人腺病毒B、D亚种基因组中简单重复序列分析
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摘要
本文以人腺病毒B亚种31条基因组序列及D亚种39条基因组序列为研究材料,利用ImperfectMicrosatelliteExtractor和DNAMAN软件对这些基因组序列中简单重复序列(SSR)的分布情况进行了系统性分析和比较。分析结果显示:人腺病毒B、D亚种基因组中简单重复序列的平均相对密度是十分接近的,但在不同类型SSR中分布情况又有所不同。D亚种中二型SSR明显高于B亚种,在两亚种一型SSR中(A)n、(T)n都是比较多的,而在两亚种二型SSR中的(CG/GC)n表现出了较高的偏好性。在同亚种多序列比对分析中,D亚种表现出了更高的稳定性。B、D亚种中SSR的这种特异性分布可能与它们的进化机制和致病性有关。
In our study, the simple sequence repeat in 31 genomes of human adenoviruses B and 39 genomes of human adenoviruses D were analyzed by the software Imperfect Microsatellite Extractor and DNAMAN. The results showed that in human adenoviruses B and D subspecies the average relative density was very similar, but the distribution of different repeat motifs was markedly different. The trinucleotide repeats had higher proportion in the D subspecies. In mononucleotide repeats the (A)n and (T)n were predominant and the (CG/GC)n were more in dinucleotide repeats in Human adenoviruses B and D subspecies. In many sequence alignment analysis of same subspecies, the D subspecies showed higher stability. The specific distribution of SSR may be related to the evolution mechanism and different pathogenicity of Human adenoviruses B and D subspecies.
In our study, the simple sequence repeat in 31 genomes of human adenoviruses B and 39 genomes of human adenoviruses D were analyzed by the software Imperfect Microsatellite Extractor and DNAMAN. The results showed that in human adenoviruses B and D subspecies the average relative density was very similar, but the distribution of different repeat motifs was markedly different. The trinucleotide repeats had higher proportion in the D subspecies. In mononucleotide repeats the (A)n and (T)n were predominant and the (CG/GC)n were more in dinucleotide repeats in Human adenoviruses B and D subspecies. In many sequence alignment analysis of same subspecies, the D subspecies showed higher stability. The specific distribution of SSR may be related to the evolution mechanism and different pathogenicity of Human adenoviruses B and D subspecies.
引文
[1]金天明,武迎红.腺病毒及腺病毒载体的研究进展[J].天津农学院学报,2007,14(2):48-51.
[2]Jones,M.,Harrach,B.,Ganac,R.D.,Gozum,M.A.,Cruz,W.P.,Riedel,B.,Pan,C.,Delwart,E.L.,Schnurr,D.P..New adenovirus species found in a patient presenting with gastroenteritis[J].J.Virol,2007,81(11):5978-5984.
[3]陈娜娜,向冬喜,郑丛龙.腺病毒及其研究进展[J].大连医科大学学报,2010,32(5):586-590.
[4]Soumitra,R.,Luk,H.V.,Sergey,K.,Rebecca,G.,Roberto,G.,Xin,Y.,Martin,k.,Arbans,S.,Qiang,W.,C.Angelica,M.,Joshua,B.P.,James,M.W..Isolation and Characterization of Adenoviruses Persistently Shed from the Gastrointestinal Tract of Non-Human Primates[J].PloS Pathogens,2009,5(7):1-7.
[5]Ming Chen,Zhongyang Tan,Jianhui Jiang,[ABD2]Mingfu Li,Hongjun Chen,Guoli Shen,Ruqin Yu.Similar distribution of simple sequence repeats in diverse completed Human Immunodeficiency Virus Type 1 genomes[J].Fen.Eun.Biol.Sos,2009,583:2959-2963.
[6]Van,Belkum,A.,Scherer,S.,Van,Alphen,L.,[ABD3]Verbrage,H.Short-sequence DNA repeats in Prokaryotic genomes[J].Microbiol.Mol.Biol.Rev,1998,62(2):275-293.
[7]Toth,G.,Gaspari,Z.,Jurka,J..Microsatellites in different Eukaryotic genomes:survey and analysis[J].Genomes Research,2000,10:967-981.
[8]彭军,谭钟扬,蔡立军,[ABD4]易丽萍,赵相艳.甲型流感病毒HA基因组的简单重复序列分布分析[J].生物信息学,2011,9(1):54-59.
[9]National Center for Biotechnology Information.Human adenovirus complete genome[DB/OL].http://www.ncbi.nlm.nih.gov/nuccore/?term=human%20adenovirus%20complete%20genome
[10]Mudunuri,S.B.,Nagarajaram,H.A..IMEX:Imperfect Microsatellite Extractor[J].Genome analysis,2007,23(10):1181-1187.
