Please use this identifier to cite or link to this item: http://repositorio.unicamp.br/jspui/handle/REPOSIP/337424
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dc.contributor.CRUESPUNIVERSIDADE ESTADUAL DE CAMPINASpt_BR
dc.contributor.authorunicampNascimento, Leandro Costa do-
dc.contributor.authorunicampJosé, Juliana-
dc.contributor.authorunicampCamargo, Eduardo Leal Oliveira-
dc.contributor.authorunicampGrassi, Maria Carolina de Barros-
dc.contributor.authorunicampPereira, Gonçalo Amarante Guimarães-
dc.contributor.authorunicampCarazzolle, Marcelo Falsarella-
dc.typeArtigopt_BR
dc.titleUnraveling the complex genome of Saccharum spontaneum using Polyploid Gene Assemblerpt_BR
dc.contributor.authorNascimento, Leandro Costa-
dc.contributor.authorYanagui, Karina-
dc.contributor.authorJose, Juliana-
dc.contributor.authorCamargo, Eduardo L. O.-
dc.contributor.authorGrassi, Maria Carolina B.-
dc.contributor.authorCunha, Camila P.-
dc.contributor.authorBressiani, Jose Prime Antonio-
dc.contributor.authorCarvalho, Guilherme M. A.-
dc.contributor.authorCarvalho, Carlos Roberto-
dc.contributor.authorPrado, Paula F.-
dc.contributor.authorMieczkowski, Piotr-
dc.contributor.authorPereira, Goncalo A. G.-
dc.contributor.authorCarazzolle, Marcelo F.-
dc.subjectCana-de-açucarpt_BR
dc.subject.otherlanguageSugarcanept_BR
dc.description.abstractThe Polyploid Gene Assembler (PGA), developed and tested in this study, represents a new strategy to perform gene-space assembly from complex genomes using low coverage DNA sequencing. The pipeline integrates reference-assisted loci and de novo assembly strategies to construct high-quality sequences focused on gene content. Pipeline validation was conducted with wheat (Triticum aestivum), a hexaploid species, using barley (Hordeum vulgare) as reference, that resulted in the identification of more than 90% of genes and several new genes. Moreover, PGA was used to assemble gene content in Saccharum spontaneum species, a parental lineage for hybrid sugarcane cultivars. Saccharum spontaneum gene sequence obtained was used to reference-guided transcriptome analysis of six different tissues. A total of 39,234 genes were identified, 60.4% clustered into known grass gene families. Thirty-seven gene families were expanded when compared with other grasses, three of them highlighted by the number of gene copies potentially involved in initial development and stress response. In addition, 3,108 promoters (many showing tissue specificity) were identified in this work. In summary, PGA can reconstruct high-quality gene sequences from polyploid genomes, as shown for wheat and S. spontaneum species, and it is more efficient than conventional genome assemblers using low coverage DNA sequencingpt_BR
dc.relation.ispartofDNA Researchpt_BR
dc.publisher.cityOxfordpt_BR
dc.publisher.countryReino Unidopt_BR
dc.publisherOxford University Presspt_BR
dc.date.issued2019-
dc.date.monthofcirculationJunept_BR
dc.language.isoengpt_BR
dc.description.volume26pt_BR
dc.description.issuenumber3pt_BR
dc.description.firstpage205pt_BR
dc.description.lastpage216pt_BR
dc.rightsAbertopt_BR
dc.sourceWOSpt_BR
dc.identifier.issn1340-2838pt_BR
dc.identifier.eissn1756-1663pt_BR
dc.identifier.doi10.1093/dnares/dsz001pt_BR
dc.identifier.urlhttps://academic.oup.com/dnaresearch/article/26/3/205/5320315pt_BR
dc.description.sponsorshipCONSELHO NACIONAL DE DESENVOLVIMENTO CIENTÍFICO E TECNOLÓGICO - CNPQpt_BR
dc.description.sponsorshipFUNDAÇÃO DE AMPARO À PESQUISA DO ESTADO DE SÃO PAULO - FAPESPpt_BR
dc.description.sponsordocumentnumber350474/2013-3; 35081/2015-1pt_BR
dc.date.available2020-03-25T23:31:18Z-
dc.date.accessioned2020-03-25T23:31:18Z-
dc.description.provenanceSubmitted by Sanches Olivia (olivias@unicamp.br) on 2020-03-25T23:31:18Z No. of bitstreams: 0. Added 1 bitstream(s) on 2020-07-20T14:19:38Z : No. of bitstreams: 1 000493010500002.pdf: 938125 bytes, checksum: b3e466ba300bd76837be3b5e6202f64c (MD5)en
dc.description.provenanceMade available in DSpace on 2020-03-25T23:31:18Z (GMT). No. of bitstreams: 0 Previous issue date: 2019en
dc.identifier.urihttp://repositorio.unicamp.br/jspui/handle/REPOSIP/337424-
dc.contributor.departmentsem informaçãopt_BR
dc.contributor.departmentsem informaçãopt_BR
dc.contributor.departmentsem informaçãopt_BR
dc.contributor.departmentsem informaçãopt_BR
dc.contributor.departmentDepartamento de Genética, Evolução e Bioagentespt_BR
dc.contributor.departmentDepartamento de Genética, Evolução, Microbiologia e Imunologiapt_BR
dc.contributor.unidadeInstituto de Biologiapt_BR
dc.subject.keywordGenome assemblypt_BR
dc.subject.keywordTranscriptomept_BR
dc.subject.keywordGene discoverypt_BR
dc.subject.keywordNew assemblerpt_BR
dc.identifier.source000493010500002pt_BR
dc.creator.orcidsem informaçãopt_BR
dc.creator.orcid0000-0002-8259-6519pt_BR
dc.creator.orcid0000-0002-4762-1555pt_BR
dc.creator.orcid0000-0001-5516-0851pt_BR
dc.creator.orcid0000-0003-4140-3482pt_BR
dc.creator.orcid0000-0002-5474-2830pt_BR
dc.type.formArtigopt_BR
dc.description.sponsorNote2014/09638-0; 2012/05890-1; 2013/08293-7pt_BR
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