柑橘衰退病毒基因组的简单重复序列分布分析
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摘要
柑橘衰退病毒(Citrus tristeza virus,CTV)属于长线性病毒科(Closteroviridae),是目前已知植物病毒中基因组最大的病毒,其引起的柑橘衰退病对全世界的柑橘产业造成着严重影响。本文以在GenBank登录的32条全长CTV基因组序列为材料,分析简单重复序列(Simple Sequence Repeats,SSRs)在其基因组序列中的分布情况。研究结果显示,在所有的CTV基因组中均有SSRs的分布,SSRs重复次数较少,二型SSRs占主导地位,未在CTV基因组序列中发现五型和六型SSRs。在32条基因组全长序列中仅在5条序列中发现四型SSRs。这是首次以柑橘病毒为材料进行的SSRs分析研究。
Citrus tristeza virus( CTV) belongs to the family of Closteroviridae,which has the biggest genome compared with the other plant viruses,and impacts on the worldwide citrus industry negatively. 32 complete genome sequences of CTV downloaded from GenBank were used to analyze the distribution of simple sequence repeats( SSRs) types. The results suggested that SSRs existed in all CTV genome sequences whereas the numbers were low. Dinucleotide repeats were the major type in CTV sequence while pentanucleotide repeats and hexanucleotide repeats were not found in CTV,and tetranucleotide repeats were rare,found in merely 5 of 32 CTV genome sequences. This is the first report about the SSRs analysis in citrus virus genome.
Citrus tristeza virus( CTV) belongs to the family of Closteroviridae,which has the biggest genome compared with the other plant viruses,and impacts on the worldwide citrus industry negatively. 32 complete genome sequences of CTV downloaded from GenBank were used to analyze the distribution of simple sequence repeats( SSRs) types. The results suggested that SSRs existed in all CTV genome sequences whereas the numbers were low. Dinucleotide repeats were the major type in CTV sequence while pentanucleotide repeats and hexanucleotide repeats were not found in CTV,and tetranucleotide repeats were rare,found in merely 5 of 32 CTV genome sequences. This is the first report about the SSRs analysis in citrus virus genome.
引文
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[12]Duran C.,Singhania R.,Raman H.,Batley J.,Edwards D.Predicting polymorphic EST-SSRs in silico[J].Mol Ecol Resour,2013,doi:10.1111/1755-0998.12078.
[13]Guyot B.,Murai K.,Fujiwara Y.,Valverde-Garduno V.,Characterization of a Megakaryocyte-specific Enhancer of the Key Hemopoietic Transcription Factor GATA1[J].Journal of Biological Chemistry,2006,2 81:13733-13742.
[14]冯海平,谭钟扬,李丹,赵相艳,李明福,欧阳清检.乙型肝炎病毒B2和C2亚型中SSRs的比较分析[J].生物信息学,2011,9(4):1672-5565.
[15]彭军,谭钟扬,蔡立军,易丽萍,赵相艳.甲型流感病毒HA基因的简单重复序列分布分析[J].生物信息学,2011,9(1):54-59.
[16]Zhao X.,Tan Z.,Feng H.,Yang R.,Li M.,Jiang J.,Shen G.,Yu R.Microsatellites in different Potyvirus genomes:Survey and analysis[J].Gene,2011,488:52-56.
[17]Jurka J.,Pethiyagoda C.Simple Repetitive DNA Sequences from Primates:Compilation and Analysis[J].Journal of Molecular Evolution,1995,40:120-126.
[18]Katti M.V.,Ranjekar P.K.,Gupta V.S.Different distribution of simple sequence repeats in eukaryotic genome sequences[J].Molecular Biology and Evolution,2001,18:1161-1167.
[19]Zhao X.,Tian Y.,Yang R.,Feng H.,Ouyang Q.,Tian Y.,Tan Z.,Li M.,Niu Y.,Jiang J.,Shen G.,Yu R.Coevolution between simple sequence repeats(SSRs)and virus genome size[J].BMC Genomics,2012,13:435.
