Building the sugarcane genome for biotechnology and identifying evolutionary trends
Autor(a) principal: | |
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Data de Publicação: | 2014 |
Outros Autores: | , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , |
Tipo de documento: | Artigo |
Idioma: | eng |
Título da fonte: | Repositório Institucional da UNESP |
Texto Completo: | http://dx.doi.org/10.1186/1471-2164-15-540 http://hdl.handle.net/11449/117308 |
Resumo: | Background: Sugarcane is the source of sugar in all tropical and subtropical countries and is becoming increasingly important for bio-based fuels. However, its large (10 Gb), polyploid, complex genome has hindered genome based breeding efforts. Here we release the largest and most diverse set of sugarcane genome sequences to date, as part of an on-going initiative to provide a sugarcane genomic information resource, with the ultimate goal of producing a gold standard genome.Results: Three hundred and seventeen chiefly euchromatic BACs were sequenced. A reference set of one thousand four hundred manually-annotated protein-coding genes was generated. A small RNA collection and a RNA-seq library were used to explore expression patterns and the sRNA landscape. In the sucrose and starch metabolism pathway, 16 non-redundant enzyme-encoding genes were identified. One of the sucrose pathway genes, sucrose-6-phosphate phosphohydrolase, is duplicated in sugarcane and sorghum, but not in rice and maize. A diversity analysis of the s6pp duplication region revealed haplotype-structured sequence composition. Examination of hom(e)ologous loci indicate both sequence structural and sRNA landscape variation. A synteny analysis shows that the sugarcane genome has expanded relative to the sorghum genome, largely due to the presence of transposable elements and uncharacterized intergenic and intronic sequences.Conclusion: This release of sugarcane genomic sequences will advance our understanding of sugarcane genetics and contribute to the development of molecular tools for breeding purposes and gene discovery. |
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Building the sugarcane genome for biotechnology and identifying evolutionary trendsSaccharumBacterial artificial chromosome sequencingPolyploidyGenomeGeneticsGrassesBackground: Sugarcane is the source of sugar in all tropical and subtropical countries and is becoming increasingly important for bio-based fuels. However, its large (10 Gb), polyploid, complex genome has hindered genome based breeding efforts. Here we release the largest and most diverse set of sugarcane genome sequences to date, as part of an on-going initiative to provide a sugarcane genomic information resource, with the ultimate goal of producing a gold standard genome.Results: Three hundred and seventeen chiefly euchromatic BACs were sequenced. A reference set of one thousand four hundred manually-annotated protein-coding genes was generated. A small RNA collection and a RNA-seq library were used to explore expression patterns and the sRNA landscape. In the sucrose and starch metabolism pathway, 16 non-redundant enzyme-encoding genes were identified. One of the sucrose pathway genes, sucrose-6-phosphate phosphohydrolase, is duplicated in sugarcane and sorghum, but not in rice and maize. A diversity analysis of the s6pp duplication region revealed haplotype-structured sequence composition. Examination of hom(e)ologous loci indicate both sequence structural and sRNA landscape variation. A synteny analysis shows that the sugarcane genome has expanded relative to the sorghum genome, largely due to the presence of transposable elements and uncharacterized intergenic and intronic sequences.Conclusion: This release of sugarcane genomic sequences will advance our understanding of sugarcane genetics and contribute to the development of molecular tools for breeding purposes and gene discovery.