Volume 35 Issue 3
May  2014
Turn off MathJax
Article Contents
Yu FAN, Dan-Dan YU, Yong-Gang YAO. Positively selected genes of the Chinese tree shrew (Tupaia belangeri chinensis) locomotion system. Zoological Research, 2014, 35(3): 240-248. doi: 10.11813/j.issn.0254-5853.2014.3.240
Citation: Yu FAN, Dan-Dan YU, Yong-Gang YAO. Positively selected genes of the Chinese tree shrew (Tupaia belangeri chinensis) locomotion system. Zoological Research, 2014, 35(3): 240-248. doi: 10.11813/j.issn.0254-5853.2014.3.240

Positively selected genes of the Chinese tree shrew (Tupaia belangeri chinensis) locomotion system

doi: 10.11813/j.issn.0254-5853.2014.3.240
  • Received Date: 2014-01-09
  • Rev Recd Date: 2014-03-17
  • Publish Date: 2014-05-08
  • While the recent release of the Chinese tree shrew (Tupaia belangeri chinensis) genome has made the tree shrew an increasingly viable experimental animal model for biomedical research, further study of the genome may facilitate new insights into the applicability of this model. For example, though the tree shrew has a rapid rate of speed and strong jumping ability, there are limited studies on its locomotion ability. In this study we used the available Chinese tree shrew genome information and compared the evolutionary pattern of 407 locomotion system related orthologs among five mammals (human, rhesus monkey, mouse, rat and dog) and the Chinese tree shrew. Our analyses identified 29 genes with significantly high ω (Ka/Ks ratio) values and 48 amino acid sites in 14 genes showed significant evidence of positive selection in the Chinese tree shrew. Some of these positively selected genes, e.g. HOXA6 (homeobox A6) and AVP (arginine vasopressin), play important roles in muscle contraction or skeletal morphogenesis. These results provide important clues in understanding the genetic bases of locomotor adaptation in the Chinese tree shrew.
  • loading
  • [1]
    Birney E, Clamp M, Durbin R. 2004. GeneWise and Genomewise. Genome Research, 14(5): 988-995.
    Cao J, Yang EB, Su JJ, Li Y, Chow P. 2003. The tree shrews: adjuncts and alternatives to primates as models for biomedical research. Journal of Medical Primatology, 32(3): 123-130.
    Cho YS, Hu L, Hou H, Lee H, Xu J, Kwon S, Oh S, Kim HM, Jho S, Kim S, Shin YA, Kim BC, Kim H, Kim CU, Luo SJ, Johnson WE, Koepfli KP, Schmidt-Kuntzel A, Turner JA, Marker L, Harper C, Miller SM, Jacobs W, Bertola LD, Kim TH, Lee S, Zhou Q, Jung HJ, Xu X, Gadhvi P, Xu P, Xiong Y, Luo Y, Pan S, Gou C, Chu X, Zhang J, Liu S, He J, Chen Y, Yang L, Yang Y, He J, Liu S, Wang J, Kim CH, Kwak H, Kim JS, Hwang S, Ko J, Kim CB, Kim S, Bayarlkhagva D, Paek WK, Kim SJ, O'brien SJ, Wang J, Bhak J. 2013. The tiger genome and comparative analysis with lion and snow leopard genomes. Nature Communications, 4: 2433.
    Davoli R, Fontanesi L, Cagnazzo M, Scotti E, Buttazzoni L, Yerle M, Russo V. 2003. Identification of SNPs, mapping and analysis of allele frequencies in two candidate genes for meat production traits: the porcine myosin heavy chain 2B (MYH4) and the skeletal muscle myosin regulatory light chain 2 (HUMMLC2B). Animal Genetics, 34(3): 221-225.
    Eberstein A, Goodgold J. 1968. Slow and fast twitch fibers in human skeletal muscle. The American Journal of Physiology, 215(3): 535-541.
    Edgar RC. 2004. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Research, 32(5): 1792-1797.
    Endo H, Rerkamuaychoke W, Kimura J, Sasaki M, Kurohmaru M, Yamada J. 1999. Functional morphology of the locomotor system in the northern smooth-tailed tree shrew (Dendrogale murina). Annals of Anatomy-Anatomischer Anzeiger, 181(4): 397-402.
    Fan Y, Huang ZY, Cao CC, Chen CS, Chen YX, Fan DD, He J, Hou HL, Hu L, Hu XT, Jiang XT, Lai R, Lang YS, Liang B, Liao SG, Mu D, Ma YY, Niu YY, Sun XQ, Xia JQ, Xiao J, Xiong ZQ, Xu L, Yang L, Zhang Y, Zhao W, Zhao XD, Zheng YT, Zhou JM, Zhu YB, Zhang GJ, Wang J, Yao YG. 2013. Genome of the Chinese tree shrew. Nature Communications, 4: 1426.
    Farah CS, Reinach FC. 1995. The troponin complex and regulation of muscle contraction. The FASEB Journal, 9(9): 755-767.
    Fuchs E, Corbach-Söhle S. 2010. Tree Shrews. In:The UFAW Handbook on the Care and Management of Laboratory and Other Research Animals. Oxford: Wiley-Blackwell, 262-275.
    Hoekstra HE, Coyne JA. 2007. The locus of evolution: evo devo and the genetics of adaptation. Evolution, 61(5): 995-1016.