[11]冯海平,谭钟扬,李丹,[ABD6]赵相艳,李明福,欧阳清检.乙型肝炎病毒B2和C2亚型中SSRs的比较分布[J].生物信息学,2011,9(4):275-280.
[12]Stallings,R.L.,Ford,A.F.,Nelson,D.,[ABD7]Torney,D.C.,Hildebrand,C.E.,Moyzis,R.K..Evolution and distribution of(GT)n repetitive sequences in mammalian genomes[J].Genomics,1991,10:807-815.
[13]Lagercrantz,U.,Ellegren,H.,Andersson,L.The abundance of various polymorphic microsatellite motifs differs between plants and vertebrates[J].Nucleic.Acids Res,1993,21:1111-1115.
[14]Paxton,R.J.,Thoren,P.A.,Tengo,J.,Estoup,A.,Pamilo,P..Mating structure and nestmate relatedness in a communal bee,Andrena jacobi(Hymenoptera,Andrenidae),using microsatellites[J].Mol.Ecol.,1996,5:511-519.
[15]Tautz,D.,Schlotterer,C..Simple sequences[J].Curr Opin Genet Dev,1994,4(6):832-837.
[16]高焕,孔杰.串联重复序列的物种差异及生物功能[J].动物学研究,2005,26(5):555-564.
[2]Jones,M.,Harrach,B.,Ganac,R.D.,Gozum,M.A.,Cruz,W.P.,Riedel,B.,Pan,C.,Delwart,E.L.,Schnurr,D.P..New adenovirus species found in a patient presenting with gastroenteritis[J].J.Virol,2007,81(11):5978-5984.
[3]陈娜娜,向冬喜,郑丛龙.腺病毒及其研究进展[J].大连医科大学学报,2010,32(5):586-590.
[4]Soumitra,R.,Luk,H.V.,Sergey,K.,Rebecca,G.,Roberto,G.,Xin,Y.,Martin,k.,Arbans,S.,Qiang,W.,C.Angelica,M.,Joshua,B.P.,James,M.W..Isolation and Characterization of Adenoviruses Persistently Shed from the Gastrointestinal Tract of Non-Human Primates[J].PloS Pathogens,2009,5(7):1-7.
[5]Ming Chen,Zhongyang Tan,Jianhui Jiang,[ABD2]Mingfu Li,Hongjun Chen,Guoli Shen,Ruqin Yu.Similar distribution of simple sequence repeats in diverse completed Human Immunodeficiency Virus Type 1 genomes[J].Fen.Eun.Biol.Sos,2009,583:2959-2963.
[6]Van,Belkum,A.,Scherer,S.,Van,Alphen,L.,[ABD3]Verbrage,H.Short-sequence DNA repeats in Prokaryotic genomes[J].Microbiol.Mol.Biol.Rev,1998,62(2):275-293.
[7]Toth,G.,Gaspari,Z.,Jurka,J..Microsatellites in different Eukaryotic genomes:survey and analysis[J].Genomes Research,2000,10:967-981.
[8]彭军,谭钟扬,蔡立军,[ABD4]易丽萍,赵相艳.甲型流感病毒HA基因组的简单重复序列分布分析[J].生物信息学,2011,9(1):54-59.
[9]National Center for Biotechnology Information.Human adenovirus complete genome[DB/OL].http://www.ncbi.nlm.nih.gov/nuccore/?term=human%20adenovirus%20complete%20genome
[10]Mudunuri,S.B.,Nagarajaram,H.A..IMEX:Imperfect Microsatellite Extractor[J].Genome analysis,2007,23(10):1181-1187.
[11]冯海平,谭钟扬,李丹,[ABD6]赵相艳,李明福,欧阳清检.乙型肝炎病毒B2和C2亚型中SSRs的比较分布[J].生物信息学,2011,9(4):275-280.
[12]Stallings,R.L.,Ford,A.F.,Nelson,D.,[ABD7]Torney,D.C.,Hildebrand,C.E.,Moyzis,R.K..Evolution and distribution of(GT)n repetitive sequences in mammalian genomes[J].Genomics,1991,10:807-815.
[13]Lagercrantz,U.,Ellegren,H.,Andersson,L.The abundance of various polymorphic microsatellite motifs differs between plants and vertebrates[J].Nucleic.Acids Res,1993,21:1111-1115.
[14]Paxton,R.J.,Thoren,P.A.,Tengo,J.,Estoup,A.,Pamilo,P..Mating structure and nestmate relatedness in a communal bee,Andrena jacobi(Hymenoptera,Andrenidae),using microsatellites[J].Mol.Ecol.,1996,5:511-519.
[15]Tautz,D.,Schlotterer,C..Simple sequences[J].Curr Opin Genet Dev,1994,4(6):832-837.
[16]高焕,孔杰.串联重复序列的物种差异及生物功能[J].动物学研究,2005,26(5):555-564.