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Biblioteca (s) : |
INIA Las Brujas. |
Fecha : |
13/11/2015 |
Actualizado : |
09/10/2019 |
Tipo de producción científica : |
Artículos en Revistas Indexadas Internacionales |
Autor : |
GARAYCOCHEA, S.; SPERANZA, P.; ALVAREZ-VALIN, F. |
Afiliación : |
SILVIA RAQUEL GARAYCOCHEA SOLSONA, INIA (Instituto Nacional de Investigación Agropecuaria), Uruguay. |
Título : |
A strategy to recover a high-quality, complete plastid sequence from low-coverage whole-genome sequencing. |
Fecha de publicación : |
2015 |
Fuente / Imprenta : |
Applications in Plant Sciences, 2015, v.3, no.10, Article number 1500022. OPEN ACCESS |
ISSN : |
2168-0450 |
DOI : |
10.3732/apps.1500022 |
Idioma : |
Inglés |
Notas : |
Article history: First published: 12 October 2015.
The authors thank Fabián Capdeville for his important support at the beginning of this work. This project received financial support from the Instituto Nacional de Investigación Agropecuaria (INIA), Uruguay. S.G. was the recipient of a Master's degree fellowship awarded by Agencia Nacional de Investigación e Innovación (ANII), Uruguay. F.A.?V. and P.S. are researchers from Sistema Nacional de Investigadores (ANII, Uruguay). |
Contenido : |
ABSTRACT.
Premise of the study: We developed a bioinformatic strategy to recover and assemble a chloroplast genome using data derived from low-coverage 454 GS FLX/Roche whole-genome sequencing. Methods: A comparative genomics approach was applied to obtain the complete chloroplast genome from a weedy biotype of rice from Uruguay. We also applied appropriate filters to discriminate reads representing novel DNA transfer events between the chloroplast and nuclear genomes. Results: From a set of 295,159 reads (96 Mb data), we assembled the chloroplast genome into two contigs. This weedy rice was classified based on 23 polymorphic regions identified by comparison with reference chloroplast genomes. We detected recent and past events of genetic material transfer between the chloroplast and nuclear genomes and estimated their occurrence frequency. Discussion: We obtained a high-quality complete chloroplast genome sequence from low-coverage sequencing data. Intergenome DNA transfer appears to be more frequent than previously thought.
© 2015 Garaycochea et al. Published by the Botanical Society of America. This work is licensed under a Creative Commons Attribution License (CC-BY-NC-SA). |
Palabras claves : |
Bioinformatic methods; BIOINFORMÁTICA; Chloroplast genome; Next-generation; Sequencing; Weedy rice. |
Thesagro : |
ARROZ; BIOLOGÍA; CIENCIA DE INFORMACIÓN; ORYZA SATIVA. |
Asunto categoría : |
F30 Genética vegetal y fitomejoramiento |
URL : |
http://www.ainfo.inia.uy/digital/bitstream/item/5184/1/Garaycochea-S.-2015.-Applications-in-plant-Sciences.pdf
https://bsapubs.onlinelibrary.wiley.com/doi/pdf/10.3732/apps.1500022
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Marc : |
LEADER 02579naa a2200301 a 4500 001 1053875 005 2019-10-09 008 2015 bl uuuu u00u1 u #d 022 $a2168-0450 024 7 $a10.3732/apps.1500022$2DOI 100 1 $aGARAYCOCHEA, S. 245 $aA strategy to recover a high-quality, complete plastid sequence from low-coverage whole-genome sequencing.$h[electronic resource] 260 $c2015 500 $aArticle history: First published: 12 October 2015. The authors thank Fabián Capdeville for his important support at the beginning of this work. This project received financial support from the Instituto Nacional de Investigación Agropecuaria (INIA), Uruguay. S.G. was the recipient of a Master's degree fellowship awarded by Agencia Nacional de Investigación e Innovación (ANII), Uruguay. F.A.?V. and P.S. are researchers from Sistema Nacional de Investigadores (ANII, Uruguay). 520 $aABSTRACT. Premise of the study: We developed a bioinformatic strategy to recover and assemble a chloroplast genome using data derived from low-coverage 454 GS FLX/Roche whole-genome sequencing. Methods: A comparative genomics approach was applied to obtain the complete chloroplast genome from a weedy biotype of rice from Uruguay. We also applied appropriate filters to discriminate reads representing novel DNA transfer events between the chloroplast and nuclear genomes. Results: From a set of 295,159 reads (96 Mb data), we assembled the chloroplast genome into two contigs. This weedy rice was classified based on 23 polymorphic regions identified by comparison with reference chloroplast genomes. We detected recent and past events of genetic material transfer between the chloroplast and nuclear genomes and estimated their occurrence frequency. Discussion: We obtained a high-quality complete chloroplast genome sequence from low-coverage sequencing data. Intergenome DNA transfer appears to be more frequent than previously thought. © 2015 Garaycochea et al. Published by the Botanical Society of America. This work is licensed under a Creative Commons Attribution License (CC-BY-NC-SA). 