Circular DNA genomics (circomics) exemplified for geminiviruses in bean crops and weeds of northeastern Brazil

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• 作者：Patricia Soares Wyant^a ; Stephan Strohmeier^a ; Benjamin Schä ; fer^a ; Bjö ; rn Krenz^a ; Iraildes Pereira Assunç ; ã ; o^b ; Gaus Silvestre de Andrade Lima^b ; Holger Jeske^a ; ^{holger.jeske@bio.uni-stuttgart.de}
• 关键词：Brazil ; Geminivirus ; Begomovirus ; Bean golden mosaic virus ; Rolling circle amplification (RCA) ; Restriction fragment length polymorphism (RFLP)
• 刊名：Virology
• 出版年：2012
• 期刊代码：108_00426822
• 类别：imm
• 出版时间：5 June, 2012
• 卷：427
• 期：2
• 页码：151-157
• 文件大小：838 K

摘要

Circomics was coined to describe the combination of rolling circle amplification (RCA), restriction fragment length polymorphism (RFLP) and pyro-sequencing to investigate the genome structures of small circular DNAs. A batch procedure is described using 61 plant samples from Asia, South America and Central America which revealed 83 contig sequences of geminiviral DNA components and 4 contig sequences of DNA satellites. The usefulness of this approach is validated for the Brazilian begomoviruses, and the sequence fidelity is determined by comparing the results with those of conventional cloning and sequencing of Bolivian begomoviruses reported recently. Therefore, circomics has been proven to be a major step forward to economize costs and labor and to characterize reliably geminiviral genomes in their population structure of the quasispecies.