The prevalence of badnaviruses in West African yams (Dioscorea cayenensis-rotundata) and evidence of endogenous pararetrovirus sequences in their genomes

Adams, 2009, Next-generation sequencing and metagenomic analysis: a universal diagnostic tool in plant virology, Molecular Plant Pathology, 10, 537, 10.1111/j.1364-3703.2009.00545.x Asiedu, 2010, Crops that feed the World Yams, Food Security, 2, 305, 10.1007/s12571-010-0085-0 Bousalem, 2009, Dilemmas caused by endogenous pararetroviruses regarding the taxonomy and diagnosis of yam (Dioscorea spp.) badnaviruses: analyses to support safe germplasm movement, Archives of Virology, 154, 297, 10.1007/s00705-009-0311-2 Briddon, 1999, Analysis of the sequence of Dioscorea alata bacilliform virus; comparison to other members of the badnavirus group, Virus Genes, 18, 277, 10.1023/A:1008076420783 Chabannes, 2013, Three infectious viral species lying in wait in the banana genome, Journal of Virology, 87, 8624, 10.1128/JVI.00899-13 Chabannes, 2013, Endogenous pararetroviruses—a reservoir of virus infection in plants, Current Opinion in Virology, 10.1016/j.coviro.2013.08.012 Cote, 2010, Micropropagation by tissue culture triggers differential expression of infectious endogenous banana streak virus sequences (eBSV) present in the B genome of natural and synthetic interspecific banana plantains, Molecular Plant Pathology, 11, 137, 10.1111/j.1364-3703.2009.00583.x Dallot, 2001, Evidence that the proliferation stage of micropropagation procedure is determinant in the expression of banana streak virus integrated into the genome of the FHIA 21 hybrid (Musa AAAB), Archives of Virology, 146, 2179, 10.1007/s007050170028 Delanoy, 2003, Development of real-time PCR for the rapid detection of episomal Banana streak virus (BSV), Plant Disease, 87, 33, 10.1094/PDIS.2003.87.1.33 Dumont, 2006, Biodiversity and domestication of yams in West Africa Eni, 2008, Sequence diversity among badnavirus isolates infecting yam (Dioscorea spp.) in Ghana, Togo, Benin and Nigeria, Archives of Virology, 153, 2263, 10.1007/s00705-008-0258-8 Eni, 2008, Survey of the incidence and distribution of five viruses infecting yams in the major yam-producing zones in Benin, Annals of Applied Biology, 156, 223 Eni, 2009, Survey of the incidence and distribution of viruses infecting yam (Dioscorea spp.) in Ghana and Togo, Annals of Applied Biology, 156, 243, 10.1111/j.1744-7348.2009.00383.x FAO, 2012 Galzi, 2013, Assessment and characterisation of the diversity of viruses infecting cultivated yams (Dioscorea spp.) in Haïti Gayral, 2009, Phylogeny of Banana streak virus reveals recent and repetitive endogenization in the genome of its banana host (Musa sp.), Journal of Molecular Evolution, 69, 65, 10.1007/s00239-009-9253-2 Gayral, 2008, A single banana streak virus integration event in the banana genome as the origin of infectious endogenous pararetrovirus, Journal of Virology, 82, 6697, 10.1128/JVI.00212-08 Gayral, 2010, Evolution of endogenous sequences of Banana streak virus: what can we learn from banana (Musa sp.) evolution?, Journal of Virology, 84, 7346, 10.1128/JVI.00401-10 Geering, 2005, Banana contains a diverse array of endogenous badnaviruses, Journal of General Virology, 86, 511, 10.1099/vir.0.80261-0 Geering, 2010, The classification and nomenclature of endogenous viruses of the family Caulimoviridae, Archives of Virology, 155, 123, 10.1007/s00705-009-0488-4 Goudou-Urbino, 1996, Aetiology and ecology of a yam mosaic disease in Burkina Faso, Tropical Science, 36, 34 Harper, 1999, Detection of episomal Banana streak virus by IC-PCR, Journal of Virological Methods, 79, 1, 10.1016/S0166-0934(98)00158-X Harper, 2005, The diversity of banana streak virus isolates in Uganda, Archives of Virology, 150, 2407, 10.1007/s00705-005-0610-1 Harper, 2002, Viral sequences integrated into plant genomes, Annual Review of Phytopathology, 140, 119, 10.1146/annurev.phyto.40.120301.105642 Harper, 1999, Integration of banana streak badnavirus into the Musa genome: molecular and cytogenetic evidence, Virology, 255, 207, 10.1006/viro.1998.9581 Harrison, 1973, Association of virus-like particles with internal brown spot of yam (Dioscorea alata), vol. 50, 335 Hull, 2000, Viral sequences integrated into plant genomes, Trends in Plant Science, 5, 362, 10.1016/S1360-1385(00)01723-4 IITA, 2012 Iskra-Caruana, 2010, A four-partner plant–virus interaction: enemies can also come from within, Molecular Plant Microbe Interactions, 23, 1394, 10.1094/MPMI-05-10-0107 Iskra-Caruana, 2014, A possible scenario for the evolution of Banana streak virus in banana, Virus Research, 10.1016/j.virusres.2014.01.005 Iskra-Caruana, 2013, The common evolutionary history of badnaviruses and banana, Infection, Genetics and Evolution, 21, 83, 10.1016/j.meegid.2013.10.013 Jakowitsch, 1999, Integrated pararetroviral sequences