Long-insert clone experimental evidence for assembly improvement and chimeric chromosomes detection in an allopentaploid beer yeast

"Lager beer is made with the hybrid Saccharomyces pastorianus. Many publicly available S. pastorianus genome assemblies are highly fragmented due to the difficulties of assembling hybrid genomes, such as the presence of homeologous chromosomes from both parental types, and translocations betwee...

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Autores: CINTIA NOEMI GOMEZ MUÑOZ, LUIS FERNANDO GARCIA ORTEGA, Javier Israel Montalvo Arredondo, Esmeralda Pérez Ortega, LUIS CASTULO DAMAS BUENROSTRO, Lina Raquel Riego Ruiz
Tipo de recurso: artículo
Estado:Versión publicada
Fecha de publicación:2021
País:México
Institución:Instituto Potosino de Investigación Científica y Tecnológica
Repositorio:Repositorio Institucional del IPICYT
OAI Identifier:oai:ipicyt.repositorioinstitucional.mx:1010/2504
Acceso en línea:http://ipicyt.repositorioinstitucional.mx/jspui/handle/1010/2504
Access Level:acceso abierto
Palabra clave:info:eu-repo/classification/Autor/Lager
info:eu-repo/classification/Autor/Yeast
info:eu-repo/classification/Autor/Hybrid
info:eu-repo/classification/Autor/Genome
info:eu-repo/classification/Autor/BAC
info:eu-repo/classification/Autor/Assembly
info:eu-repo/classification/Autor/Translocations
info:eu-repo/classification/cti/2
info:eu-repo/classification/cti/24
info:eu-repo/classification/cti/2409
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spelling Long-insert clone experimental evidence for assembly improvement and chimeric chromosomes detection in an allopentaploid beer yeastCINTIA NOEMI GOMEZ MUÑOZLUIS FERNANDO GARCIA ORTEGAJavier Israel Montalvo ArredondoEsmeralda Pérez OrtegaLUIS CASTULO DAMAS BUENROSTROLina Raquel Riego Ruizinfo:eu-repo/classification/Autor/Lagerinfo:eu-repo/classification/Autor/Yeastinfo:eu-repo/classification/Autor/Hybridinfo:eu-repo/classification/Autor/Genomeinfo:eu-repo/classification/Autor/BACinfo:eu-repo/classification/Autor/Assemblyinfo:eu-repo/classification/Autor/Translocationsinfo:eu-repo/classification/cti/2info:eu-repo/classification/cti/24info:eu-repo/classification/cti/2409info:eu-repo/classification/cti/2409"Lager beer is made with the hybrid Saccharomyces pastorianus. Many publicly available S. pastorianus genome assemblies are highly fragmented due to the difficulties of assembling hybrid genomes, such as the presence of homeologous chromosomes from both parental types, and translocations between them. To improve the assembly of a previously sequenced lager yeast hybrid Saccharomyces sp. 790 and elucidate its genome structure, we proposed the use of alternative experimental evidence. We determined the phylogenetic position of Saccharomyces sp. 790 and established it as S. pastorianus 790. Then, we obtained from this yeast a bacterial artificial chromosome (BAC) genomic library with its BAC-end sequences (BESs). To analyze these data, we developed a pipeline (applicable to other assemblies) that classifies BES pairs alignments according to their orientation. For the case of S. pastorianus 790, paired-end BESs alignments validated parts of the assembly and unpaired-end ones suggested contig joins or misassemblies. Importantly, the BACs library was preserved and used for verification experiments. Unpaired-end alignments were used to upgrade the previous assembly and provided an improved detection of translocations. With this, we proposed a genome structure of S. pastorianus 790, which was similar to that of other lager yeasts; however, when we estimated chromosome copy number and experimentally measured its genome size, we discovered that one key difference is the outstanding S. pastorianus 790 ploidy level (allopentaploid). Altogether, our results show the value of