A gene-rich fraction analysis of the Passiflora edulis genome reveals highly conserved microsyntenic regions with two related Malpighiales species
Autor(a) principal: | |
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Data de Publicação: | 2018 |
Outros Autores: | , , , , , , , , , |
Tipo de documento: | Artigo |
Idioma: | eng |
Título da fonte: | Repositório Institucional da UNESP |
Texto Completo: | http://dx.doi.org/10.1038/s41598-018-31330-8 http://hdl.handle.net/11449/164581 |
Resumo: | Passiflora edulis is the most widely cultivated species of passionflowers, cropped mainly for industrialized juice production and fresh fruit consumption. Despite its commercial importance, little is known about the genome structure of P. edulis. To fill in this gap in our knowledge, a genomic library was built, and now completely sequenced over 100 large-inserts. Sequencing data were assembled from long sequence reads, and structural sequence annotation resulted in the prediction of about 1,900 genes, providing data for subsequent functional analysis. The richness of repetitive elements was also evaluated. Microsyntenic regions of P. edulis common to Populus trichocarpa and Manihot esculenta, two related Malpighiales species with available fully sequenced genomes were examined. Overall, gene order was well conserved, with some disruptions of collinearity identified as rearrangements, such as inversion and translocation events. The microsynteny level observed between the P. edulis sequences and the compared genomes is surprising, given the long divergence time that separates them from the common ancestor. P. edulis gene-rich segments are more compact than those of the other two species, even though its genome is much larger. This study provides a first accurate gene set for P. edulis, opening the way for new studies on the evolutionary issues in Malpighiales genomes. |
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A gene-rich fraction analysis of the Passiflora edulis genome reveals highly conserved microsyntenic regions with two related Malpighiales speciesPassiflora edulis is the most widely cultivated species of passionflowers, cropped mainly for industrialized juice production and fresh fruit consumption. Despite its commercial importance, little is known about the genome structure of P. edulis. To fill in this gap in our knowledge, a genomic library was built, and now completely sequenced over 100 large-inserts. Sequencing data were assembled from long sequence reads, and structural sequence annotation resulted in the prediction of about 1,900 genes, providing data for subsequent functional analysis. The richness of repetitive elements was also evaluated. Microsyntenic regions of P. edulis common to Populus trichocarpa and Manihot esculenta, two related Malpighiales species with available fully sequenced genomes were examined. Overall, gene order was well conserved, with some disruptions of collinearity identified as rearrangements, such as inversion and translocation events. The microsynteny level observed between the P. edulis sequences and the compared genomes is surprising, given the long divergence time that separates them from the common ancestor. P. edulis gene-rich segments are more compact than those of the other two species, even though its genome is much larger. This study provides a first accurate gene set for P. edulis, opening the way for new studies on the evolutionary issues in Malpighiales genomes.Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)Univ Sao Paulo, Dept Genet, Escola Super Agr Luiz de Queiroz, BR-13418900 Piracicaba, BrazilINRA, Ctr Natl Ressources Genom Vegetales, F-31326 Castanet Tolosan, FranceUniv Estadual Campinas, Inst Biol, Dept Biol Vegetal, BR-13083862 Campinas, SP, BrazilUCA, INRA, UMR 1095, GDEC, F-63000 Clermont Ferrand, FranceUniv Estadual Paulista, Dept Tecnol, Fac Ciencias Agr & Vet, BR-14884900 Jaboticabal, BrazilUniv Estadual Paulista, Dept Tecnol, Fac Ciencias Agr & Vet, BR-14884900 Jaboticabal, BrazilFAPESP: 2014/25215-2FAPESP: 2013/11196-3FAPESP: 2017/04216-9Nature Publishing GroupUniversidade de São Paulo (USP)INRAUniversidade Estadual de Campinas (UNICAMP)UCAUniversidade Estadual Paulista (Unesp)Munhoz, Carla FreitasCosta, Zirlane PortugalCauz-Santos, Luiz AugustoEgoavil Reategui, Alina CarmenRodde, NathalieCauet, StephaneDornelas, Marcelo CarnierLeroy, PhilippeVarani, Alessandro de Mello [UNESP]Berges, HeleneCarneiro Vieira, Maria Lucia2018-11-26T17:55:11Z2018-11-26T17:55:11Z2018-08-29info:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/article18application/pdfhttp://dx.doi.org/10.1038/s41598-018-31330-8Scientific Reports. London: Nature Publishing Group, v. 8, 18 p., 2018.2045-2322http://hdl.handle.net/11449/16458110.1038/s41598-018-31330-8WOS:000443003800031WOS000443003800031.pdfWeb of Sciencereponame:Repositório Institucional da UNESPinstname:Universidade Estadual Paulista (UNESP)instacron:UNESPengScientific Reports1,533info:eu-repo/semantics/openAccess2024-06-07T15:31:34Zoai:repositorio.unesp.br:11449/164581Repositório InstitucionalPUBhttp://repositorio.unesp.br/oai/requestopendoar:29462024-08-05T15:29:10.215608Repositório Institucional da UNESP - Universidade Estadual Paulista (UNESP)false |
dc.title.none.fl_str_mv |
A gene-rich fraction analysis of the Passiflora edulis genome reveals highly conserved microsyntenic regions with two related Malpighiales species |