650 $aARROZ 650 $aBIOLOGÍA 650 $aCIENCIA DE INFORMACIÓN 650 $aORYZA SATIVA 653 $aBioinformatic methods 653 $aBIOINFORMÁTICA 653 $aChloroplast genome 653 $aNext-generation 653 $aSequencing 653 $aWeedy rice 700 1 $aSPERANZA, P. 700 1 $aALVAREZ-VALIN, F. 773 $tApplications in Plant Sciences, 2015$gv.3, no.10, Article number 1500022. OPEN ACCESS
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Registro original : |
INIA Las Brujas (LB) |
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Biblioteca (s) : |
INIA Las Brujas. |
Fecha actual : |
20/06/2015 |
Actualizado : |
20/06/2015 |
Tipo de producción científica : |
Informes Agroclimáticos |
Autor : |
GIMENEZ, A.; CASTAÑO, J.; FUREST, J.; CAL, A.; TISCORNIA, G. |
Afiliación : |
AGUSTIN EDUARDO GIMENEZ FUREST, INIA (Instituto Nacional de Investigación Agropecuaria), Uruguay; JOSE PEDRO CASTAÑO SANCHEZ, INIA (Instituto Nacional de Investigación Agropecuaria), Uruguay; JOSE MARIA FUREST CROCCO, INIA (Instituto Nacional de Investigación Agropecuaria), Uruguay; ADRIAN TABARE CAL ALVAREZ, INIA (Instituto Nacional de Investigación Agropecuaria), Uruguay; GUADALUPE TISCORNIA TOSAR, INIA (Instituto Nacional de Investigación Agropecuaria), Uruguay. |
Título : |
Informe Agroclimático 2012 - Situación a Enero. |
Fecha de publicación : |
2012 |
Fuente / Imprenta : |
Montevideo (Uruguay): INIA, 2012., |
Páginas : |
4 p. |
Idioma : |
Español |
Palabras claves : |
AGROCLIMA; AGROCLIMATOLOGÍA; BOLETIN AGROCLIMÁTICO; CARACTERIZACIÓN AGROCLIMÁTICA; DIRECCION VIENTO; ESTACIONES AGROMETEOROLOGICAS; ESTACIONES AUTOMATICAS; ESTACIONES INIA; ESTADO DEL TIEMPO; ESTRÉS HÍDRICO; GRAFICAS AGROCLIMATICOS; GRAS; HELIOFANOGRAFO; INFORMACION SATELITAL; INUNDACIONES; LLUVIAS DIARIAS; MAXIMA; MEDIA; MINIMA; PANEL SOLAR; PERSPECTIVAS CLIMATICAS; PLUVIOMETRO; PRECIPITACION NACIONAL; PREVENCION HELADAS; PRONOSTICO; SENSOR; SIMETRICO; TANQUE A; TERMOCUPLAS; TERMOHIDROGRAFO; VARIABLES AGROCLIMATICAS; VELETA. |
Thesagro : |
AGROCLIMATOLOGIA; CAMBIO CLIMATICO; CLIMA; CLIMATOLOGIA; ESTACIONES METEOROLOGICAS; ESTRES HIDRICO; EVAPORACION; EVAPOTRANSPIRACION; HUMEDAD; HUMEDAD RELATIVA; LLUVIA; METEOROLOGIA; PERSPECTIVAS; PLUVIOMETROS; PRONOSTICO DEL TIEMPO; SENSORES; SISTEMAS; SISTEMAS DE INFORMACION; SUELO; TEMPERATURA; TERMOMETROS. |
Asunto categoría : |
P40 Meteorología y climatología |
URL : |
http://www.ainfo.inia.uy/digital/bitstream/item/4707/1/Inf.Agr.-enero-2012.pdf
http://www.inia.uy/Publicaciones/Paginas/publicacion-2456.aspx
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Marc : |
LEADER 02071nam a2200793 a 4500 001 1052863 005 2015-06-20 008 2012 bl uuuu u0uu1 u #d 100 1 $aGIMENEZ, A. 245 $aInforme Agroclimático 2012 - Situación a Enero.$h[electronic resource] 260 $aMontevideo (Uruguay): INIA, 2012.,$c2012 300 $a4 p. 650 $aAGROCLIMATOLOGIA 650 $aCAMBIO CLIMATICO 650 $aCLIMA 650 $aCLIMATOLOGIA 650 $aESTACIONES METEOROLOGICAS 650 $aESTRES HIDRICO 650 $aEVAPORACION 650 $aEVAPOTRANSPIRACION 650 $aHUMEDAD 650 $aHUMEDAD RELATIVA 650 $aLLUVIA 650 $aMETEOROLOGIA 650 $aPERSPECTIVAS 650 $aPLUVIOMETROS 650 $aPRONOSTICO DEL TIEMPO 650 $aSENSORES 650 $aSISTEMAS 650 $aSISTEMAS DE INFORMACION 650 $aSUELO 650 $aTEMPERATURA 650 $aTERMOMETROS 653 $aAGROCLIMA 653 $aAGROCLIMATOLOGÍA 653 $aBOLETIN AGROCLIMÁTICO 653 $aCARACTERIZACIÓN AGROCLIMÁTICA 653 $aDIRECCION VIENTO 653 $aESTACIONES AGROMETEOROLOGICAS 653 $aESTACIONES AUTOMATICAS 653 $aESTACIONES INIA 653 $aESTADO DEL TIEMPO 653 $aESTRÉS HÍDRICO 653 $aGRAFICAS AGROCLIMATICOS 653 $aGRAS 653 $aHELIOFANOGRAFO 653 $aINFORMACION SATELITAL 653 $aINUNDACIONES 653 $aLLUVIAS DIARIAS 653 $aMAXIMA 653 $aMEDIA 653 $aMINIMA 653 $aPANEL SOLAR 653 $aPERSPECTIVAS CLIMATICAS 653 $aPLUVIOMETRO 653 $aPRECIPITACION NACIONAL 653 $aPREVENCION HELADAS 653 $aPRONOSTICO 653 $aSENSOR 653 $aSIMETRICO 653 $aTANQUE A 653 $aTERMOCUPLAS 653 $aTERMOHIDROGRAFO 653 $aVARIABLES AGROCLIMATICAS 653 $aVELETA 700 1 $aCASTAÑO, J. 700 1 $aFUREST, J. 700 1 $aCAL, A. 700 1 $aTISCORNIA, G.
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