Unraveling the complex genome of Saccharum spontaneum using Polyploid Gene Assembler

Autor(es):Mostrar menos -

Nascimento, Leandro Costa ^{[1, 2]} ; Yanagui, Karina ^[1] ; Jose, Juliana ^[1] ; Camargo, Eduardo L. O. ^{[1, 3]} ; Grassi, Maria Carolina B. ^[1] ; Cunha, Camila P. ^[4] ; Bressiani, Jose Prime Antonio ^[3] ; Carvalho, Guilherme M. A. ^[5] ; Carvalho, Carlos Roberto ^[5] ; Prado, Paula F. ^[1] ; Mieczkowski, Piotr ^[6] ; Pereira, Goncalo A. G. ^[1] ; Carazzolle, Marcelo F. ^[1]

Afiliação do(s) autor(es)

^[1] Univ Estadual Campinas, Inst Biol, Dept Genet Evolucao Microbiol & Imunol, LGE, Campinas, SP - Brazil

^[2] Univ Estadual Campinas, Lab Cent Tecnol Alto Desempenho LaCTAD, Campinas, SP - Brazil

^[3] GranBio Investimentos SA, Biocelere Agroind Ltda, Campinas, SP - Brazil

^[4] CNPEM, Lab Nacl Ciencia & Tecnol Bioetanol CTBE, Campinas, SP - Brazil

^[5] Univ Fed Vicosa, Dept Biol Geral, Lab Citogenet & Citometria, Vicosa, MG - Brazil

^[6] Univ N Carolina, Dept Genet, Chapel Hill, NC 27515 - USA

• Tipo de documento: Artigo Científico
• Fonte: DNA Research; v. 26, n. 3, p. 205-216, JUN 2019.
• Citações Web of Science: 1

Resumo

The 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 sequencing. (AU)

• Processo FAPESP: 13/08293-7 - CECC - Centro de Engenharia e Ciências Computacionais
• Beneficiário: Munir Salomao Skaf
• Modalidade de apoio: Auxílio à Pesquisa - Centros de Pesquisa, Inovação e Difusão - CEPIDs
• Processo FAPESP: 14/09638-0 - Montagem e análises comparativas de genomas dos fungos fitopatógenos Moniliophthora (Agaricales, Basidiomycota) obtidos por sequenciamento de larga escala, usando métodos computacionais de alta performance
• Beneficiário: Juliana José
• Modalidade de apoio: Bolsas no Brasil - Pós-Doutorado
• Processo FAPESP: 12/05890-1 - Genoma de Saccharum spontaneum para o desenvolvimento da cana energia
• Beneficiário: Karina Yanagui de Almeida
• Modalidade de apoio: Bolsas no Brasil - Doutorado