define a unique class of dispersed repetitive DNA in plants, Proceedings of the National Academy of Sciences USA, 96, 13241, 10.1073/pnas.96.23.13241 James, 2011, Development of a novel rolling-circle amplification technique to detect Banana streak virus that also discriminates between integrated and episomal virus sequences, Plant Disease, 95, 57, 10.1094/PDIS-07-10-0519 Kenyon, 2008, Yams (Dioscorea spp.) from the South Pacific Islands contain many novel badnaviruses: implications for international movement of yam germplasm, Archives of Virology, 153, 877, 10.1007/s00705-008-0062-5 Kenyon, 2001, An overview of viruses infecting Dioscorea yams in Sub-Saharan Africa, 432 King, 2012, Virus taxonomy Kunii, 2004, Reconstruction of putative DNA virus from endogenous rice tungro bacilliform virus-like sequences in the rice genome: implications for integration and evolution, BMC Genomics, 5, 80, 10.1186/1471-2164-5-80 Le Provost, 2006, Improved detection of episomal banana streak viruses by multiplex immunocapture PCR, Journal of Virological Methods, 137, 7, 10.1016/j.jviromet.2006.05.021 Lockhart, 1986, Purification and serology of a bacilliform virus associated with banana streak disease, Phytopathology, 76, 995, 10.1094/Phyto-76-995 Lockhart, 2000, Characterization and genomic analysis of tobacco vein clearing virus, a plant pararetrovirus that is transmitted vertically and related to sequences integrated in the host genome, Journal of General Virology, 81, 1579, 10.1099/0022-1317-81-6-1579 Lodhi, 1994, A simple and efficient method for DNA extraction from grapevine cultivars. Vitis species and Ampelopsis, Plant Molecular Biology Reporter, 12, 6, 10.1007/BF02668658 Mantell, 1978, Incidence of internal brown spot disease in white Lisbon Yams (Dioscorea alata) during storage, Experimental Agriculture, 14, 167, 10.1017/S0014479700008589 Matzke, 2004, Endogenous pararetroviruses of allotetraploid Nicotiana tabacum and its diploid progenitors, N. sylvestris and N. tomentosiformis, Biological Journal of the Linnean Society, 82, 627, 10.1111/j.1095-8312.2004.00347.x Mette, 2002, Endogenous viral sequences and their potential contribution to heritable virus resistance in plants, EMBO Journal, 21, 461, 10.1093/emboj/21.3.461 Mignouna, 2008, Genomics of yams, a common source of food and medicine in the tropics, 549, 10.1007/978-0-387-71219-2_23 Muller, 2011, High molecular variability of sugarcane bacilliform viruses in Guadeloupe implying the existence of at least three new species, Virus Research, 160, 414, 10.1016/j.virusres.2011.06.016 Mumford, 1997, Rapid single-tube immunocapture RT-PCR for the detection of two yam potyviruses, Journal of Virological Methods, 69, 73, 10.1016/S0166-0934(97)00141-9 Ndowora, 1999, Evidence that badnavirus infection in Musa can originate from integrated pararetroviral sequences, Virology, 255, 214, 10.1006/viro.1998.9582 Noreen, 2007, Distinct expression of Petunia vein clearing virus and the DNA transposon dTph1 in two Petunia hybrida lines is correlated with differences in histone modification and siRNA production, Plant Journal, 50, 219, 10.1111/j.1365-313X.2007.03040.x Perrier, 2003, Data analysis methods, 43 Phillips, 1999, The partial characterization of badnavirus infecting the Greater asiatic or water yam (Dioscorea alata), Journal of Phytopathology, 147, 265, 10.1111/j.1439-0434.1999.tb03829.x Rector, 2004, A sequence-independent strategy for detection and cloning of circular DNA virus genomes by using multiply primed rolling-circle amplification, Journal of Virology, 78, 4993, 10.1128/JVI.78.10.4993-4998.2004 Richert-Pöggeler, 2003, Induction of infectious petunia vein clearing (pararetro)virus from endogenous provirus in petunia, EMBO Journal, 22, 4836, 10.1093/emboj/cdg443 Scarcelli, 2006, Genetic nature of yams (Dioscorea sp.) domesticated by farmers in Benin (West Africa), Genetic Resources and Crop Evolution, 53, 121, 10.1007/s10722-004-1950-5 Seal, 2007, Molecular analysis of a full-length sequence of a new yam badnavirus from Dioscorea sansibarensis, Archives of Virology, 152, 819, 10.1007/s00705-006-0888-7 Staginnus, 2009, Suggestions for a nomenclature of endogenous pararetroviral sequences in plants, Archives of Virology, 154, 1189, 10.1007/s00705-009-0412-y Staginnus, 2007, Endogenous pararetroviral sequences in tomato (Solanum lycopersicum) and related species, BMC Plant Biology, 7, 24, 10.1186/1471-2229-7-24 Tamiru, 2013, Whole genome sequencing of Guinea yam (Dioscorea rotundata), 20 Wylie, 1993, A polymerase chain reaction assay for cucumber mosaic virus in lupin seeds, Australian Journal of Agricultural Research, 44, 41, 10.1071/AR9930041 Yang, 2003, Sequence diversity of South Pacific isolates of Taro bacilliform virus and the development of a PCR-based diagnostic test, Archives of Virology, 148, 1957, 10.1007/s00705-003-0163-0