macaques due to lineage-specific duplication. In summary, this study presents a large-scale transcriptomic comparison between MMU and MFA and between macaques and humans. The discovery of gene expression variations not only enhances the biomedical utility of macaque models but also contributes to the wider field of primate genomics. |
| doi_str_mv | 10.24272/j.issn.2095-8137.2023.322 |
| format | Article |
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, MMU) and crab-eating macaques (
, MFA) serve as crucial nonhuman primate biomedical models with different phenotypes. To date, however, large-scale comparative transcriptome research between these two species has not yet been fully explored. Here, we conducted systematic comparisons utilizing newly sequenced RNA-seq data from 84 samples (41 MFA samples and 43 MMU samples) encompassing 14 common tissues. Our findings revealed a small fraction of genes (3.7%) with differential expression between the two species, as well as 36.5% of genes with tissue-specific expression in both macaques. Comparison of gene expression between macaques and humans indicated that 22.6% of orthologous genes displayed differential expression in at least two tissues. Moreover, 19.41% of genes that overlapped with macaque-specific structural variants showed differential expression between humans and macaques. Of these, the
gene exhibited elevated expression in humans compared to macaques due to lineage-specific duplication. In summary, this study presents a large-scale transcriptomic comparison between MMU and MFA and between macaques and humans. The discovery of gene expression variations not only enhances the biomedical utility of macaque models but also contributes to the wider field of primate genomics.</description><identifier>ISSN: 2095-8137</identifier><identifier>ISSN: 0254-5853</identifier><identifier>EISSN: 2095-8137</identifier><identifier>DOI: 10.24272/j.issn.2095-8137.2023.322</identifier><identifier>PMID: 38485500</identifier><language>eng</language><publisher>China: Kunming Institute of Zoology, The Chinese Academy of Sciences</publisher><subject>Animals ; Brain research ; Consortia ; Eating ; Euthanasia ; Gene expression ; Genes ; Genomes ; Genomics ; Macaca mulatta ; Marine crustaceans ; Monkeys & apes ; Neurosciences ; Phenotypes ; Phenotypic variations ; Quality control ; Tissue ; Transcriptomes ; Transcriptomics</subject><ispartof>Dōngwùxué yánjiū, 2024-03, Vol.45 (2), p.299-310</ispartof><rights>Copyright Kunming Institute of Zoology, The Chinese Academy of Sciences Mar 2024</rights><rights>Copyright © 2024 Editorial Office of Zoological Research, Kunming Institute of Zoology, Chinese Academy of Sciences. 2024 Editorial Office of Zoological Research, Kunming Institute of Zoology, Chinese Academy of Sciences</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><link.rule.ids>314,776,780,881,27901,27902</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/38485500$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Mao, Yu-Xiang</creatorcontrib><creatorcontrib>Li, Yamei</creatorcontrib><creatorcontrib>Yang, Zikun</creatorcontrib><creatorcontrib>Xu, Ning</creatorcontrib><creatorcontrib>Zhang, Shilong</creatorcontrib><creatorcontrib>Wang, Xuankai</creatorcontrib><creatorcontrib>Yang, Xiangyu</creatorcontrib><creatorcontrib>Sun, Qiang</creatorcontrib><creatorcontrib>Mao, Yafei</creatorcontrib><creatorcontrib>中国科学院大学, 北京 100049, 中国</creatorcontrib><creatorcontrib>中国科学院神经科学研究所神经科学国家重点实验室, 脑科学与智能技术卓越创新中心, 上海 200031, 中国</creatorcontrib><creatorcontrib>中国科学院遗传进化与动物模型重点实验室, 云南 昆明 650201, 中国</creatorcontrib><creatorcontrib>Shanghai Center for Brain Science and Brain-Inspired Intelligence Technology, Shanghai 201210, China</creatorcontrib><creatorcontrib>Center for Genomic Research, International Institutes of Medicine, Fourth Affiliated Hospital, Zhejiang University, Yiwu, Zhejiang 322000, China</creatorcontrib><creatorcontrib>上海交通大学致远学院, 上海 200240, 中国</creatorcontrib><creatorcontrib>Institute of Neuroscience, State Key Laboratory of Neuroscience, Center for Excellence in Brain Science & Intelligence Technology, Chinese Academy of Sciences, Shanghai 200031, China</creatorcontrib><creatorcontrib>Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Ministry of Education, Shanghai Jiao Tong University, Shanghai 200030, China</creatorcontrib><creatorcontrib>上海交通大学Bio-X研究院, 遗传发育与精神神经疾病教育部重点实验室, 上海 200030, 