02579naa a2200301 a 450000100080000000500110000800800410001902200140006002400300007410000200010424501340012426000090025850004880026752012050075565000100196065000140197065000280198465000170201265300260202965300200205565300230207565300200209865300150211865300150213370000170214870000220216577300900218710538752019-10-09       2015    bl uuuu     u00u1 u    #d  a2168-04507 a10.3732/apps.15000222DOI1 aGARAYCOCHEA, S.  aA strategy to recover a high-quality, complete plastid sequence from low-coverage whole-genome sequencing.h[electronic resource]  c2015  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).  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).  aARROZ  aBIOLOGÍA  aCIENCIA DE INFORMACIÓN  aORYZA SATIVA  aBioinformatic methods  aBIOINFORMÁTICA  aChloroplast genome  aNext-generation  aSequencing  aWeedy rice1 aSPERANZA, P.1 aALVAREZ-VALIN, F.  tApplications in Plant Sciences, 2015gv.3, no.10, Article number 1500022. OPEN ACCESS