    Huynen MA, Gabaldon T, Snel B. 2005. Variation and evolution of biomolecular systems: searching for functional relevance. FEBS Letters, 579(8): 1839-1845.
    Kosakovsky Pond SL, Murrell B, Fourment M, Frost SD, Delport W, Scheffler K. 2011. A random effects branch-site model for detecting episodic diversifying selection. Molecular Biology and Evolution, 28(11): 3033-3043.
    Lindblad-Toh K, Garber M, Zuk O, Lin MF, Parker BJ, Washietl S, Kheradpour P, Ernst J, Jordan G, Mauceli E, Ward LD, Lowe CB, Holloway AK, Clamp M, Gnerre S, Alfoldi J, Beal K, Chang J, Clawson H, Cuff J, Di Palma F, Fitzgerald S, Flicek P, Guttman M, Hubisz MJ, Jaffe DB, Jungreis I, Kent WJ, Kostka D, Lara M, Martins AL, Massingham T, Moltke I, Raney BJ, Rasmussen MD, Robinson J, Stark A, Vilella AJ, Wen J, Xie X, Zody MC, Baldwin J, Bloom T, Chin CW, Heiman D, Nicol R, Nusbaum C, Young S, Wilkinson J, Worley KC, Kovar CL, Muzny DM, Gibbs RA, Cree A, Dihn HH, Fowler G, Jhangiani S, Joshi V, Lee S, Lewis LR, Nazareth LV, Okwuonu G, Santibanez J, Warren WC, Mardis ER, Weinstock GM, Wilson RK, Delehaunty K, Dooling D, Fronik C, Fulton L, Fulton B, Graves T, Minx P, Sodergren E, Birney E, Margulies EH, Herrero J, Green ED, Haussler D, Siepel A, Goldman N, Pollard KS, Pedersen JS, Lander ES, Kellis M. 2011. A high-resolution map of human evolutionary constraint using 29 mammals. Nature, 478: 476-482.
    Macarthur DG, North KN. 2004. A gene for speed? The evolution and function of alpha-actinin-3. BioEssays, 26(7): 786-795.
    Mcginnis S, Madden TL. 2004. BLAST: at the core of a powerful and diverse set of sequence analysis tools. Nucleic Acids Research, 32(2): W20-W25.
    Murphy WJ, Pevzner PA, O'brien SJ. 2004. Mammalian phylogenomics comes of age. Trends in Genetics, 20(12): 631-639.
    Norman B, Esbjornsson M, Rundqvist H, Osterlund T, Von Walden F, Tesch PA. 2009. Strength, power, fiber types, and mRNA expression in trained men and women with different ACTN3 R577X genotypes. Journal of Applied Physiology, 106(3): 959-965.
    Peng YZ, Ye ZZ, Zou RJ, Wang YX, Tian BP, Ma YY, Shi LM. 1991. Biology of Chinese Tree Shrews (Tupaia belangeri chinensis). Kunming, China: Yunnan Science and Technology Press.
    Salmikangas P, Van Der Ven PF, Lalowski M, Taivainen A, Zhao F, Suila H, Schroder R, Lappalainen P, Furst DO, Carpen O. 2003. Myotilin, the limb-girdle muscular dystrophy 1A (LGMD1A) protein, cross-links actin filaments and controls sarcomere assembly. Human Molecular Genetics, 12(2): 189-203.
    Schmidt M, Schilling N. 2007. Fiber type distribution in the shoulder muscles of the tree shrew, the cotton-top tamarin, and the squirrel monkey related to shoulder movements and forelimb loading. Journal of Human Evolution, 52(4): 401-419.
    Sellers JR. 2000. Myosins: a diverse superfamily. Biochimica et Biophysica Acta, 1496(1): 3-22.
    Tamura K, Peterson D, Peterson N, Stecher G, Nei M, Kumar S. 2011. MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Molecular Biology and Evolution, 28(10): 2731-2739.
    The Chimpanzee Sequencing and Analysis Consortium. 2005. Initial sequence of the chimpanzee genome and comparison with the human genome. Nature, 437: 69-87.
    Tiso N, Majetti M, Stanchi F, Rampazzo A, Zimbello R, Nava A, Danieli GA. 1999. Fine mapping and genomic structure of ACTN2, the human gene coding for the sarcomeric isoform of alpha-actinin-2, expressed in skeletal and cardiac muscle. Biochemical and Biophysical Research Communications, 265(1): 256-259.
    Wellik DM. 2007. Hox patterning of the vertebrate axial skeleton. Developmental Dynamics, 236(9): 2454-2463.
    Xu L, Zhang Y, Liang B, Lu LB, Chen CS, Chen YB, Zhou JM, Yao YG. 2013. Tree shrews under the spot light: emerging model of human diseases. Zoological Research, 34(2): 59-69. (in Chinese)
    Yang Z. 2007. PAML 4: phylogenetic analysis by maximum likelihood. Molecular Biology and Evolution, 24(8): 1586-1591.
    Zeng YN, Shen YY, Zhang YP. 2013. Genome-wide scan reveals the molecular mechanisms of functional differentiation of Myotis lucifugus and Pteropus vampyrus. Zoological Research, 34(3): 221-227. (in Chinese)
    Zhang Z, Li J, Zhao XQ, Wang J, Wong GK, Yu J. 2006. KaKs_Calculator: calculating Ka and Ks through model selection and model averaging. Genomics Proteomics Bioinformatics, 4(4): 259-263.
  • Relative Articles

