Jakowitsch J, Mette MF, van der Winden J, Matzke MA, Matzke AJM: Integrated pararetroviral sequences define a unique class of dispersed repetitive DNA in plants. Proc Nat Acad Sci. 1999, 96: 13241-13264. 10.1073/pnas.96.23.13241.
Article
PubMed
CAS
PubMed Central
Google Scholar
Lockart BE, Menke J, Dahal G, Olszewski NE: 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. J Gen Virol. 2000, 81: 1579-1585.
Article
Google Scholar
Gregor W, Mette MF, Staginnus C, Matzke M, Matzke AJM: A distinct endogenous pararetrovirus family in Nicotiana tomentosiformis, a diploid progenitor of polyploid tobacco. Plant Physiol. 2004, 134: 1191-1199. 10.1104/pp.103.031112.
Article
PubMed
CAS
PubMed Central
Google Scholar
Hansen CN, Harper G, Heslop-Harrison JS: Characterization of pararetrovirus-like sequences in the genome of potato (Solanum tuberosum). Cytogenet Genome Res. 2005, 110: 559-565. 10.1159/000084989.
Article
PubMed
CAS
Google Scholar
Harper G, Osuji JO, Heslop-Harrison JS, Hull R: Integration of Banana Streak Badnavirus into the Musa genome: molecular and cytogenetic evidence. Virology. 1999, 255: 207-213. 10.1006/viro.1998.9581.
Article
PubMed
CAS
Google Scholar
Ndowora T, Dahal G, LaFleur D, Harper G, Hull R, Olszewski NE, Lockhart B: Evidence that badnavirus infection in Musa can originate from integrated pararetroviral sequences. Virology. 1999, 255: 214-220. 10.1006/viro.1998.9582.
Article
PubMed
CAS
Google Scholar
Geering ADW, Olszewski NE, Harper G, Lockhart BEL, Hull R, Thomas JE: Banana contains a diverse array of endogenous badnaviruses. J Gen Virol. 2005, 86: 511-520. 10.1099/vir.0.80261-0.
Article
PubMed
CAS
Google Scholar
Richert-Pöggeler KR, Noreen F, Schwarzacher T, Harper G, Hohn T: Induction of infectious petunia vein clearing (pararetro) virus from endogeeous provirus in petunia. EMBO J. 2003, 22: 4836-4845. 10.1093/emboj/cdg443.
Article
PubMed
PubMed Central
Google Scholar
Kunii M, Kanda M, Nagano H, Uyeda I, Kishima Y, Sano Y: Reconstruction of putative DNA virus from endogenous rice tungro bacilliform virus-like sequences in the rice genome: implications for integration and evolution. BMC Genomics. 2004, 5: 80-10.1186/1471-2164-5-80.
Article
PubMed
PubMed Central
Google Scholar
Harper G, Hull R, Lockhart B, Olszewski N: Viral sequences integrated into plant genomes. Annu Rev Phytopathol. 2002, 40: 119-136. 10.1146/annurev.phyto.40.120301.105642.
Article
PubMed
CAS
Google Scholar
Lheureux F, Carreel F, Jenny C, Lockhart BEL, Iskra-Caruana ML: Identification of genetic markers linked to banana streak disease expression in inter-specific Musa hybrids. Theor Appl Genet. 2003, 106: 594-598.
PubMed
CAS
Google Scholar
Dallot S, Acuna P, Rivera C, Ramirez P, Cote F, Lockhart BEL, Caruana ML: Evidence that the proliferation stage of micropropagation procedure is determant in the expression of Banana streak virus integrated into the genome of FHIA 21 hybrid (Musa AAAB). Arch Virol. 2001, 146: 2179-2190. 10.1007/s007050170028.
Article
PubMed
CAS
Google Scholar
Harper G, Dahal G, Thottappilly G, Hull R: Detection of episomal banana strek badnavirus by IC-PCR. JVirol Methods. 1999, 79: 1-8. 10.1016/S0166-0934(98)00158-X.
Article
CAS
Google Scholar
Hull R, Harper G, Lockhart B: Viral sequences integrated into plant genomes. Trends Plant Sci. 2000, 5: 362-365. 10.1016/S1360-1385(00)01723-4.
Article
PubMed
CAS
Google Scholar
Mette MF, Kanno T, Aufsatz W, Jakowitsch J, Van der Winden J, Matzke MA, Matzke AJM: Endogenous viral sequences and their potential contribution to heritable virus resistance in plants. EMBO J. 2002, 21: 461-469. 10.1093/emboj/21.3.461.
