title: Circular DNA genomics (circomics) exemplified for geminiviruses in bean crops and weeds of northeastern Brazil.
abstract: 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.
authors.affiliation: Institute of Biology, Department of Molecular Biology and Plant Virology, University of Stuttgart, Pfaffenwaldring 57, 70550 Stuttgart, Germany.
authors.forename: Patricia Soares
authors.initials: PS
authors.lastname: Wyant
authors.forename: Stephan
authors.initials: S
authors.lastname: Strohmeier
authors.forename: Benjamin
authors.initials: B
authors.lastname: Schäfer
authors.forename: Björn
authors.initials: B
authors.lastname: Krenz
authors.forename: Iraildes Pereira
authors.initials: IP
authors.lastname: Assunção
authors.forename: Gaus Silvestre de Andrade
authors.initials: GS
authors.lastname: Lima
authors.forename: Holger
authors.initials: H
authors.lastname: Jeske
mesh_terms: D001938:Brazil; D004270:DNA, Circular / Q000235:genetics*; D004279:DNA, Viral / Q000235:genetics*; D007887:Fabaceae / Q000821:virology*; D017791:Geminiviridae / Q000235:genetics*; D015967:Gene Expression Regulation, Viral; D023281:Genomics; D021141:Nucleic Acid Amplification Techniques; D010802:Phylogeny; D010935:Plant Diseases / Q000821:virology; D057685:Plant Weeds / Q000821:virology*
chemical_list: D004270:DNA, Circular; D004279:DNA, Viral