Analysis of Three Sugarcane Homo/Homeologous Regions Suggests Independent Polyploidization Events of Saccharum officinarum and Saccharum spontaneum
| Autor: | Paulo Cavalcanti Gomes Ferreira, Danilo Augusto Sforça, João Paulo Kitajima, Mariane de Mendonça Vilela, Renato Vicentini, Clícia Grativol, Claudio Benicio Cardoso-Silva, Nathalia de Setta, Michel Vincentz, Anete Pereira de Souza, Luiz Eduardo Vieira Del Bem, Marie-Anne Van Sluys, Guilherme M. Q. Cruz |
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| Rok vydání: | 2017 |
| Předmět: |
0301 basic medicine
Genome evolution genome evolution Genes Plant Synteny Genome homo/homeologues expression Polyploidy 03 medical and health sciences Polyploid Saccharum officinarum sugarcane Botany Genetics Selection Genetic Gene Ecology Evolution Behavior and Systematics Plant Proteins Polymorphism Genetic biology autopolyploidization Saccharum spontaneum Haplotype food and beverages biology.organism_classification Saccharum 030104 developmental biology Haplotypes EVOLUÇÃO DNA Transposable Elements R570 Research Article |
| Zdroj: | Repositório Institucional da USP (Biblioteca Digital da Produção Intelectual) Universidade de São Paulo (USP) instacron:USP Genome Biology and Evolution |
| Popis: | 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. |
| Databáze: | OpenAIRE |
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