Article
PubMed
CAS
PubMed Central
Google Scholar
Meins F, Si-Ammour A, Blevins T: RNA silencing systems and their relevance to plant development. Annu Rev Cell Dev Biol. 2005, 21: 297-318. 10.1146/annurev.cellbio.21.122303.114706.
Article
PubMed
CAS
Google Scholar
Voinnet O, Pinto Y, Baulcombe DC: Suppression of gene silencing: a general strategy used by diverse DNA and RNA viruses of plants. Proc Natl Acad Sci USA. 1999, 96: 14147-14152. 10.1073/pnas.96.24.14147.
Article
PubMed
CAS
PubMed Central
Google Scholar
Covey SN, Al-Kaff NS: Plant DNA viruses and gene silencing. Plant Mol Biol. 2000, 43: 307-322. 10.1023/A:1006408101473.
Article
PubMed
CAS
Google Scholar
Matzke MA, Birchler JA: RNAi-mediated pathways in the nucleus. Nat Rev Genet. 2005, 6: 24-34. 10.1038/nrg1500.
Article
PubMed
CAS
Google Scholar
Arumuganathan K, Earle ED: Nuclear DNA content of some important plant species. Plant Mol Biol Rep. 1991, 9: 208-218.
Article
CAS
Google Scholar
Tanksley SD, Ganal MW, Prince JP, de Vicente MC, Bonierbale MW, Broun P, Fulton TM, Giovannoni JJ, Grandillo S, Martin GB, et al: High density molecular linkage maps of the tomato and potato genomes. Genetics. 1992, 132: 1141-1160.
PubMed
CAS
PubMed Central
Google Scholar
Mueller LA, Tanksley SD, Giovannoni JJ, van Eck J, Stack S, Choi D, Kim BD, Chen M, Cheng Z, Li C, et al: The tomato sequencing project, the first cornerstone of the International Solanaceae Project (SOL). Comp Funct Genom. 2005, 6: 153-158. 10.1002/cfg.468.
Article
CAS
Google Scholar
Peterson DG, Price HJ, Johnston JS, Stack SM: DNA content of heterochromatin and euchromatin in tomato (Lycopersicon esculentum) pachytene chromosomes. Genome. 1996, 39: 77-82.
Article
PubMed
CAS
Google Scholar
Budiman MA, Mao L, Wood TC, Wing RA: A deep-coverage tomato BAC library and prospects toward development of an STC framework for genome sequencing. Genome Res. 2000, 10: 129-136.
PubMed
CAS
PubMed Central
Google Scholar
Peterson DG, Pearson WR, Stack SM: Characterization of the tomato (Lycopersicon esculentum) genome using in vitro and in-situ DNA reassociation. Genome. 1998, 41: 346-356. 10.1139/gen-41-3-346.
Article
CAS
Google Scholar
Guyot R, Cheng X, Su Y, Cheng Z, Schlagenhauf E, Keller B, Ling HQ: Complex organization and evolution of the tomato pericentromeric region at the FER gene locus. Plant Physiol. 2005, 138: 1205-1215. 10.1104/pp.104.058099.
Article
PubMed
CAS
PubMed Central
Google Scholar
Vidavsky F, Czosnek H: Tomato breeding lines resistant and tolerant to tomato yellow leaf curl virus issued from Lycopersicon hirsutum . Phytopathol. 1998, 88: 910-914. 10.1094/PHYTO.1998.88.9.910.
Article
CAS
Google Scholar
Kabelka E, Franchino B, Francis DM: Two loci from Lycopersicon hirsutum LA407 confer resistance to strains of Clavibacter michiganensis subsp. Michiganensis. Phytopathol. 2002, 92: 504-510. 10.1094/PHYTO.2002.92.5.504.
Article
CAS
Google Scholar
Scott JW, Harbaugh BK: Micro-Tom – a miniature dwarf tomato. Florida Agr Expt Sta Circ. 1989, 370: 1-6.
Google Scholar
Yang TJ, Lee J, Chang SB, Yu Y, de Yong H, Wing RA: In-depth sequence analysis of the tomato chromosome 12 centromeric region: identification of a large CAA block and characterization of pericentromere retrotransposons. Chromosoma. 2005, 114: 103-117. 10.1007/s00412-005-0342-8.
