Contrasting genetic structure between two begomoviruses infecting the same leguminous hosts Roberto Ramos Sobrinho, 1 Ce ´ sar Augusto Diniz Xavier, 1 Hermano Monteiro de Barros Pereira, 1 Gaus Silvestre de Andrade Lima, 2 Iraı ´ldes Pereira Assunc ¸a ˜o, 2 Eduardo Seiti Gomide Mizubuti, 1 Siobain Duffy 3 and Francisco Murilo Zerbini 1 Correspondence Siobain Duffy duffy@aesop.rutgers.edu Francisco Murilo Zerbini zerbini@ufv.br Received 15 April 2014 Accepted 11 July 2014 1 Departamento de Fitopatologia/BIOAGRO, Universidade Federal de Vic ¸osa, Vic ¸ osa, MG 36570-900, Brazil 2 Departamento de Fitossanidade/CECA, Universidade Federal de Alagoas, Rio Largo, AL 57100-000, Brazil 3 Department of Ecology, Evolution and Natural Resources, Rutgers, The State University Of New Jersey, New Brunswick, NJ 08901, USA Begomoviruses are whitefly-transmitted, ssDNA plant viruses and are among the most damaging pathogens causing epidemics in economically important crops worldwide. Wild/non-cultivated plants play a crucial epidemiological role, acting as begomovirus reservoirs and as ‘mixing vessels’ where recombination can occur. Previous work suggests a higher degree of genetic variability in begomovirus populations from non-cultivated hosts compared with cultivated hosts. To assess this supposed host effect on the genetic variability of begomovirus populations, cultivated (common bean, Phaseolus vulgaris, and lima bean, Phaseolus lunatus) and non-cultivated (Macroptilium lathyroides) legume hosts were sampled from two regions of Brazil. A total of 212 full-length DNA-A genome segments were sequenced from samples collected between 2005 and 2012, and populations of the begomoviruses Bean golden mosaic virus (BGMV) and Macroptilium yellow spot virus (MaYSV) were obtained. We found, for each begomovirus species, similar genetic variation between populations infecting cultivated and non-cultivated hosts, indicating that the presumed genetic variability of the host did not a priori affect viral variability. We observed a higher degree of genetic variation in isolates from MaYSV populations than BGMV populations, which was explained by numerous recombination events in MaYSV. MaYSV and BGMV showed distinct distributions of genetic variation, with the BGMV population (but not MaYSV) being structured by both host and geography. INTRODUCTION Viruses belonging to the family Geminiviridae have circular ssDNA genomes and are widely distributed in tropical and subtropical regions, infecting several economically important crop species (Legg & Fauquet, 2004; Morales, 2006). The family is divided into seven genera (Becurtovirus, Begomovirus, Curtovirus , Eragrovirus , Mastrevirus , Topocuvirus and Turncurtovirus ) according to the type of insect vector, host range, genome organization and phylogeny (Varsani et al., 2014). Viruses classified within the genus Begomovirus are transmitted by the whitefly Bemisia tabaci (Brown et al., 2012). Begomo- viruses usually found in the New World have two genomic components known as DNA-A and DNA-B, but only the DNA-A is used in the taxonomic classification of bipartite begomoviruses (Brown et al., 2012). The DNA-A contains genes involved in replication and encapsidation, while the DNA-B contains genes responsible for intra- and inter- cellular movement (Hanley-Bowdoin et al., 2013). Begomo- viruses are among the most damaging pathogens infecting cultivated plants worldwide (Legg & Fauquet, 2004; Morales & Anderson, 2001; Navas-Castillo et al., 2011; Varma & Malathi, 2003), and specifically limit production of tomatoes, peppers and legumes in the New World (Morales, 2006; Navas-Castillo et al., 2011). In Brazil, Bean golden mosaic virus (BGMV) has been an important pathogen infecting beans The GenBank/EMBL/DDBJ accession numbers for the sequences reported in this paper are KJ939707–KJ939918. Four supplementary tables are available with the online version of this paper. Journal of General Virology (2014), 95, 2540–2552 DOI 10.1099/vir.0.067009-0 2540 067009 G 2014 The Authors Printed in Great Britain