中国</creatorcontrib><creatorcontrib>浙江大学医学院附属第四医院, 国际健康医学研究院, 基因组研究中心, 浙江 义乌 322000, 中国</creatorcontrib><creatorcontrib>University of Chinese Academy of Sciences, Beijing 100049, China</creatorcontrib><creatorcontrib>Key Laboratory of Genetic Evolution & Animal Models, Chinese Academy of Sciences, Kunming, Yunnan 650201, China</creatorcontrib><creatorcontrib>Zhiyuan College, Shanghai Jiao Tong University, Shanghai 200240, China</creatorcontrib><creatorcontrib>上海脑科学与类脑研究中心, 上海 201210, 中国</creatorcontrib><title>Comparative transcriptome analysis between rhesus macaques ( Macaca mulatta ) and crab-eating macaques ( M. fascicularis )</title><title>Dōngwùxué yánjiū</title><addtitle>Zool Res</addtitle><description>Understanding gene expression variations between species is pivotal for deciphering the evolutionary diversity in phenotypes. Rhesus macaques (
, MMU) and crab-eating macaques (
, MFA) serve as crucial nonhuman primate biomedical models with different phenotypes. To date, however, large-scale comparative transcriptome research between these two species has not yet been fully explored. Here, we conducted systematic comparisons utilizing newly sequenced RNA-seq data from 84 samples (41 MFA samples and 43 MMU samples) encompassing 14 common tissues. Our findings revealed a small fraction of genes (3.7%) with differential expression between the two species, as well as 36.5% of genes with tissue-specific expression in both macaques. Comparison of gene expression between macaques and humans indicated that 22.6% of orthologous genes displayed differential expression in at least two tissues. Moreover, 19.41% of genes that overlapped with macaque-specific structural variants showed differential expression between humans and macaques. Of these, the
gene exhibited elevated expression in humans compared to macaques due to lineage-specific duplication. In summary, this study presents a large-scale transcriptomic comparison between MMU and MFA and between macaques and humans. The discovery of gene expression variations not only enhances the biomedical utility of macaque models but also contributes to the wider field of primate genomics.</description><subject>Animals</subject><subject>Brain research</subject><subject>Consortia</subject><subject>Eating</subject><subject>Euthanasia</subject><subject>Gene expression</subject><subject>Genes</subject><subject>Genomes</subject><subject>Genomics</subject><subject>Macaca mulatta</subject><subject>Marine crustaceans</subject><subject>Monkeys & apes</subject><subject>Neurosciences</subject><subject>Phenotypes</subject><subject>Phenotypic variations</subject><subject>Quality 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Affiliated Hospital, Zhejiang University, Yiwu, Zhejiang 322000, China</creatorcontrib><creatorcontrib>上海交通大学致远学院, 上海 200240, 中国</creatorcontrib><creatorcontrib>Institute of Neuroscience, State Key Laboratory of Neuroscience, Center for Excellence in Brain Science & Intelligence Technology, Chinese Academy of Sciences, Shanghai 200031, China</creatorcontrib><creatorcontrib>Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Ministry of Education, Shanghai Jiao Tong University, Shanghai 200030, China</creatorcontrib><creatorcontrib>上海交通大学Bio-X研究院, 遗传发育与精神神经疾病教育部重点实验室, 上海 200030, 中国</creatorcontrib><creatorcontrib>浙江大学医学院附属第四医院, 国际健康医学研究院, 基因组研究中心, 浙江 义乌 322000, 中国</creatorcontrib><creatorcontrib>University of Chinese Academy of Sciences, Beijing 100049, China</creatorcontrib><creatorcontrib>Key Laboratory of Genetic Evolution & Animal Models, Chinese Academy of Sciences, Kunming, Yunnan 650201, China</creatorcontrib><creatorcontrib>Zhiyuan 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100049, 中国</aucorp><aucorp>中国科学院神经科学研究所神经科学国家重点实验室, 脑科学与智能技术卓越创新中心, 上海 200031, 中国</aucorp><aucorp>中国科学院遗传进化与动物模型重点实验室, 云南 昆明 650201, 中国</aucorp><aucorp>Shanghai Center for Brain Science and Brain-Inspired Intelligence Technology, Shanghai 201210, China</aucorp><aucorp>Center for Genomic Research, International Institutes of Medicine, Fourth Affiliated Hospital, Zhejiang University, Yiwu, Zhejiang 322000, China</aucorp><aucorp>上海交通大学致远学院, 上海 200240, 中国</aucorp><aucorp>Institute of Neuroscience, State Key Laboratory of Neuroscience, Center for Excellence in Brain Science & Intelligence Technology, Chinese Academy of Sciences, Shanghai 200031, China</aucorp><aucorp>Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Ministry of Education, Shanghai Jiao Tong