title |
A gene-rich fraction analysis of the Passiflora edulis genome reveals highly conserved microsyntenic regions with two related Malpighiales species |
spellingShingle |
A gene-rich fraction analysis of the Passiflora edulis genome reveals highly conserved microsyntenic regions with two related Malpighiales species Munhoz, Carla Freitas |
title_short |
A gene-rich fraction analysis of the Passiflora edulis genome reveals highly conserved microsyntenic regions with two related Malpighiales species |
title_full |
A gene-rich fraction analysis of the Passiflora edulis genome reveals highly conserved microsyntenic regions with two related Malpighiales species |
title_fullStr |
A gene-rich fraction analysis of the Passiflora edulis genome reveals highly conserved microsyntenic regions with two related Malpighiales species |
title_full_unstemmed |
A gene-rich fraction analysis of the Passiflora edulis genome reveals highly conserved microsyntenic regions with two related Malpighiales species |
title_sort |
A gene-rich fraction analysis of the Passiflora edulis genome reveals highly conserved microsyntenic regions with two related Malpighiales species |
author |
Munhoz, Carla Freitas |
author_facet |
Munhoz, Carla Freitas Costa, Zirlane Portugal Cauz-Santos, Luiz Augusto Egoavil Reategui, Alina Carmen Rodde, Nathalie Cauet, Stephane Dornelas, Marcelo Carnier Leroy, Philippe Varani, Alessandro de Mello [UNESP] Berges, Helene Carneiro Vieira, Maria Lucia |
author_role |
author |
author2 |
Costa, Zirlane Portugal Cauz-Santos, Luiz Augusto Egoavil Reategui, Alina Carmen Rodde, Nathalie Cauet, Stephane Dornelas, Marcelo Carnier Leroy, Philippe Varani, Alessandro de Mello [UNESP] Berges, Helene Carneiro Vieira, Maria Lucia |
author2_role |
author author author author author author author author author author |
dc.contributor.none.fl_str_mv |
Universidade de São Paulo (USP) INRA Universidade Estadual de Campinas (UNICAMP) UCA Universidade Estadual Paulista (Unesp) |
dc.contributor.author.fl_str_mv |
Munhoz, Carla Freitas Costa, Zirlane Portugal Cauz-Santos, Luiz Augusto Egoavil Reategui, Alina Carmen Rodde, Nathalie Cauet, Stephane Dornelas, Marcelo Carnier Leroy, Philippe Varani, Alessandro de Mello [UNESP] Berges, Helene Carneiro Vieira, Maria Lucia |
description |
Passiflora edulis is the most widely cultivated species of passionflowers, cropped mainly for industrialized juice production and fresh fruit consumption. Despite its commercial importance, little is known about the genome structure of P. edulis. To fill in this gap in our knowledge, a genomic library was built, and now completely sequenced over 100 large-inserts. Sequencing data were assembled from long sequence reads, and structural sequence annotation resulted in the prediction of about 1,900 genes, providing data for subsequent functional analysis. The richness of repetitive elements was also evaluated. Microsyntenic regions of P. edulis common to Populus trichocarpa and Manihot esculenta, two related Malpighiales species with available fully sequenced genomes were examined. Overall, gene order was well conserved, with some disruptions of collinearity identified as rearrangements, such as inversion and translocation events. The microsynteny level observed between the P. edulis sequences and the compared genomes is surprising, given the long divergence time that separates them from the common ancestor. P. edulis gene-rich segments are more compact than those of the other two species, even though its genome is much larger. This study provides a first accurate gene set for P. edulis, opening the way for new studies on the evolutionary issues in Malpighiales genomes. |
publishDate |
2018 |
dc.date.none.fl_str_mv |
2018-11-26T17:55:11Z 2018-11-26T17:55:11Z 2018-08-29 |
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://dx.doi.org/10.1038/s41598-018-31330-8 Scientific Reports. London: Nature Publishing Group, v. 8, 18 p., 2018. 2045-2322 http://hdl.handle.net/11449/164581 10.1038/s41598-018-31330-8 WOS:000443003800031 WOS000443003800031.pdf |
url |
http://dx.doi.org/10.1038/s41598-018-31330-8 http://hdl.handle.net/11449/164581 |
identifier_str_mv |
Scientific Reports. London: Nature Publishing Group, v. 8, 18 p., 2018. 2045-2322 10.1038/s41598-018-31330-8 WOS:000443003800031 WOS000443003800031.pdf |
dc.language.iso.fl_str_mv |
eng |
language |
eng |
dc.relation.none.fl_str_mv |
Scientific Reports 1,533 |
dc.rights.driver.fl_str_mv |
info:eu-repo/semantics/openAccess |
eu_rights_str_mv |
openAccess |
dc.format.none.fl_str_mv |
18 application/pdf |
dc.publisher.none.fl_str_mv |
Nature Publishing Group |
publisher.none.fl_str_mv |
Nature Publishing Group |
dc.source.none.fl_str_mv |
Web of Science reponame:Repositório Institucional da UNESP instname:Universidade Estadual Paulista (UNESP) instacron:UNESP |
instname_str |
Universidade Estadual Paulista (UNESP) |
instacron_str |
UNESP |
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UNESP |
reponame_str |
Repositório Institucional da UNESP |
collection |
Repositório Institucional da UNESP |
repository.name.fl_str_mv |
Repositório Institucional da UNESP - Universidade Estadual Paulista (UNESP) |
repository.mail.fl_str_mv |
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1808128519099645952 |