Assembly of the 373k gene space of the polyploid sugarcane genome reveals reservoirs of functional diversity in the world's leading biomass crop

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dc.contributorLaboratório Especial de Toxinologia Aplicada (LETA)pt_BR
dc.contributor.authorSouza, Glaucia Mendespt_BR
dc.contributor.authorVan Sluys, Marie-Annept_BR
dc.contributor.authorLembke, Carolina Gimilianipt_BR
dc.contributor.authorLee, Hayanpt_BR
dc.contributor.authorMargarido, Gabriel Rodrigues Alvespt_BR
dc.contributor.authorHotta, Carlos Takeshipt_BR
dc.contributor.authorGaiarsa, Jonas Weissmannpt_BR
dc.contributor.authorDiniz, Augusto Limapt_BR
dc.contributor.authorOliveira, Mauro de Medeirospt_BR
dc.contributor.authorFerreira, Sávio de Siqueirapt_BR
dc.contributor.authorNishiyama Junior, Milton Yutakapt_BR
dc.contributor.authorten-Caten, Felipept_BR
dc.contributor.authorRagagnin, Geovani Tolfopt_BR
dc.contributor.authorAndrade, Pablo de Moraispt_BR
dc.contributor.authorSouza, Robson Francisco dept_BR
dc.contributor.authorNicastro, Gianlucca Gonçalvespt_BR
dc.contributor.authorPandya, Ravipt_BR
dc.contributor.authorKim, Changsoopt_BR
dc.contributor.authorGuo, Huipt_BR
dc.contributor.authorDurham, Alan Mitchellpt_BR
dc.contributor.authorCarneiro, Monalisa Sampaiopt_BR
dc.contributor.authorZhang, Jisenpt_BR
dc.contributor.authorZhang, Xingtanpt_BR
dc.contributor.authorZhang, Qingpt_BR
dc.contributor.authorMing, Raypt_BR
dc.contributor.authorSchatz, Michael Cpt_BR
dc.contributor.authorDavidson, Bobpt_BR
dc.contributor.authorPaterson, Andrew Hpt_BR
dc.contributor.authorHeckerman, Davidpt_BR
dc.date.accessioned2020-07-09T21:25:39Z-
dc.date.available2020-07-09T21:25:39Z-
dc.date.issued2019-
dc.identifier.citationSouza GM, Van Sluys M-A, Lembke CG, Lee H, Margarido GRA, Hotta CT, et al. Assembly of the 373k gene space of the polyploid sugarcane genome reveals reservoirs of functional diversity in the world's leading biomass crop. Gigascience. 2019 Nov;8(12):1-18. doi:10.1093/gigascience/giz129.pt_BR
dc.identifier.issn2047-217X-
dc.identifier.urihttps://repositorio.butantan.gov.br/handle/butantan/2873-
dc.description.abstractBackground: Sugarcane cultivars are polyploid interspecific hybrids of giant genomes, typically with 10–13 sets of chromosomes from 2 Saccharum species. The ploidy, hybridity, and size of the genome, estimated to have >10 Gb, pose a challenge for sequencing. Results: Here we present a gene space assembly of SP80-3280, including 373,869 putative genes and their potential regulatory regions. The alignment of single-copy genes in diploid grasses to the putative genes indicates that we could resolve 2–6 (up to 15) putative homo(eo)logs that are 99.1% identical within their coding sequences. Dissimilarities increase in their regulatory regions, and gene promoter analysis shows differences in regulatory elements within gene families that are expressed in a species-specific manner. We exemplify these differences for sucrose synthase (SuSy) and phenylalanine ammonia-lyase (PAL), 2 gene families central to carbon partitioning. SP80-3280 has particular regulatory elements involved in sucrose synthesis not found in the ancestor Saccharum spontaneum. PAL regulatory elements are found in co-expressed genes related to fiber synthesis within gene networks defined during plant growth and maturation. Comparison with sorghum reveals predominantly bi-allelic variations in sugarcane, consistent with the formation of 2 "subgenomes" after their divergence ~3.8–4.6 million years ago and reveals single-nucleotide variants that may underlie their differences. Conclusions: This assembly represents a large step towards a whole-genome assembly of a commercial sugarcane cultivar. It includes a rich diversity of genes and homo(eo)logous resolution for a representative fraction of the gene space, relevant to improve biomass and food production.pt_BR
dc.description.sponsorshipFundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)pt_BR
dc.description.sponsorshipNational Science Foundation (NSF)pt_BR
dc.description.sponsorshipNational Institutes of Health (NIH)pt_BR