Article
PubMed
CAS
Google Scholar
Vosman B, Arens P: Molecular characterization of GATA/GACA microsatellite repeats in tomato. Genome. 1997, 40: 25-33.
Article
PubMed
CAS
Google Scholar
Chang SB: Cytogenetic and molecular studies on tomato chromosomes using diploid tomato and tomato monosomic additions in tetraploid potatoe. PhD Thesis. 2004, Wageningen University; Laboratory of Genetics
Google Scholar
Smulders MJM, Bredemeijer G, Rus-Kortekaas W, Arens P, Vosman B: Use of short microsatellites from database sequences to generate polymorphisms among Lycopersicon esculentum cultivars and accessions of other Lycopersicon species. Theor Appl Genet. 1997, 97: 264-272. 10.1007/s001220050409.
Article
Google Scholar
Carrington JC, Kasschau KD, Johansen LK: Activation and suppression of RNA silencing by plant viruses. Virology. 2001, 281: 1-5. 10.1006/viro.2000.0812.
Article
PubMed
CAS
Google Scholar
Baulcombe D: Viral suppression of systemic silencing. Trends Microbiol. 2002, 10: 306-308. 10.1016/S0966-842X(02)02387-9.
Article
PubMed
CAS
Google Scholar
Vargason JM, Szittya G, Burgyan J, Hall TM: Size selective recognition of siRNA by an RNA silencing suppressor. Cell. 2003, 115: 799-811. 10.1016/S0092-8674(03)00984-X.
Article
PubMed
CAS
Google Scholar
Chapman EJ, Prokhnevsky AI, Gopinath K, Dolja VV, Carrington JC: Viral RNA silencing suppressors inhibit the microRNA pathway at an intermediate step. Genes Dev. 2004, 18: 1179-1186. 10.1101/gad.1201204.
Article
PubMed
CAS
PubMed Central
Google Scholar
Baulcombe DC, Molnar A: Crystal structure of p19-a universal suppressor of RNA silencing. Trends Biochem Sci. 2004, 29: 279-281. 10.1016/j.tibs.2004.04.007.
Article
PubMed
CAS
Google Scholar
Bucher E, Prins M: RNA silencing: A natural resistance mechanism in plants. Natural Resistance Mechanisms of Plants to Viruses. Edited by: Loebenstein G, Carr JP. 2006, Springer Netherlands, 3a:
Google Scholar
Lakatos L, Csorba T, Pantaleo V, Chapman EJ, Carrington JC, Liu Y-P, Dolja VV, fernandez Calvino L, Lopéz-Moya jj, Burgyan J: Small RNA binding is a common strategy to suppress RNA silencing by several viral suppressors. EMBO J. 2006, 25: 2768-2780. 10.1038/sj.emboj.7601164.
Article
PubMed
CAS
PubMed Central
Google Scholar
Peralta IE, Spooner DM: Granule-bound starch synthase (GBSSI) gene phylogeny of wild tomatoes (Solanum L. section Lycopersicon [Mill.] Wettst. subsection Lycopersicon.). American Journal of Botany. 2001, 88: 1888-1902. 10.2307/3558365.
Article
PubMed
CAS
Google Scholar
Hull R: Matthews' Plant Virology. 2002, San Diego: Academic Press
Google Scholar
De Kochko A, Verdaguer B, Taylor N, Carcamo R, Beachy RN, Fauquet C: Cassava vein mosaic virus (CsVMV), type species for a new genus of plant double stranded viruses?. Arch Virol. 1998, 143: 945-962. 10.1007/s007050050344.
Article
PubMed
CAS
Google Scholar
Richert-Pöggeler KR, Sheperd RJ: Petunia vein clearing virus: a plant pararetrovirus with the core sequences for an integrase function. Virology. 1997, 236: 137-146. 10.1006/viro.1997.8712.
Article
PubMed
Google Scholar
Heslop-Harrison JS: Comparative genome organization in plants: from sequence and markers to chromatin and chromosomes. Plant Cell. 2000, 12: 617-635. 10.1105/tpc.12.5.617.
Article
PubMed
CAS
PubMed Central
Google Scholar
Devos KM, Brown JKM, Bennetzen JL: Genome size reduction through illegitimate recombination counteracts genome expansion in Arabidopsis . Genome Res. 2002, 12: 1075-1079. 10.1101/gr.132102.
