title: Analysis of Three Sugarcane Homo/Homeologous Regions Suggests Independent Polyploidization Events of Saccharum officinarum and Saccharum spontaneum.
abstract: Whole genome duplication has played an important role in plant evolution and diversification. Sugarcane is an important crop with a complex hybrid polyploid genome, for which the process of adaptation to polyploidy is still poorly understood. In order to improve our knowledge about sugarcane genome evolution and the homo/homeologous gene expression balance, we sequenced and analyzed 27 BACs (Bacterial Artificial Chromosome) of sugarcane R570 cultivar, containing the putative single-copy genes LFY (seven haplotypes), PHYC (four haplotypes), and TOR (seven haplotypes). Comparative genomic approaches showed that these sugarcane loci presented a high degree of conservation of gene content and collinearity (synteny) with sorghum and rice orthologous regions, but were invaded by transposable elements (TE). All the homo/homeologous haplotypes of LFY, PHYC, and TOR are likely to be functional, because they are all under purifying selection (dN/dS ≪ 1). However, they were found to participate in a nonequivalently manner to the overall expression of the corresponding gene. SNPs, indels, and amino acid substitutions allowed inferring the S. officinarum or S. spontaneum origin of the TOR haplotypes, which further led to the estimation that these two sugarcane ancestral species diverged between 2.5 and 3.5 Ma. In addition, analysis of shared TE insertions in TOR haplotypes suggested that two autopolyploidization may have occurred in the lineage that gave rise to S. officinarum, after its divergence from S. spontaneum.
authors.affiliation: Centro de Biologia Molecular e Engenharia Genética, Departamento de Biologia Vegetal, Instituto de Biologia, Universidade Estadual de Campinas, Campinas, SP, Brazil.
authors.forename: Mariane de Mendonça
authors.initials: MM
authors.lastname: Vilela
authors.affiliation: Centro de Biologia Molecular e Engenharia Genética, Departamento de Biologia Vegetal, Instituto de Biologia, Universidade Estadual de Campinas, Campinas, SP, Brazil.
authors.forename: Luiz Eduardo
authors.initials: LE
authors.lastname: Del Bem
authors.affiliation: Departamento de Botânica, Instituto de Biociências, Universidade de São Paulo, SP, Brazil.
authors.forename: Marie-Anne
authors.initials: MA
authors.lastname: Van Sluys
authors.affiliation: Universidade Federal do ABC (UFABC), São Bernardo do Campo, SP, Brazil.
authors.forename: Nathalia
authors.initials: N
authors.lastname: de Setta
authors.affiliation: Mendelics Análise Genômica SA, São Paulo, SP, Brazil.
authors.forename: João Paulo
authors.initials: JP
authors.lastname: Kitajima
authors.affiliation: Departamento de Botânica, Instituto de Biociências, Universidade de São Paulo, SP, Brazil.
authors.forename: Guilherme Marcelo Queiroga
authors.initials: GM
authors.lastname: Cruz
authors.affiliation: Centro de Biologia Molecular e Engenharia Genética, Departamento de Biologia Vegetal, Instituto de Biologia, Universidade Estadual de Campinas, Campinas, SP, Brazil.
authors.forename: Danilo Augusto
authors.initials: DA
authors.lastname: Sforça
authors.affiliation: Centro de Biologia Molecular e Engenharia Genética, Departamento de Biologia Vegetal, Instituto de Biologia, Universidade Estadual de Campinas, Campinas, SP, Brazil.
authors.forename: Anete Pereira
authors.initials: AP
authors.lastname: de Souza
authors.affiliation: Universidade Federal do Rio de Janeiro, RJ, Brazil.
authors.forename: Paulo Cavalcanti Gomes
authors.initials: PC
authors.lastname: Ferreira
authors.affiliation: Laboratório de Química e Função de Proteínas e Peptídeos, Centro de Biociências e Biotecnologia, Universidade Estadual do Norte Fluminense Darcy Ribeiro, Parque Califórnia, Campos dos Goytacazes, RJ, Brazil.
authors.forename: Clícia
authors.initials: C
authors.lastname: Grativol
authors.affiliation: Centro de Biologia Molecular e Engenharia Genética, Departamento de Biologia Vegetal, Instituto de Biologia, Universidade Estadual de Campinas, Campinas, SP, Brazil.
authors.forename: Claudio Benicio
authors.initials: CB
authors.lastname: Cardoso-Silva
authors.affiliation: Centro de Biologia Molecular e Engenharia Genética, Departamento de Biologia Vegetal, Instituto de Biologia, Universidade Estadual de Campinas, Campinas, SP, Brazil.
authors.forename: Renato
authors.initials: R
authors.lastname: Vicentini
authors.affiliation: Centro de Biologia Molecular e Engenharia Genética, Departamento de Biologia Vegetal, Instituto de Biologia, Universidade Estadual de Campinas, Campinas, SP, Brazil.
authors.forename: Michel
authors.initials: M
authors.lastname: Vincentz
mesh_terms: D004251:DNA Transposable Elements; D017343:Genes, Plant; D006239:Haplotypes; D010940:Plant Proteins / Q000235:genetics; D011110:Polymorphism, Genetic; D011123:Polyploidy; D031786:Saccharum / Q000145:classification / Q000235:genetics*; D012641:Selection, Genetic; D026801:Synteny
chemical_list: D004251:DNA Transposable Elements; D010940:Plant Proteins
keywords: R570; autopolyploidization; genome evolution; homo/homeologues expression; sugarcane