DNA Research, 2019, 26(3), 205–216 doi: 10.1093/dnares/dsz001 Advance Access Publication Date: 14 February 2019 Full Paper Full Paper Unraveling the complex genome of Saccharum spontaneum using Polyploid Gene Assembler Leandro Costa Nascimento1,2, Karina Yanagui1, Juliana Jose1, Eduardo L. O. Camargo1,3, Maria Carolina B. Grassi1, Camila P. Cunha4, Jose´ Antonio Bressiani3, Guilherme M. A. Carvalho5, Carlos Roberto Carvalho5, Paula F. Prado1, Piotr Mieczkowski6, Gonc¸alo A. G. Pereira1*, and Marcelo F. Carazzolle1 1Laborato´rio de Genoˆmica e bioEnergia (LGE), Departamento de Gene´tica, Evoluc¸ao,~ Microbiologia e Imunologia, Instituto de Biologia, Universidade Estadual de Campinas, Campinas, SP, Brazil, 2Laborato´rio Central de Tecnologias de Alto Desempenho (LaCTAD), Universidade Estadual de Campinas, Campinas, SP, Brazil, 3Biocelere Agroindustrial Ltda, GranBio Investimentos S.A., Campinas, SP, Brazil, 4Laborato´rio Nacional de Cieˆncia e Tecnologia do Bioetanol (CTBE), Centro Nacional de Pesquisas em Energia e Materiais (CNPEM), Campinas, SP, Brazil, 5Laborato´rio de Citogene´tica e Citometria, Departamento de Biologia Geral, Universidade Federal de Vic¸osa, Vic¸osa, MG, Brazil, and 6Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA *To whom correspondence should be addressed. Tel. þ55 19 3521 6237. Fax. þ55 19 3521 6185. Email:
[email protected] Edited by Prof. Kazuhiro Sato Received 22 October 2018; Editorial decision 10 January 2019; Accepted 21 January 2019 Abstract 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 se- quencing. The pipeline integrates reference-assisted loci and de novo assembly strategies to construct high-quality sequences focused on gene content.