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)International Consortium for Sugarcane BiotechnologyConsortium for Plant Biotechnology ResearchUniv. Georgia Office of the Vice President for ResearchUniv Sao Paulo, Inst Biociencias, Dept Bot, BR-05508090 Sao Paulo, BrazilUniv Fed ABC, BR-09210170 Santo Andre, BrazilUniv Sao Paulo, Dept Genet, Escola Super Agr Luiz de Queiroz, BR-13418900 Piracicaba, SP, BrazilUniv Estadual Campinas, Ctr Biol Mol & Engn Genet, BR-13083875 Campinas, SP, BrazilUniv Estadual Paulista, Inst Biociencias, Dept Genet, BR-18618000 Botucatu, SP, BrazilInst Quim, Dept Bioquim, BR-05508900 Sao Paulo, SP, BrazilINRA CNRGV, F-31326 Castanet Tolosan, FranceDept Biol Celular & Genet UFRN, BR-59072970 Natal, RN, BrazilUniv Fed Sao Carlos, Ctr Ciencias Agr, Araras, SP, BrazilUniv Georgia, Dept Plant Biol, Athens, GA 30602 USAUniv Georgia, Dept Crop & Soil Sci, Athens, GA 30602 USAUniv Georgia, Dept Genet, Athens, GA 30602 USACIRAD, UMR1096, F-34398 Montpellier 5, FranceMendel Genom Anal, Sao Paulo, BrazilUniv Estadual Paulista, Inst Biociencias, Dept Genet, BR-18618000 Botucatu, SP, BrazilFAPESP: 08/52074-0FAPESP: 10/05591-9FAPESP: 08/58031-0FAPESP: 08/52197-4FAPESP: 08/52146-0FAPESP: 09/51632-1FAPESP: 09/09217-7FAPESP: 08/58243-8FAPESP: 09/09116-6FAPESP: 11/05317-7FAPESP: 08/54201-9International Consortium for Sugarcane Biotechnology24Consortium for Plant Biotechnology ResearchDE-FG36-02GO12026Biomed Central LtdUniversidade de São Paulo (USP)Universidade Federal do ABC (UFABC)Universidade Estadual de Campinas (UNICAMP)Universidade Estadual Paulista (Unesp)Inst QuimINRA CNRGVDept Biol Celular & Genet UFRNUniversidade Federal de São Carlos (UFSCar)Univ GeorgiaCIRADMendel Genom AnalSetta, Nathalia deMonteiro-Vitorello, Claudia BarrosMetcalfe, Cushla JaneQueiroga Cruz, Guilherme MarceloDel Bem, Luiz EduardoVicentini, RenatoSilveira Nogueira, Fabio Tebaldi [UNESP]Campos, Roberta AlvaresNunes, Sideny LimaGasperazzo Turrini, Paula CristinaVieira, Andreia PrataOchoa Cruz, Edgar AndresSilveira Correa, Tatiana CarolineHotta, Carlos TakeshiVarani, Alessandro de MelloVautrin, SoniaTrindade, Adilson Silva daVilela, Mariane de MendoncaLembke, Carolina GimilianiSato, Paloma MiekoAndrade, Rodrigo Fandino deNishiyama, Milton YutakaCardoso-Silva, Claudio BenicioScortecci, Katia CastanhoFranco Garcia, Antonio AugustoCarneiro, Monalisa SampaioKim, ChangsooPaterson, Andrew H.Berges, HeleneD'Hont, AngeliqueSouza, Anete Pereira deSouza, Glaucia MendesVincentz, MichelKitajima, Joao PauloVan Sluys, Marie-Anne2015-03-18T15:55:48Z2015-03-18T15:55:48Z2014-06-30info:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/article17application/pdfhttp://dx.doi.org/10.1186/1471-2164-15-540Bmc Genomics. London: Biomed Central Ltd, v. 15, 17 p., 2014.1471-2164http://hdl.handle.net/11449/11730810.1186/1471-2164-15-540WOS:000339583200001WOS000339583200001.pdfWeb of Sciencereponame:Repositório Institucional da UNESPinstname:Universidade Estadual Paulista (UNESP)instacron:UNESPengBmc Genomics3.7302,110info:eu-repo/semantics/openAccess2023-10-14T06:03:51Zoai:repositorio.unesp.br:11449/117308Repositório InstitucionalPUBhttp://repositorio.unesp.br/oai/requestopendoar:29462023-10-14T06:03:51Repositório Institucional da UNESP - Universidade Estadual Paulista (UNESP)false |
