Fecha/hora: 09/06/2024 21:20:43

Biblioteca(s): | INIA Las Brujas.
Tipo de la producción científica: | Artículos en Revistas Indexadas Internacionales
Circulación/Nivel: | Internacional - --
Fecha corriente: | 13/11/2015
Fecha de la última actualización: | 09/10/2019
Autoria: | 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.
Año 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-Clave: | Bioinformatic methods; BIOINFORMÁTICA; Chloroplast genome; Next-generation; Sequencing; Weedy rice.
Thesagro: | ARROZ; BIOLOGÍA; CIENCIA DE INFORMACIÓN; ORYZA SATIVA.
Categoría del tema: | 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

Registro original: | INIA Las Brujas (LB)
Ejemplares: | LB - (100797-1) - PXI - AP - DD -  -  -  - DIS