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Issue:ISSN 1000-7083
          CN 51-1193/Q
Director:Sichuan Association for Science and Technology
Sponsored by:Sichuan Society of Zoologists; Chengdu Giant Panda Breeding Research Foundation; Sichuan Association of Wildlife Conservation; Sichuan University
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Your Position :Home->Past Journals Catalog->2019 Vol.38 No.6

Characteristics of Alu Family in Four Old World Monkey Genomes
Author of the article:ZHANG Xueyan, YU Haoyang, SUN Tianlin, QIU Shi, CAI Yansen, LI Jing*
Author's Workplace:Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, Sichuan Key Laboratory of Conservation Biology on Endangered Wildlife, College of Life Sciences, Sichuan University, Chengdu 610065, China
Key Words:Old World monkey; transposable element; Alu family; polymorphic Alu locus; species-specific Alu locus
Abstract:In order to clarify the influence of transposable elements (TEs) on the genomic diversity and evolution of Old World monkeys, this study provided TEs annotation for the 4 Old World monkey species:olive baboon (Papio anubis), rhesus macaque (Macaca mulatta), green monkey (Chlorocebus sabaeus) and proboscis monkey (Nasalis larvatus) based on Repbase database. The types and divergence rates of TEs in the 4 species were analyzed by focusing on the primate-specific Alu families, the insertion/deletion polymorphic Alu loci, and the species-specific Alu (SSA) loci. The results showed that the Alu transposons had more than a million copies (except N. larvatus). The composition and distribution of TEs in the 4 genomes were consistent with their evolutionary relationship. TEs characteristics of P. anubis were similar with M. mulatta, but different from C. sabaeus and N. larvatus. A large number of insertion/deletion polymorphic Alu loci were identified in the 4 genomes by comparative-genomic analysis. We further identified 7 882 SSA loci, and more than 95% of them were belonging to the AluY family. The SSA of the 3 Cercopithecinae species were mainly composed of the AluYRa1 subfamily, while in the N. larvatus were mainly composed of the Alu YRa2 subfamily. The study revealed that the transposition activity of the Alu family might play a significant role in the evolution and the genomic diversity of the Old World monkey.
2019,38(6): 638-645 收稿日期:2019-05-07
Batzer MA, Deininger PL. 2002. Alu repeats and human genomic diversity[J]. Nature Reviews Genetics, 3(5):370-379.
Deininger PL, Batzer MA. 2002. Mammalian retroelements[J]. Genome Research, 12(10):1455-1465.
Deininger PL. 2011. Alu elements:know the SINEs[J]. Genome Biology, 12(12):236. DOI:10.1186/gb-2011-12-12-236.
Dewannieux M, Esnault C, Heidmann T. 2003. LINE-mediated retrotransposition of marked Alu sequences[J]. Nature Genetics, 35(1):41-48.
Feschotte C. 2008. Transposable elements and the evolution of regulatory networks[J]. Nature Reviews Genetics, 9(5):397-405.
Han K, Konkel MK, Xing JC, et al. 2007. Mobile DNA in Old World monkeys:a glimpse through the rhesus macaque genome[J]. Science, 316(5882):238-240.
Konkel MK, Walker JA, Batzer MA. 2010. LINEs and SINEs of primate evolution[J]. Evolutionary Anthropology:Issues, News, and Reviews, 19(6):236-249.
Konkel MK, Wang J, Liang P, et al. 2007. Identification and characterization of novel polymorphic LINE-1 insertions through comparison of two human genome sequence assemblies[J]. Gene, 390(1-2):28-38.
Lander ES, Linton LM, Birren B, et al. 2001. Initial sequencing and analysis of the human genome[J]. Nature, 409(6822):860-921.
Liu GE, Alkan C, Jiang L, et al. 2009. Comparative analysis of Alu repeats in primate genomes[J]. Genome Research, 19(5):876-885.
Mclain AT, Carman GW, Fullerton ML, et al. 2013. Analysis of western lowland gorilla (Gorilla gorilla gorilla) specific Alu repeats[J]. Mobile DNA, 4(1):26. DOI:10.1186/1759-8753-4-26.
Meijaard E, Nijman V, Supriatna J. 2008. Nasalis larvatus[DB/OL].[2019-01-30]. The IUCN Red List of Threatened Species 2008:e. T14352A4434312.
Peng CJ, Niu LL, Deng JB, et al. 2018. Can-SINE dynamics in the giant panda and three other Caniformia genomes[J]. Mobile DNA, 9(1):32. DOI:10.1186/s13100-018-0137-0.
Perelman P, Johnson WE,Roos C, et al. 2011. A molecular phylogeny of living primates[J]. PLoS Genetics, 7(3):e1001342. DOI:10.1371/journal.pgen.1001342.
Pozzi L, Hodgson JA, Burrell AS, et al. 2014. Primate phylogenetic relationships and divergence dates inferred from complete mitochondrial genomes[J]. Molecular Phylogenetics and Evolution, 75:165-183.
Ray DA, Xing JC, Hedges DJ, et al. 2005. Alu insertion loci and platyrrhine primate phylogeny[J]. Molecular Phylogenetics and Evolution, 35(1):117-126.
Roy-Engel AM, Batzer MA, Deininger PL. 2008. Evolution of human retrosequences:Alu[M]//Langley RJ, Renno T. Encyclopedia of life sciences. Chichester:John Wiley & Sons, Ltd.
Salem AH, Ray DA, Xing JC, et al. 2003. Alu elements and hominid phylogenetics[J]. Proceedings of the National Academy of Sciences of the United States of America, 100(22):12787-12791.
Tchitchek N, Jacquelin B, Wincker P, et al. 2012. Expression sequence tag library derived from peripheral blood mononuclear cells of the Chlorocebus sabaeus[J]. BMC Genomics, 13:279. DOI:10.1186/1471-2164-13-279.
Wicker T, Sabot F, Hua-Van A, et al. 2007. A unified classification system for eukaryotic transposable elements[J]. Nature Reviews Genetics, 8(12):973-982.
Zhou X, Wang B, Pan Q, et al. 2014. Whole-genome sequencing of the snub-nosed monkey provides insights into folivory and evolutionary history[J]. Nature Genetics, 46(12):1303-1310.
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