Portuguese wild grapevine genome re-sequencing (Vitis vinifera sylvestris)
Autor(a) principal: | |
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Data de Publicação: | 2020 |
Outros Autores: | , , , , , |
Tipo de documento: | Artigo |
Idioma: | eng |
Título da fonte: | Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos) |
Texto Completo: | http://hdl.handle.net/10400.5/20566 |
Resumo: | The first genome of Vitis vinifera vinifera (PN40024), published in 2007, boosted grapevine related studies. While this reference genome is a suitable tool for the overall studies in the field, it lacks the ability to unveil changes accumulated during V. v. vinifera domestication. The subspecies V. v. sylvestris preserves wild characteristics, making it a good material to provide insights into V. v. vinifera domestication. The difference in the reproductive strategy between both subspecies is one of the characteristics that set them apart. While V. v. vinifera flowers are hermaphrodite, V. v. sylvestris is mostly dioecious. In this paper, we compare the re-sequencing of the genomes from a male and a female individual of the wild sylvestris, against the reference vinifera genome (PN40024). Variant analysis reveals a low number but with high impact modifications in coding regions, essentially nonsynonymous single nucleotide polymorphisms and frame shifts caused by insertions and deletions. The sex-locus was manually inspected, and the results obtained are in line with the most recent works related with wild grapevine sex. In this paper we also describe for the first time RNA editing in transcripts of 14 genes in the sex-determining region, including VviYABBY and VviPLATZ |
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Portuguese wild grapevine genome re-sequencing (Vitis vinifera sylvestris)Vitis vinifera sylvestrisgenome re-sequencingThe first genome of Vitis vinifera vinifera (PN40024), published in 2007, boosted grapevine related studies. While this reference genome is a suitable tool for the overall studies in the field, it lacks the ability to unveil changes accumulated during V. v. vinifera domestication. The subspecies V. v. sylvestris preserves wild characteristics, making it a good material to provide insights into V. v. vinifera domestication. The difference in the reproductive strategy between both subspecies is one of the characteristics that set them apart. While V. v. vinifera flowers are hermaphrodite, V. v. sylvestris is mostly dioecious. In this paper, we compare the re-sequencing of the genomes from a male and a female individual of the wild sylvestris, against the reference vinifera genome (PN40024). Variant analysis reveals a low number but with high impact modifications in coding regions, essentially nonsynonymous single nucleotide polymorphisms and frame shifts caused by insertions and deletions. The sex-locus was manually inspected, and the results obtained are in line with the most recent works related with wild grapevine sex. In this paper we also describe for the first time RNA editing in transcripts of 14 genes in the sex-determining region, including VviYABBY and VviPLATZNatureRepositório da Universidade de LisboaRamos, Miguel J.N.Coito, João L.Faísca-Silva, DavidCunha, JorgeCosta, M.Manuela R.Amâncio, SaraRocheta, Margarida2020-11-13T09:40:47Z20202020-01-01T00:00:00Zinfo:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/articleapplication/pdfhttp://hdl.handle.net/10400.5/20566engScientific Reports (2020) 10:18993https://doi.org/10.1038/s41598-020-76012-6info:eu-repo/semantics/openAccessreponame:Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos)instname:Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informaçãoinstacron:RCAAP2023-03-06T14:49:58Zoai:www.repository.utl.pt:10400.5/20566Portal AgregadorONGhttps://www.rcaap.pt/oai/openaireopendoar:71602024-03-19T17:05:16.136134Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos) - Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informaçãofalse |
dc.title.none.fl_str_mv |
Portuguese wild grapevine genome re-sequencing (Vitis vinifera sylvestris) |
title |
Portuguese wild grapevine genome re-sequencing (Vitis vinifera sylvestris) |
spellingShingle |