dc.description.sponsorshipConselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)pt_BR
dc.description.sponsorshipCoordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)pt_BR
dc.format.extent1-18pt_BR
dc.languageengpt_BR
dc.publisherBioMed Centralpt_BR
dc.relation.ispartofGigaSciencept_BR
dc.rightsOpen Accesspt_BR
dc.titleAssembly of the 373k gene space of the polyploid sugarcane genome reveals reservoirs of functional diversity in the world's leading biomass croppt_BR
dc.typeArticlept_BR
dc.identifier.doi10.1093/gigascience/giz129pt_BR
dc.identifier.urlhttps://doi.org/10.1093/gigascience/giz129pt_BR
dc.contributor.externalUniversidade de São Paulo (USP)¦¦Brasilpt_BR
dc.contributor.externalJoint Genome Institute¦¦Estados Unidospt_BR
dc.contributor.externalMicrosoft Redmond campus¦¦Estados Unidospt_BR
dc.contributor.externalChungnam National University¦¦Coréia do Sulpt_BR
dc.contributor.externalUniversity of Georgia¦¦Estados Unidospt_BR
dc.contributor.externalUniversidade Federal de São Carlos (UFSCar)¦¦Brasilpt_BR
dc.contributor.externalFujian Agriculture and Forestry University¦¦Chinapt_BR
dc.contributor.externalUniversity of Illinois at Urbana-Champaign¦¦Estados Unidospt_BR
dc.contributor.externalJohns Hopkins University (JHU)¦¦Estados Unidospt_BR
dc.publisher.cityLondonpt_BR
dc.identifier.citationvolume8pt_BR
dc.identifier.citationissue12pt_BR
dc.subject.keywordallelept_BR
dc.subject.keywordbioenergypt_BR
dc.subject.keywordbiomasspt_BR
dc.subject.keywordgenomept_BR
dc.subject.keywordpolyploidpt_BR
dc.relation.ispartofabbreviatedGigasciencept_BR
dc.identifier.citationabntv. 8, n. 12, p. 1-18, nov. 2019pt_BR
dc.identifier.citationvancouver2019 Nov;8(12):1-18pt_BR
dc.publisher.countryEnglandpt_BR
dc.contributor.butantanNishiyama Junior, Milton Yutaka|:Pesquisador|:Laboratório Especial de Toxinologia Aplicada (LETA)|:pt_BR
dc.sponsorship.butantanConselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)¦¦304 360/2014–7pt_BR
dc.sponsorship.butantanConselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)¦¦308 197/2010–0pt_BR
dc.sponsorship.butantanConselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)¦¦159094/2014–3pt_BR
dc.sponsorship.butantanConselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)¦¦309566/2015–0pt_BR
dc.sponsorship.butantanCoordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)¦¦454337pt_BR
dc.sponsorship.butantanFundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)¦¦2012/51062–3pt_BR
dc.sponsorship.butantanFundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)¦¦2016/17545-8pt_BR
dc.sponsorship.butantanFundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)¦¦2014/50921-8pt_BR
dc.sponsorship.butantanFundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)¦¦2008/52146-0pt_BR
dc.sponsorship.butantanFundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)¦¦2008/52074-0pt_BR
dc.sponsorship.butantanFundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)¦¦2011/50761–2pt_BR
dc.sponsorship.butantanFundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)¦¦2015/22993–7pt_BR
dc.sponsorship.butantanFundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)¦¦2013/18322–4pt_BR
dc.sponsorship.butantanFundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)¦¦2015/15346–5pt_BR
dc.sponsorship.butantanFundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)¦¦2017/02270–6pt_BR
dc.sponsorship.butantanFundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)¦¦2013/23048–9pt_BR
dc.sponsorship.butantanFundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)¦¦2016/06917–1pt_BR
dc.sponsorship.butantanFundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)¦¦2013/07467–1pt_BR
dc.sponsorship.butantanFundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)¦¦2017/02842–0pt_BR
dc.sponsorship.butantanFundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)¦¦pt_BR
dc.sponsorship.butantanNational Institutes of Health (NIH)¦¦R01-HG006677pt_BR
dc.sponsorship.butantanNational Science Foundation (NSF)¦¦1350041pt_BR
dc.sponsorship.butantanNational Science Foundation (NSF)¦¦0115903pt_BR
dc.identifier.bvsccBR78.1pt_BR
dc.identifier.bvsdbIBProdpt_BR
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