dc.title.none.fl_str_mv |
Building the sugarcane genome for biotechnology and identifying evolutionary trends |
title |
Building the sugarcane genome for biotechnology and identifying evolutionary trends |
spellingShingle |
Building the sugarcane genome for biotechnology and identifying evolutionary trends Setta, Nathalia de Saccharum Bacterial artificial chromosome sequencing Polyploidy Genome Genetics Grasses |
title_short |
Building the sugarcane genome for biotechnology and identifying evolutionary trends |
title_full |
Building the sugarcane genome for biotechnology and identifying evolutionary trends |
title_fullStr |
Building the sugarcane genome for biotechnology and identifying evolutionary trends |
title_full_unstemmed |
Building the sugarcane genome for biotechnology and identifying evolutionary trends |
title_sort |
Building the sugarcane genome for biotechnology and identifying evolutionary trends |
author |
Setta, Nathalia de |
author_facet |
Setta, Nathalia de Monteiro-Vitorello, Claudia Barros Metcalfe, Cushla Jane Queiroga Cruz, Guilherme Marcelo Del Bem, Luiz Eduardo Vicentini, Renato Silveira Nogueira, Fabio Tebaldi [UNESP] Campos, Roberta Alvares Nunes, Sideny Lima Gasperazzo Turrini, Paula Cristina Vieira, Andreia Prata Ochoa Cruz, Edgar Andres Silveira Correa, Tatiana Caroline Hotta, Carlos Takeshi Varani, Alessandro de Mello Vautrin, Sonia Trindade, Adilson Silva da Vilela, Mariane de Mendonca Lembke, Carolina Gimiliani Sato, Paloma Mieko Andrade, Rodrigo Fandino de Nishiyama, Milton Yutaka Cardoso-Silva, Claudio Benicio Scortecci, Katia Castanho Franco Garcia, Antonio Augusto Carneiro, Monalisa Sampaio Kim, Changsoo Paterson, Andrew H. Berges, Helene D'Hont, Angelique Souza, Anete Pereira de Souza, Glaucia Mendes Vincentz, Michel Kitajima, Joao Paulo Van Sluys, Marie-Anne |
author_role |
author |
author2 |
Monteiro-Vitorello, Claudia Barros Metcalfe, Cushla Jane Queiroga Cruz, Guilherme Marcelo Del Bem, Luiz Eduardo Vicentini, Renato Silveira Nogueira, Fabio Tebaldi [UNESP] Campos, Roberta Alvares Nunes, Sideny Lima Gasperazzo Turrini, Paula Cristina Vieira, Andreia Prata Ochoa Cruz, Edgar Andres Silveira Correa, Tatiana Caroline Hotta, Carlos Takeshi Varani, Alessandro de Mello Vautrin, Sonia Trindade, Adilson Silva da Vilela, Mariane de Mendonca Lembke, Carolina Gimiliani Sato, Paloma Mieko Andrade, Rodrigo Fandino de Nishiyama, Milton Yutaka Cardoso-Silva, Claudio Benicio Scortecci, Katia Castanho Franco Garcia, Antonio Augusto Carneiro, Monalisa Sampaio Kim, Changsoo Paterson, Andrew H. Berges, Helene D'Hont, Angelique Souza, Anete Pereira de Souza, Glaucia Mendes Vincentz, Michel Kitajima, Joao Paulo Van Sluys, Marie-Anne |
author2_role |
author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author |
dc.contributor.none.fl_str_mv |
Universidade de São Paulo (USP) Universidade Federal do ABC (UFABC) Universidade Estadual de Campinas (UNICAMP) Universidade Estadual Paulista (Unesp) Inst Quim INRA CNRGV Dept Biol Celular & Genet UFRN Universidade Federal de São Carlos (UFSCar) Univ Georgia CIRAD Mendel Genom Anal |
dc.contributor.author.fl_str_mv |