    [1] Qi Chen, Zhao-Xia Ma, Li-Bin Xia, Zhen-Ni Ye, Bao-Ling Liu, Tie-Kun Ma, Peng-Fei Bao, Xing-Fei Wu, Cong-Tao Yu, Dai-Ping Ma, Yuan-Yuan Han, Wen-Guang Wang, De-Xuan Kuang, Jie-Jie Dai, Rong-Ping Zhang, Min Hu, Hong Shi, Wen-Lin Wang, Yan-Jiao Li. A tree shrew model for steroid-associated osteonecrosis. Zoological Research, 2020, 41(5): 564-568.  doi: 10.24272/j.issn.2095-8137.2020.061
    [2] Jing Zhang, Rong-Can Luo, Xiao-Yong Man, Long-Bao Lv, Yong-Gang Yao, Min Zheng. The anatomy of the skin of the Chinese tree shrew is very similar to that of human skin. Zoological Research, 2020, 41(2): 208-212.  doi: 10.24272/j.issn.2095-8137.2020.028
    [3] Yu Fan, Mao-Sen Ye, Jin-Yan Zhang, Ling Xu, Dan-Dan Yu, Tian-Le Gu, Yu-Lin Yao, Jia-Qi Chen, Long-Bao Lv, Ping Zheng, Dong-Dong Wu, Guo-Jie Zhang, Yong-Gang Yao. Chromosomal level assembly and population sequencing of the Chinese tree shrew genome. Zoological Research, 2019, 40(6): 506-521.  doi: 10.24272/j.issn.2095-8137.2019.063
    [4] Li-Ping Jiang, Qiu-Shuo Shen, Cui-Ping Yang, Yong-Bin Chen. Establishment of basal cell carcinoma animal model in Chinese tree shrew (Tupaia belangeri chinensis). Zoological Research, 2017, 38(4): 180-190.  doi: 10.24272/j.issn.2095-8137.2017.045
    [5] Yong-Gang Yao. Creating animal models, why not use the Chinese tree shrew (Tupaia belangeri chinensis)?. Zoological Research, 2017, 38(3): 118-126.  doi: 10.24272/j.issn.2095-8137.2017.032
    [6] Cai-Yun WANG, Yun-Han MA, Da-Jian HE, Shi-Hua YANG. cDNA cloning and sequence analysis of pluripotency genes in tree shrews (Tupaia belangeri). Zoological Research, 2013, 34(2): 127-131.  doi: 10.3724/SP.J.1141.2013.02127
    [7] Xiao-Yun WU, Yun-Hai LI, Qing CHANG, Lin-Qiang ZHANG, Sha-Sha LIAO, Bin LIANG. Streptozotocin induction of type 2 diabetes in tree shrew. Zoological Research, 2013, 34(2): 108-115.  doi: 10.3724/SP.J.1141.2013.02108
    [8] Xiao-Hong LIU, Yong-Gang YAO. Characterization of 12 polymorphic microsatellite markers in the Chinese tree shrew (Tupaia belangeri chinensis). Zoological Research, 2013, 34(E2): 13362-E.  doi: 10.3724/SP.J.1141.2013.E02E62
    [9] SUN Yong-Mei, YANG Jian-Zhen, SUN Hua-Ying, MA Yuan-Ye, WANG Jian-Hong. Establishment of tree shrew chronic morphine dependent model. Zoological Research, 2012, 33(1): 14-18.  doi: 10.3724/SP.J.1141.2012.01014