Portuguese wild grapevine genome re-sequencing (Vitis vinifera sylvestris) Ramos, Miguel J.N. Vitis vinifera sylvestris genome re-sequencing |
title_short |
Portuguese wild grapevine genome re-sequencing (Vitis vinifera sylvestris) |
title_full |
Portuguese wild grapevine genome re-sequencing (Vitis vinifera sylvestris) |
title_fullStr |
Portuguese wild grapevine genome re-sequencing (Vitis vinifera sylvestris) |
title_full_unstemmed |
Portuguese wild grapevine genome re-sequencing (Vitis vinifera sylvestris) |
title_sort |
Portuguese wild grapevine genome re-sequencing (Vitis vinifera sylvestris) |
author |
Ramos, Miguel J.N. |
author_facet |
Ramos, Miguel J.N. Coito, João L. Faísca-Silva, David Cunha, Jorge Costa, M.Manuela R. Amâncio, Sara Rocheta, Margarida |
author_role |
author |
author2 |
Coito, João L. Faísca-Silva, David Cunha, Jorge Costa, M.Manuela R. Amâncio, Sara Rocheta, Margarida |
author2_role |
author author author author author author |
dc.contributor.none.fl_str_mv |
Repositório da Universidade de Lisboa |
dc.contributor.author.fl_str_mv |
Ramos, Miguel J.N. Coito, João L. Faísca-Silva, David Cunha, Jorge Costa, M.Manuela R. Amâncio, Sara Rocheta, Margarida |
dc.subject.por.fl_str_mv |
Vitis vinifera sylvestris genome re-sequencing |
topic |
Vitis vinifera sylvestris genome re-sequencing |
description |
The first genome of Vitis vinifera vinifera (PN40024), published in 2007, boosted grapevine related studies. While this reference genome is a suitable tool for the overall studies in the field, it lacks the ability to unveil changes accumulated during V. v. vinifera domestication. The subspecies V. v. sylvestris preserves wild characteristics, making it a good material to provide insights into V. v. vinifera domestication. The difference in the reproductive strategy between both subspecies is one of the characteristics that set them apart. While V. v. vinifera flowers are hermaphrodite, V. v. sylvestris is mostly dioecious. In this paper, we compare the re-sequencing of the genomes from a male and a female individual of the wild sylvestris, against the reference vinifera genome (PN40024). Variant analysis reveals a low number but with high impact modifications in coding regions, essentially nonsynonymous single nucleotide polymorphisms and frame shifts caused by insertions and deletions. The sex-locus was manually inspected, and the results obtained are in line with the most recent works related with wild grapevine sex. In this paper we also describe for the first time RNA editing in transcripts of 14 genes in the sex-determining region, including VviYABBY and VviPLATZ |
publishDate |
2020 |
dc.date.none.fl_str_mv |
2020-11-13T09:40:47Z 2020 2020-01-01T00:00:00Z |
dc.type.status.fl_str_mv |
info:eu-repo/semantics/publishedVersion |
dc.type.driver.fl_str_mv |
info:eu-repo/semantics/article |
format |
article |
status_str |
publishedVersion |
dc.identifier.uri.fl_str_mv |
http://hdl.handle.net/10400.5/20566 |
url |
http://hdl.handle.net/10400.5/20566 |
dc.language.iso.fl_str_mv |
eng |
language |
eng |
dc.relation.none.fl_str_mv |
Scientific Reports (2020) 10:18993 https://doi.org/10.1038/s41598-020-76012-6 |
dc.rights.driver.fl_str_mv |
info:eu-repo/semantics/openAccess |
eu_rights_str_mv |
openAccess |
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application/pdf |
dc.publisher.none.fl_str_mv |
Nature |
publisher.none.fl_str_mv |
Nature |
dc.source.none.fl_str_mv |
reponame:Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos) instname:Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informação instacron:RCAAP |
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Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informação |
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RCAAP |
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RCAAP |
reponame_str |
Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos) |
collection |
Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos) |
repository.name.fl_str_mv |
Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos) - Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informação |
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1799131144991539200 |