Setta, Nathalia de Monteiro-Vitorello, Claudia Barros Metcalfe, Cushla Jane Queiroga Cruz, Guilherme Marcelo Del Bem, Luiz Eduardo Vicentini, Renato Silveira Nogueira, Fabio Tebaldi [UNESP] Campos, Roberta Alvares Nunes, Sideny Lima Gasperazzo Turrini, Paula Cristina Vieira, Andreia Prata Ochoa Cruz, Edgar Andres Silveira Correa, Tatiana Caroline Hotta, Carlos Takeshi Varani, Alessandro de Mello Vautrin, Sonia Trindade, Adilson Silva da Vilela, Mariane de Mendonca Lembke, Carolina Gimiliani Sato, Paloma Mieko Andrade, Rodrigo Fandino de Nishiyama, Milton Yutaka Cardoso-Silva, Claudio Benicio Scortecci, Katia Castanho Franco Garcia, Antonio Augusto Carneiro, Monalisa Sampaio Kim, Changsoo Paterson, Andrew H. Berges, Helene D'Hont, Angelique Souza, Anete Pereira de Souza, Glaucia Mendes Vincentz, Michel Kitajima, Joao Paulo Van Sluys, Marie-Anne |
dc.subject.por.fl_str_mv |
Saccharum Bacterial artificial chromosome sequencing Polyploidy Genome Genetics Grasses |
topic |
Saccharum Bacterial artificial chromosome sequencing Polyploidy Genome Genetics Grasses |
description |
Background: Sugarcane is the source of sugar in all tropical and subtropical countries and is becoming increasingly important for bio-based fuels. However, its large (10 Gb), polyploid, complex genome has hindered genome based breeding efforts. Here we release the largest and most diverse set of sugarcane genome sequences to date, as part of an on-going initiative to provide a sugarcane genomic information resource, with the ultimate goal of producing a gold standard genome.Results: Three hundred and seventeen chiefly euchromatic BACs were sequenced. A reference set of one thousand four hundred manually-annotated protein-coding genes was generated. A small RNA collection and a RNA-seq library were used to explore expression patterns and the sRNA landscape. In the sucrose and starch metabolism pathway, 16 non-redundant enzyme-encoding genes were identified. One of the sucrose pathway genes, sucrose-6-phosphate phosphohydrolase, is duplicated in sugarcane and sorghum, but not in rice and maize. A diversity analysis of the s6pp duplication region revealed haplotype-structured sequence composition. Examination of hom(e)ologous loci indicate both sequence structural and sRNA landscape variation. A synteny analysis shows that the sugarcane genome has expanded relative to the sorghum genome, largely due to the presence of transposable elements and uncharacterized intergenic and intronic sequences.Conclusion: This release of sugarcane genomic sequences will advance our understanding of sugarcane genetics and contribute to the development of molecular tools for breeding purposes and gene discovery. |
publishDate |
2014 |
dc.date.none.fl_str_mv |
2014-06-30 2015-03-18T15:55:48Z 2015-03-18T15:55:48Z |
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/10.1186/1471-2164-15-540 Bmc Genomics. London: Biomed Central Ltd, v. 15, 17 p., 2014. 1471-2164 http://hdl.handle.net/11449/117308 10.1186/1471-2164-15-540 WOS:000339583200001 WOS000339583200001.pdf |
url |
http://dx.doi.org/10.1186/1471-2164-15-540 http://hdl.handle.net/11449/117308 |
identifier_str_mv |
Bmc Genomics. London: Biomed Central Ltd, v. 15, 17 p., 2014. 1471-2164 10.1186/1471-2164-15-540 WOS:000339583200001 WOS000339583200001.pdf |
dc.language.iso.fl_str_mv |
eng |
language |
eng |
dc.relation.none.fl_str_mv |
Bmc Genomics 3.730 2,110 |
dc.rights.driver.fl_str_mv |
info:eu-repo/semantics/openAccess |
eu_rights_str_mv |
openAccess |
dc.format.none.fl_str_mv |
17 application/pdf |
dc.publisher.none.fl_str_mv |
Biomed Central Ltd |
publisher.none.fl_str_mv |
Biomed Central Ltd |
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 |
institution |
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 |
|
_version_ |
1797789389026230272 |