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(Reference retrieved automatically from Web of Science through information on FAPESP grant and its corresponding number as mentioned in the publication by the authors.)

Unraveling the complex genome of Saccharum spontaneum using Polyploid Gene Assembler

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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]
Total Authors: 13
[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
Total Affiliations: 6
Document type: Journal article
Source: DNA Research; v. 26, n. 3, p. 205-216, JUN 2019.
Web of Science Citations: 1

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)

FAPESP's process: 13/08293-7 - CCES - Center for Computational Engineering and Sciences
Grantee:Munir Salomao Skaf
Support Opportunities: Research Grants - Research, Innovation and Dissemination Centers - RIDC
FAPESP's process: 14/09638-0 - Assemblage and comparative analysis of phytopathogenic fungi genomes of Moniliophthora (Agaricales, Basidiomycota) obtained by large-scale sequencing using high-performance computational methods
Grantee:Juliana José
Support Opportunities: Scholarships in Brazil - Post-Doctoral
FAPESP's process: 12/05890-1 - Saccharum spontaneum genome for development of energy cane
Grantee:Karina Yanagui de Almeida
Support Opportunities: Scholarships in Brazil - Doctorate