    [10] ZHANG Yuan-Xu, PING Shu-Huang, YANG Shi-Hua. Morphological characteristics and cryodamage of Chinese tree shrew (Tupaia belangeri chinensis) sperm. Zoological Research, 2012, 33(1): 29-36.  doi: 10.3724/SP.J.1141.2012.01029
    [11] SHEN Pei-Qing, ZHENG Hong, LIU Ru-Wen, CHEN Li-Ling, LI Bo, HE Bao-Li, LI Jin-Tao, BE. Progress and prospect in research on laboratory tree shrew in China. Zoological Research, 2011, 32(1): 109-114.  doi: 10.3724/SP.J.1141.2011.01109
    [12] YE Zhi-zhang, PENG Yen-zhang, PAN Ru-liang, WANG Hong. Arterial System in Chinese Tree Shrew (Tupaia belangeri chinensis). Zoological Research, 1990, 11(2): 131-138.
    [13] TIAN Bao-ping, PEN Yian-zhang, HOU Yi-di. Investigation of Parasites on Chinese Tree Shrews. Zoological Research, 1989, 10(zk): 90-110.
    [14] YE Zhi-zhang, PENG Yan-zhang, PAN Ru-liang, WANG Hong. The spinal plexus of Tree shrew(Tupaia belangeri chinensis). Zoological Research, 1989, 10(2): 107-114.
    [15] ZOU Ru-jing, JI Wei-zhi, SHA Ling-li, LU Jin-ming, YAN Ye, YANG Ke-qin. Reproduction in Tree Shrew (Tupaia belangeri chinensis). Zoological Research, 1987, 8(3): 231-237.
    [16] WANG Ying-xiang. Taxonomic Research on Burma-Chinese tree Shrew,Tupaia belangeri (Wagner),from Southern China. Zoological Research, 1987, 8(3): 213-230.
    [17] WU Jia-yan. Study of System and Distribution of Chinese Takin (Budorcas taxicolor Hodgson,1850). Zoological Research, 1986, 7(2): 167-175.
    [18] ZHANG Bei, LIU Zu-dong. The Physico-Chemical Determination of the Hemoglobin of Tree Shrew. Zoological Research, 1986, 7(3): 251-254.
    [19] DAI Chang-bo et al.. Studies on Experimental Infection of Tree Shrew With Herpes Simplex Virus Type Ⅱ. Zoological Research, 1985, 6(3): 258-276.
    [20] ZOU Ru-jing, DAI Wei, BEN Kun-long, SONG Bao-yun. Blood Picture of the Tree Shrew (Tupaia Belanger). Zoological Research, 1983, 4(3): 291-294.
  • 加载中


    通讯作者: 陈斌, bchen63@163.com
    • 1. 

      沈阳化工大学材料科学与工程学院 沈阳 110142

    1. 本站搜索
    2. 百度学术搜索
    3. 万方数据库搜索
    4. CNKI搜索

    Article Metrics

    Article views (627) PDF downloads(1512) Cited by()
    Proportional views


    DownLoad:  Full-Size Img  PowerPoint