combining bioinformatic analyses with experimental data such as long-insert clone information to improve a short-read assembly of a hybrid genome."Oxford University Press2021info:eu-repo/semantics/articleinfo:eu-repo/semantics/publishedVersionapplication/pdfhttp://ipicyt.repositorioinstitucional.mx/jspui/handle/1010/2504reponame:Repositorio Institucional del IPICYTinstname:Instituto Potosino de Investigación Científica y Tecnológicainstacron:IPICYTinfo:eu-repo/semantics/altIdentifier/DOI/https://doi.org/10.1093/g3journal/jkab088citation:Cintia Gómez-Muñoz, Luis Fernando García-Ortega, Javier Montalvo-Arredondo, Esmeralda Pérez-Ortega, Luis Cástulo Damas-Buenrostro, Lina Riego-Ruiz, Long-insert clone experimental evidence for assembly improvement and chimeric chromosomes detection in an allopentaploid beer yeast, G3 Genes|Genomes|Genetics, Volume 11, Issue 7, July 2021, jkab088, https://doi.org/10.1093/g3journal/jkab088info:eu-repo/semantics/openAccesshttp://creativecommons.org/licenses/by-nc-nd/4.0oai:ipicyt.repositorioinstitucional.mx:1010/25042024-08-28T03:17:55Z
dc.title.none.fl_str_mv Long-insert clone experimental evidence for assembly improvement and chimeric chromosomes detection in an allopentaploid beer yeast
title Long-insert clone experimental evidence for assembly improvement and chimeric chromosomes detection in an allopentaploid beer yeast
spellingShingle Long-insert clone experimental evidence for assembly improvement and chimeric chromosomes detection in an allopentaploid beer yeast
CINTIA NOEMI GOMEZ MUÑOZ
info:eu-repo/classification/Autor/Lager
info:eu-repo/classification/Autor/Yeast
info:eu-repo/classification/Autor/Hybrid
info:eu-repo/classification/Autor/Genome
info:eu-repo/classification/Autor/BAC
info:eu-repo/classification/Autor/Assembly
info:eu-repo/classification/Autor/Translocations
info:eu-repo/classification/cti/2
info:eu-repo/classification/cti/24
info:eu-repo/classification/cti/2409
info:eu-repo/classification/cti/2409
title_short Long-insert clone experimental evidence for assembly improvement and chimeric chromosomes detection in an allopentaploid beer yeast
title_full Long-insert clone experimental evidence for assembly improvement and chimeric chromosomes detection in an allopentaploid beer yeast
title_fullStr Long-insert clone experimental evidence for assembly improvement and chimeric chromosomes detection in an allopentaploid beer yeast
title_full_unstemmed Long-insert clone experimental evidence for assembly improvement and chimeric chromosomes detection in an allopentaploid beer yeast
title_sort Long-insert clone experimental evidence for assembly improvement and chimeric chromosomes detection in an allopentaploid beer yeast
dc.creator.none.fl_str_mv CINTIA NOEMI GOMEZ MUÑOZ
LUIS FERNANDO GARCIA ORTEGA
Javier Israel Montalvo Arredondo
Esmeralda Pérez Ortega
LUIS CASTULO DAMAS BUENROSTRO
Lina Raquel Riego Ruiz
author CINTIA NOEMI GOMEZ MUÑOZ
author_facet CINTIA NOEMI GOMEZ MUÑOZ
LUIS FERNANDO GARCIA ORTEGA
Javier Israel Montalvo Arredondo
Esmeralda Pérez Ortega
LUIS CASTULO DAMAS BUENROSTRO
Lina Raquel Riego Ruiz
author_role author
author2 LUIS FERNANDO GARCIA ORTEGA
Javier Israel Montalvo Arredondo
Esmeralda Pérez Ortega
LUIS CASTULO DAMAS BUENROSTRO
Lina Raquel Riego Ruiz
author2_role author
author
author
author
author
dc.subject.none.fl_str_mv info:eu-repo/classification/Autor/Lager
info:eu-repo/classification/Autor/Yeast
info:eu-repo/classification/Autor/Hybrid
info:eu-repo/classification/Autor/Genome
info:eu-repo/classification/Autor/BAC
info:eu-repo/classification/Autor/Assembly
info:eu-repo/classification/Autor/Translocations
info:eu-repo/classification/cti/2
info:eu-repo/classification/cti/24
info:eu-repo/classification/cti/2409
info:eu-repo/classification/cti/2409
topic info:eu-repo/classification/Autor/Lager
