The Gypsy Database (GyDB) of mobile genetic elements: release 2.0

This article introduces the second release of the Gypsy Database of Mobile Genetic Elements (GyDB 2.0): a research project devoted to the evolutionary dynamics of viruses and transposable elements based on their phylogenetic classification (per lineage and protein domain). The Gypsy Database (GyDB) is a long-term project that is continuously progressing, and that owing to the high molecular diversity of mobile elements requires to be completed in several stages. GyDB 2.0 has been powered with a wiki to allow other researchers participate in the project. The current database stage and scope are long terminal repeats (LTR) retroelements and relatives. GyDB 2.0 is an update based on the analysis of Ty3/Gypsy, Retroviridae, Ty1/Copia and Bel/Pao LTR retroelements and the Caulimoviridae pararetroviruses of plants. Among other features, in terms of the aforementioned topics, this update adds: (i) a variety of descriptions and reviews distributed in multiple web pages; (ii) protein-based phylogenies, where phylogenetic levels are assigned to distinct classified elements; (iii) a collection of multiple alignments, lineage-specific hidden Markov models and consensus sequences, called GyDB collection; (iv) updated RefSeq databases and BLAST and HMM servers to facilitate sequence characterization of new LTR retroelement and caulimovirus queries; and (v) a bibliographic server. GyDB 2.0 is available at http://gydb.org

Spatially structured genetic diversity of the Amerindian yam (Dioscorea trifida L.) assessed by SSR and ISSR markers in Southern Brazil

Dioscorea trifida L. (Dioscoreaceae) is among the economically most important cultivated Amerindian yam species, whose origin and domestication are still unresolved issues. in order to estimate the genetic diversity maintained by traditional farmers in Brazil, 53 accessions of D. trifida from 11 municipalities in the states of São Paulo, Santa Catarina, Mato Grosso and Amazonas were characterized on the basis of eight Simple Sequence Repeats (SSR) and 16 Inter Simple Sequence Repeats (ISSR) markers. the level of polymorphism among the accessions was high, 95 % for SSR and 75.8 % for ISSR. the SSR marker showed higher discrimination power among accessions compared to ISSR, with D parameter values of 0.79 and 0.44, respectively. Although SSR and ISSR markers led to dendrograms with different topologies, both separated the accessions into three main groups: I-Ubatuba-SP; II-Iguape-SP and Santa Catarina; and III-Mato Grosso. the accessions from Amazonas State were classified in group II with SSR and in a separate group with ISSR. Bayesian and principal coordinate analyzes conducted with both molecular markers corroborated the classification into three main groups. Higher variation was found within groups in the AMOVA analysis for both markers (66.5 and 60.6 % for ISSR and SSR, respectively), and higher Shannon diversity index was found for group II with SSR. Significant but low correlations were found between genetic and geographic distances (r = 0.08; p = 0.0007 for SSR and r = 0.16; p = 0.0002 for ISSR). Therefore, results from both markers showed a slight spatially structured genetic diversity in D. trifida accessions maintained by small traditional farmers in Brazil.Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)Univ São Paulo, Luiz de Queiroz Coll Agr, Dept Genet, BR-13400970 São Paulo, BrazilUniversidade Federal de São Paulo, Dept Biol Sci, BR-09972270 São Paulo, BrazilUniv Calif Davis, Dept Plant Sci MS1, Sect Crop & Ecosyst Sci, Davis, CA 95616 USAUniversidade Federal de São Paulo, Dept Biol Sci, BR-09972270 São Paulo, BrazilFAPESP: 2007/04805-2Web of Scienc

Potentialité d'invasion, en Méditerranée occidentale, par des potyvirus proches du Papaya ringspot virus (PRSV)

Supplément 1National audienc

Occurrence of potyviruses on yam (Dioscorea spp.) in Colombia and first molecular characterization of Yam mild mosaic virus

BGPI - Equipe 6International audienceA survey to determine the prevalence of potyviruses on yams, Dioscorea alata and D. cayenensis-rotundata, was undertaken in Colombia. Two hundred fifty leaf samples showing mottling symptoms were collected on the Atlantic coast and analyzed by antigen-coated plate enzyme-linked immunosorbent assay with universal potyvirus monoclonal antibodies (Agdia, Elkhart, IN). Potyviruses were detected in 70% (165/235) of the D. alata and in 66% (10/15) of the D. cayenensis-rotundata samples. The presence of Yam mild mosaic virus (YMMV) was indicated in some of these samples by immunocapture reverse-transcriptase polymerase chain reaction performed as previously reported (1). A 600-bp fragment that included the core and C-terminal region of the coat protein gene (CP) and the 3' untranslated region (3'UTR) was amplified from a D. alata isolate using universal potyvirus primers (1), cloned, and sequenced (EMBL Acc. AJ311725). Comparison with the two previously published YMMV sequences revealed 96.1 and 97.4% identity for the deduced amino acid sequence in the CP region, 74.1 and 83.2% nucleotide identity in the 3'UTR for Papua New Guinea (AB022424 [2]) and Martinique (AJ250336) isolates, respectively. YMMV is known to be widespread on D. alata in Africa and the South Pacific and has been recently identified in the Caribbean (1). To our knowledge, this is the first report of its occurrence in Colombia. A study of its incidence and genetic diversity in South America has been undertaken

Detection of plum pox potyvirus and analysis of its molecular variability using immunocapture-PCR

International audienc