Portuguese wild grapevine genome re-sequencing (Vitis vinifera sylvestris)

Detalhes bibliográficos
Autor(a) principal: Ramos, Miguel J.N.
Data de Publicação: 2020
Outros Autores: Coito, João L., Faísca-Silva, David, Cunha, Jorge, Costa, M.Manuela R., Amâncio, Sara, Rocheta, Margarida
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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spelling 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
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dc.relation.none.fl_str_mv Scientific Reports (2020) 10:18993
https://doi.org/10.1038/s41598-020-76012-6
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