info:eu-repo/classification/Autor/Yeast
info:eu-repo/classification/Autor/Hybrid
info:eu-repo/classification/Autor/Genome
info:eu-repo/classification/Autor/BAC
info:eu-repo/classification/Autor/Assembly
info:eu-repo/classification/Autor/Translocations
info:eu-repo/classification/cti/2
info:eu-repo/classification/cti/24
info:eu-repo/classification/cti/2409
info:eu-repo/classification/cti/2409
description "Lager beer is made with the hybrid Saccharomyces pastorianus. Many publicly available S. pastorianus genome assemblies are highly fragmented due to the difficulties of assembling hybrid genomes, such as the presence of homeologous chromosomes from both parental types, and translocations between them. To improve the assembly of a previously sequenced lager yeast hybrid Saccharomyces sp. 790 and elucidate its genome structure, we proposed the use of alternative experimental evidence. We determined the phylogenetic position of Saccharomyces sp. 790 and established it as S. pastorianus 790. Then, we obtained from this yeast a bacterial artificial chromosome (BAC) genomic library with its BAC-end sequences (BESs). To analyze these data, we developed a pipeline (applicable to other assemblies) that classifies BES pairs alignments according to their orientation. For the case of S. pastorianus 790, paired-end BESs alignments validated parts of the assembly and unpaired-end ones suggested contig joins or misassemblies. Importantly, the BACs library was preserved and used for verification experiments. Unpaired-end alignments were used to upgrade the previous assembly and provided an improved detection of translocations. With this, we proposed a genome structure of S. pastorianus 790, which was similar to that of other lager yeasts; however, when we estimated chromosome copy number and experimentally measured its genome size, we discovered that one key difference is the outstanding S. pastorianus 790 ploidy level (allopentaploid). Altogether, our results show the value of combining bioinformatic analyses with experimental data such as long-insert clone information to improve a short-read assembly of a hybrid genome."
publishDate 2021
dc.date.none.fl_str_mv 2021
dc.type.none.fl_str_mv info:eu-repo/semantics/article
info:eu-repo/semantics/publishedVersion
format article
status_str publishedVersion
dc.identifier.none.fl_str_mv http://ipicyt.repositorioinstitucional.mx/jspui/handle/1010/2504
url http://ipicyt.repositorioinstitucional.mx/jspui/handle/1010/2504
dc.relation.none.fl_str_mv info:eu-repo/semantics/altIdentifier/DOI/https://doi.org/10.1093/g3journal/jkab088
citation:Cintia Gómez-Muñoz, Luis Fernando García-Ortega, Javier Montalvo-Arredondo, Esmeralda Pérez-Ortega, Luis Cástulo Damas-Buenrostro, Lina Riego-Ruiz, Long-insert clone experimental evidence for assembly improvement and chimeric chromosomes detection in an allopentaploid beer yeast, G3 Genes|Genomes|Genetics, Volume 11, Issue 7, July 2021, jkab088, https://doi.org/10.1093/g3journal/jkab088
dc.rights.none.fl_str_mv info:eu-repo/semantics/openAccess
http://creativecommons.org/licenses/by-nc-nd/4.0
eu_rights_str_mv openAccess
rights_invalid_str_mv http://creativecommons.org/licenses/by-nc-nd/4.0
dc.format.none.fl_str_mv application/pdf
dc.publisher.none.fl_str_mv Oxford University Press
publisher.none.fl_str_mv Oxford University Press
dc.source.none.fl_str_mv reponame:Repositorio Institucional del IPICYT
instname:Instituto Potosino de Investigación Científica y Tecnológica
instacron:IPICYT
instname_str Instituto Potosino de Investigación Científica y Tecnológica
instacron_str IPICYT
institution IPICYT
reponame_str Repositorio Institucional del IPICYT
collection Repositorio Institucional del IPICYT
repository.name.fl_str_mv
repository.mail.fl_str_mv
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