A strategy to recover a high-quality, complete plastid sequence from low-coverage whole-genome sequencing.
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...
Guardat en:
| Autor principal: | |
|---|---|
| Altres autors: | , |
| Format: | article |
| Idioma: | anglès |
| Publicat: |
2015
|
| Matèries: | |
| Accés en línia: | https://ainfo.inia.uy/consulta/busca?b=pc&id=53875&biblioteca=vazio&busca=53875&qFacets=53875 |
| Etiquetes: |
Sense etiquetes, Sigues el primer a etiquetar aquest registre!
|
| _version_ | 1868890121787408384 |
|---|---|
| author | GARAYCOCHEA, S. |
| author2 | SPERANZA, P. ALVAREZ-VALIN, F. |
| author2_role | author author |
| author_browse | ALVAREZ-VALIN, F. GARAYCOCHEA, S. SPERANZA, P. |
| author_facet | GARAYCOCHEA, S. SPERANZA, P. ALVAREZ-VALIN, F. |
| author_role | author |
| collection | AINFO |
| dc.creator.none.fl_str_mv | GARAYCOCHEA, S. SPERANZA, P. ALVAREZ-VALIN, F. |
| dc.date.none.fl_str_mv | 2015 2022-12-16T20:41:49Z 2022-12-16T20:41:49Z 2022-12-16T20:41:49Z |
| dc.identifier.none.fl_str_mv | https://ainfo.inia.uy/consulta/busca?b=pc&id=53875&biblioteca=vazio&busca=53875&qFacets=53875 |
| dc.language.none.fl_str_mv | en eng |
| dc.rights.none.fl_str_mv | info:eu-repo/semantics/openAccess Acceso abierto |
| dc.source.none.fl_str_mv | reponame:AINFO instname:Instituto Nacional de Investigación Agropecuaria instacron:Instituto Nacional de Investigación Agropecuaria |
| dc.subject.none.fl_str_mv | BIOINFORMÁTICA Bioinformatic methods Chloroplast genome Next-generation Sequencing Weedy rice BIOLOGÍA CIENCIA DE INFORMACIÓN ARROZ ORYZA SATIVA |
| dc.title.none.fl_str_mv | A strategy to recover a high-quality, complete plastid sequence from low-coverage whole-genome sequencing. |
| dc.type.none.fl_str_mv | Article PublishedVersion info:eu-repo/semantics/article info:eu-repo/semantics/publishedVersion |
| description | 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). |
| eu_rights_str_mv | openAccess |
| format | article |
| id | anni_8a32b48a36778646c1b42e7a4b76dedf |
| instacron_str | Instituto Nacional de Investigación Agropecuaria |
| institution | Instituto Nacional de Investigación Agropecuaria |
| instname_str | Instituto Nacional de Investigación Agropecuaria |
| language | eng |
| language_invalid_str_mv | en |
| network_acronym_str | anni |
| network_name_str | oai-lr-anni |
| oai_identifier_str | oai:redi.anii.org.uy:20.500.12381/2459 |
| publishDate | 2015 |
| publishDateSort | 2015 |
| reponame_str | AINFO |
| repository.mail.fl_str_mv | |
| repository.name.fl_str_mv | |
| repository_id_str | |
| rights_invalid_str_mv | Acceso abierto |
| spelling | A strategy to recover a high-quality, complete plastid sequence from low-coverage whole-genome sequencing.GARAYCOCHEA, S.SPERANZA, P.ALVAREZ-VALIN, F.BIOINFORMÁTICABioinformatic methodsChloroplast genomeNext-generationSequencingWeedy riceBIOLOGÍACIENCIA DE INFORMACIÓNARROZORYZA SATIVAABSTRACT.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).2022-12-16T20:41:49Z2022-12-16T20:41:49Z20152022-12-16T20:41:49ZArticlePublishedVersioninfo:eu-repo/semantics/articleinfo:eu-repo/semantics/publishedVersionhttps://ainfo.inia.uy/consulta/busca?b=pc&id=53875&biblioteca=vazio&busca=53875&qFacets=53875reponame:AINFOinstname:Instituto Nacional de Investigación Agropecuariainstacron:Instituto Nacional de Investigación Agropecuariaenenginfo:eu-repo/semantics/openAccessAcceso abiertooai:redi.anii.org.uy:20.500.12381/24592026-02-10T17:37:28Z |
| spellingShingle | A strategy to recover a high-quality, complete plastid sequence from low-coverage whole-genome sequencing. GARAYCOCHEA, S. BIOINFORMÁTICA Bioinformatic methods Chloroplast genome Next-generation Sequencing Weedy rice BIOLOGÍA CIENCIA DE INFORMACIÓN ARROZ ORYZA SATIVA |
| status_str | publishedVersion |
| title | A strategy to recover a high-quality, complete plastid sequence from low-coverage whole-genome sequencing. |
| title_full | A strategy to recover a high-quality, complete plastid sequence from low-coverage whole-genome sequencing. |
| title_fullStr | A strategy to recover a high-quality, complete plastid sequence from low-coverage whole-genome sequencing. |
| title_full_unstemmed | A strategy to recover a high-quality, complete plastid sequence from low-coverage whole-genome sequencing. |
| title_short | A strategy to recover a high-quality, complete plastid sequence from low-coverage whole-genome sequencing. |
| title_sort | A strategy to recover a high-quality, complete plastid sequence from low-coverage whole-genome sequencing. |
| topic | BIOINFORMÁTICA Bioinformatic methods Chloroplast genome Next-generation Sequencing Weedy rice BIOLOGÍA CIENCIA DE INFORMACIÓN ARROZ ORYZA SATIVA |
| url | https://ainfo.inia.uy/consulta/busca?b=pc&id=53875&biblioteca=vazio&busca=53875&qFacets=53875 |