University, Shanghai 200030, China</aucorp><aucorp>上海交通大学Bio-X研究院, 遗传发育与精神神经疾病教育部重点实验室, 上海 200030, 中国</aucorp><aucorp>浙江大学医学院附属第四医院, 国际健康医学研究院, 基因组研究中心, 浙江 义乌 322000, 中国</aucorp><aucorp>University of Chinese Academy of Sciences, Beijing 100049, China</aucorp><aucorp>Key Laboratory of Genetic Evolution & Animal Models, Chinese Academy of Sciences, Kunming, Yunnan 650201, China</aucorp><aucorp>Zhiyuan College, Shanghai Jiao Tong University, Shanghai 200240, China</aucorp><aucorp>上海脑科学与类脑研究中心, 上海 201210, 中国</aucorp><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Comparative transcriptome analysis between rhesus macaques ( Macaca mulatta ) and crab-eating macaques ( M. fascicularis )</atitle><jtitle>Dōngwùxué yánjiū</jtitle><addtitle>Zool Res</addtitle><date>2024-03-18</date><risdate>2024</risdate><volume>45</volume><issue>2</issue><spage>299</spage><epage>310</epage><pages>299-310</pages><issn>2095-8137</issn><issn>0254-5853</issn><eissn>2095-8137</eissn><abstract>Understanding gene expression variations between species is pivotal for deciphering the evolutionary diversity in phenotypes. Rhesus macaques (
, MMU) and crab-eating macaques (
, MFA) serve as crucial nonhuman primate biomedical models with different phenotypes. To date, however, large-scale comparative transcriptome research between these two species has not yet been fully explored. Here, we conducted systematic comparisons utilizing newly sequenced RNA-seq data from 84 samples (41 MFA samples and 43 MMU samples) encompassing 14 common tissues. Our findings revealed a small fraction of genes (3.7%) with differential expression between the two species, as well as 36.5% of genes with tissue-specific expression in both macaques. Comparison of gene expression between macaques and humans indicated that 22.6% of orthologous genes displayed differential expression in at least two tissues. Moreover, 19.41% of genes that overlapped with macaque-specific structural variants showed differential expression between humans and macaques. Of these, the
gene exhibited elevated expression in humans compared to macaques due to lineage-specific duplication. In summary, this study presents a large-scale transcriptomic comparison between MMU and MFA and between macaques and humans. The discovery of gene expression variations not only enhances the biomedical utility of macaque models but also contributes to the wider field of primate genomics.</abstract><cop>China</cop><pub>Kunming Institute of Zoology, The Chinese Academy of Sciences</pub><pmid>38485500</pmid><doi>10.24272/j.issn.2095-8137.2023.322</doi><tpages>12</tpages><oa>free_for_read</oa></addata></record> |
| fulltext | fulltext |
| identifier | ISSN: 2095-8137 |
| ispartof | Dōngwùxué yánjiū, 2024-03, Vol.45 (2), p.299-310 |
| issn | 2095-8137 0254-5853 2095-8137 |
| language | eng |
| recordid | cdi_proquest_journals_3104150992 |
| source | Elektronische Zeitschriftenbibliothek - Frei zugängliche E-Journals; PubMed Central |
| subjects | Animals Brain research Consortia Eating Euthanasia Gene expression Genes Genomes Genomics Macaca mulatta Marine crustaceans Monkeys & apes Neurosciences Phenotypes Phenotypic variations Quality control Tissue Transcriptomes Transcriptomics |
| title | Comparative transcriptome analysis between rhesus macaques ( Macaca mulatta ) and crab-eating macaques ( M. fascicularis ) |
| url | https://sfx.bib-bvb.de/sfx_tum?ctx_ver=Z39.88-2004&ctx_enc=info:ofi/enc:UTF-8&ctx_tim=2025-02-03T08%3A49%3A00IST&url_ver=Z39.88-2004&url_ctx_fmt=infofi/fmt:kev:mtx:ctx&rfr_id=info:sid/primo.exlibrisgroup.com:primo3-Article-proquest_pubme&rft_val_fmt=info:ofi/fmt:kev:mtx:journal&rft.genre=article&rft.atitle=Comparative%20transcriptome%20analysis%20between%20rhesus%20macaques%20(%20Macaca%20mulatta%20)%20and%20crab-eating%20macaques%20(%20M.%20fascicularis%20)&rft.jtitle=D%C5%8Dngw%C3%B9xu%C3%A9%20y%C3%A1nji%C5%AB&rft.au=Mao,%20Yu-Xiang&rft.aucorp=%E4%B8%AD%E5%9B%BD%E7%A7%91%E5%AD%A6%E9%99%A2%E5%A4%A7%E5%AD%A6,%20%E5%8C%97%E4%BA%AC%20100049,%20%E4%B8%AD%E5%9B%BD&rft.date=2024-03-18&rft.volume=45&rft.issue=2&rft.spage=299&rft.epage=310&rft.pages=299-310&rft.issn=2095-8137&rft.eissn=2095-8137&rft_id=info:doi/10.24272/j.issn.2095-8137.2023.322&rft_dat=%3Cproquest_pubme%3E3104150992%3C/proquest_pubme%3E%3Curl%3E%3C/url%3E&disable_directlink=true&sfx.directlink=off&sfx.report_link=0&rft_id=info:oai/&rft_pqid=3104150992&rft_id=info:pmid/38485500&rfr_iscdi=true |