Article
PubMed
CAS
PubMed Central
Google Scholar
Matzke M, Gregor W, Mette MF, Aufsatz W, Kanno T, Jakowitsch J, Matzke AJM: Endogenous pararetroviruses of allotetraploid Nicotiana tabacum and its diploid progenitors, N.sylvestris and N. tomentosiformis. Biol J Linnean Soc. 2004, 82: 627-638. 10.1111/j.1095-8312.2004.00347.x.
Article
Google Scholar
Schwarzacher T: DNA, chromosomes and in situ hybridization. Genome. 2003, 46: 953-962. 10.1139/g03-119.
Article
PubMed
CAS
Google Scholar
Noreen F, Akbergenov R, Hohn T, Richert-Pöggeler KR: Distinct expression of endogenous Petunia vein clearing virus and theDNA transposon dTph1 in two Petunia hybridalines is correlated with differences in histone modification and siRNA production. The Plant J. 2007,
Google Scholar
Hamilton A, Voinnet O, Chappell L, Baulcombe D: Two classes of short interfereing RNA in RNA silencing. EMBO J. 2002, 21: 4671-4679. 10.1093/emboj/cdf464.
Article
PubMed
CAS
PubMed Central
Google Scholar
Baulcombe D: RNA silencing in plants. Nature. 2004, 431: 356-363. 10.1038/nature02874.
Article
PubMed
CAS
Google Scholar
Almeida R, Allshire RC: RNA silencing and genome regulation. Trends Cell Biol. 2005, 15: 251-258. 10.1016/j.tcb.2005.03.006.
Article
PubMed
CAS
Google Scholar
Wassenegger M: The role of the RNAi machinery in heterochromatin formation. Cell. 2005, 122: 13-16. 10.1016/j.cell.2005.06.034.
Article
PubMed
CAS
Google Scholar
Altschul SF, Madden TL, Schäffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ: Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 1997, 25: 3389-3402. 10.1093/nar/25.17.3389.
Article
PubMed
CAS
PubMed Central
Google Scholar
Thompson JD, Higgins DG, Gibson TJ: CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, positions-specific gap penalties and weight matrix choice. Nucleic Acids Res. 1994, 22: 4673-4680. 10.1093/nar/22.22.4673.
Article
PubMed
CAS
PubMed Central
Google Scholar
Thompson JD, Gibson TJ, Plewniak F, Jeanmougin F, Higgins DG: The ClustalX windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res. 1997, 24: 4876-4882. 10.1093/nar/25.24.4876.
Article
Google Scholar
Mette MF, Aufsatz W, Kanno T, Daxinger L, Rovina P, Matzke M, Matzke AJM: Analysis of double-stranded RNA and small RNAs involved in RNA-mediated transcriptional gene silencing. Meth Mol Biol: RNA silencing. Edited by: Carmichael GG. 2005, Totowa:Humana Press, 74-82.
Google Scholar
Beczner L, Horváth J, Romhany I, Förster H: Studies on the etiology of tuber necrotic ringspot disease in potato. Potato Res. 1984, 27: 339-352. 10.1007/BF02357646.
Article
Google Scholar
Martelli GP, Gallitelli D, Russo M: Tombusviruses. The Plant Viruses. Edited by: Koenig R. 1988, New York: Plenum Press, 3: 13-72.
Chapter
Google Scholar
Schwarzacher T, Heslop-Harrison JS: Practical in situ hybridization. 2000, Oxford: BIOS Scientific Publishers
Google Scholar
Zhong XB, De Jong JH, Zabel P: Preparation of tomato meiotic pachytene and mitotic metaphase chromosomes for fluorescence in situ hybridization (FISH). Chromosome Res. 1996, 4: 24-28. 10.1007/BF02254940.
Article
PubMed
CAS
Google Scholar
Gerlach WL, Bedbrook JR: Cloning and characterization of ribosomal RNA genes from wheat and barley. Nucleic Acids Res. 1979, 7: 1869-1885. 10.1093/nar/7.7.1869.
Article
PubMed
CAS
PubMed Central
Google Scholar
Mishra SK, Tripp J, Winkelhaus S, Tschiersch B, Theres K, Nover L, Scharf KD: In the complex family of heat stress transcription factors, HsfA1 has a unique role as master regulator of thermotolerance in tomato. Genes Dev. 2002, 16: 1555-1567. 10.1101/gad.228802.
Article
PubMed
CAS
PubMed Central
Google Scholar