Satellyptus: analysis and database of microsatellites from ESTs of Eucalyptus
| Autor: | Regina Maria Barreto Cicarelli, Gustavo Arbex Avelar, José Fernando Garcia, Eloiza Helena Tajara da Silva, Paulo Cezar Ceresini, Elaine Costa Souza, Laercio Ribeiro Porto Neto, Ivan Rizzo Guillherme, Marco Túlio Alves da Silva, Carlos Norberto Fischer, Cristina Lacerda Soares Petrarolha Silva, Robson Fernando Missio, Danyelle Cristine Marini, Maurício Bacci Júnior, Ivo Gregorio, André Ricardo Carvalho Marcon |
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| Přispěvatelé: | ETH-Zentrum Swiss Federal Institute of Technology Institute of Plant Sciences/Phytopathology, Universidade Estadual Paulista (Unesp), Fundação Educacional de Andradina Faculdades Integradas Stella Maris |
| Jazyk: | angličtina |
| Rok vydání: | 2005 |
| Předmět: |
lcsh:QH426-470
Database Gene ontology food and beverages Biology computer.software_genre Eucalyptus SSR lcsh:Genetics Genetic marker Small sequence repeats Genetics bioinformatics tool genetic markers Genetic markers Microsatellite gene ontology Bioinformatics tool Molecular Biology computer small sequence repeats |
| Zdroj: | Genetics and Molecular Biology, 28 (3) SciELO Repositório Institucional da UNESP Universidade Estadual Paulista (UNESP) instacron:UNESP Genetics and Molecular Biology v.28 n.3 suppl.0 2005 Genetics and Molecular Biology Sociedade Brasileira de Genética (SBG) instacron:SBG Genetics and Molecular Biology, Vol 28, Iss 3, Pp 589-600 (2005) Genetics and Molecular Biology, Volume: 28, Issue: 3 Supplement, Pages: 589-600, Published: 2005 |
| ISSN: | 1415-4757 1678-4685 |
| Popis: | The main goal of our research was to search for SSRs in the Eucalyptus EST FORESTs database (using a software for mining SSR-motifs). With this objective, we created a database for cataloging Eucalyptus EST-derived SSRs, and developed a bioinformatics tool, named Satellyptus, for finding and analyzing microsatellites in the Eucalyptus EST database. The search for microsatellites in the FORESTs database containing 71,115 Eucalyptus EST sequences (52.09 Mb) revealed 20,530 SSRs in 15,621 ESTs. The SSR abundance detected on the Eucalyptus ESTs database (29% or one microsatellite every four sequences) is considered very high for plants. Amongst the categories of SSR motifs, the dimeric (37%) and trimeric ones (33%) predominated. The AG/CT motif was the most frequent (35.15%) followed by the trimeric CCG/CGG (12.81%). From a random sample of 1,217 sequences, 343 microsatellites in 265 SSR-containing sequences were identified. Approximately 48% of these ESTs containing microsatellites were homologous to proteins with known biological function. Most of the microsatellites detected in Eucalyptus ESTs were positioned at either the 5 or 3 end. Our next priority involves the design of flanking primers for codominant SSR loci, which could lead to the development of a set of microsatellite-based markers suitable for marker-assisted Eucalyptus breeding programs. Genetics and Molecular Biology, 28 (3) ISSN:1415-4757 ISSN:1678-4685 |
| Databáze: | OpenAIRE |
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