[2]Yang Z.N.,Mathews D.M.,Dodds J.A.,Mirkov T.E.Molecular characterization of isolate of citrus tristeza virus that cause severe symptoms in sweet orange[J].Virus Genes,1999,19:131-142.
[3]Vives M.C.,Rubio L.,López C.,Navas-Castillo J.,AlbiachMarti M.R.,Dawson W.O.,Guerri J.,Flores R.,Moreno P.The complete genome sequence of the major component of a mild citrus tristeza virus isolate[J].Journal of General Virology,1999,80:811-816.
[4]Karasev A.V.,Dawson W.O.,Hilf M.E.,Garnsey S.M.Molecular biology of citrus tristeza virus:implications for disease diagnosis and control[J].Acta Horticulturae,1998,472:333-337.
[5]余冬冬,刘永清,王国平.柑橘衰退病毒研究进展[J].果树学报,2003,20(3):224-229.
[6]Roistacher C.N.Should we introduce protective isolates of Citrus tristeza virus[J].Citrograph,1992,77:5-9.
[7]赵学源,蒋元晖,张权柄,邱柱石,苏维芳.柑桔苗黄型衰退病毒的分布情况和六种酸橙砧木对它的反应[J].植物病理学报,1979,9(1):61-64.
[8]周常勇,赵学源,蒋元晖,戴胜根,唐科志,杨方云,黄森,杨育龙,李宗明,王兆兰,张高明,谭晓,张学武.柚矮化病调查和病原鉴定[J].中国南方果树,1998,27(3):20-21.
[9]Zhang L.,Yuan D.,Yu S.,Li Z.,Cao Y,Miao Z,Qian H.,Tang K.Preference of simple sequence repeats in coding and non-coding regions of Arabidopsis thaliana[J].Bioinformatics,2004,20:1081-1086.
[10]Usdin K.The biological effects of simple tandem repeats:Lessons from the repeat expansion diseases[J].Genome Research,2008,18:1011-1019.
[11]Rauscher G.,Simko I.Development of genomic SSR markers for fingerprinting lettuce(Lactuca sativa L.)cultivars and mapping genes[J].BMC Plant Biology,2013,doi:10.1186/1471-2229-13-11.
[12]Duran C.,Singhania R.,Raman H.,Batley J.,Edwards D.Predicting polymorphic EST-SSRs in silico[J].Mol Ecol Resour,2013,doi:10.1111/1755-0998.12078.
[13]Guyot B.,Murai K.,Fujiwara Y.,Valverde-Garduno V.,Characterization of a Megakaryocyte-specific Enhancer of the Key Hemopoietic Transcription Factor GATA1[J].Journal of Biological Chemistry,2006,2 81:13733-13742.
[14]冯海平,谭钟扬,李丹,赵相艳,李明福,欧阳清检.乙型肝炎病毒B2和C2亚型中SSRs的比较分析[J].生物信息学,2011,9(4):1672-5565.
[15]彭军,谭钟扬,蔡立军,易丽萍,赵相艳.甲型流感病毒HA基因的简单重复序列分布分析[J].生物信息学,2011,9(1):54-59.
[16]Zhao X.,Tan Z.,Feng H.,Yang R.,Li M.,Jiang J.,Shen G.,Yu R.Microsatellites in different Potyvirus genomes:Survey and analysis[J].Gene,2011,488:52-56.
[17]Jurka J.,Pethiyagoda C.Simple Repetitive DNA Sequences from Primates:Compilation and Analysis[J].Journal of Molecular Evolution,1995,40:120-126.
[18]Katti M.V.,Ranjekar P.K.,Gupta V.S.Different distribution of simple sequence repeats in eukaryotic genome sequences[J].Molecular Biology and Evolution,2001,18:1161-1167.
[19]Zhao X.,Tian Y.,Yang R.,Feng H.,Ouyang Q.,Tian Y.,Tan Z.,Li M.,Niu Y.,Jiang J.,Shen G.,Yu R.Coevolution between simple sequence repeats(SSRs)and virus genome size[J].BMC Genomics,2012,13:435.