High-throughput gene and SNP discovery in ucalyptus grandis, an uncharacterized genome

• Autor(a) principal: Novaes, Evandro
• Data de Publicação: 2008
• Outros Autores: Drost, Derek R., Farmerie, William G., Pappas Júnior, Georgios J., Grattapaglia, Dario, Sederoff, Ronald R., Kirst, Matias
• Tipo de documento: Artigo
• Idioma: eng
• Título da fonte: Repositório Institucional da UCB
• Texto Completo: http://twingo.ucb.br:8080/jspui/handle/10869/475; https://repositorio.ucb.br:9443/jspui/handle/123456789/7675
• topic: Eucalyptus; EST; Genolyptus; Sequenciamento de EST; Single Feature Polymorphism; SNPs

With the purpose of generating the first broad survey of gene sequences in Eucalyptus grandis, the most widely planted hardwood tree species, we used 454 technology to sequence and assemble 148 Mbp of expressed sequences (EST). EST sequences were generated from a normalized cDNA pool comprised of multiple tissues and genotypes, promoting discovery of homologues to almost half of Arabidopsis genes, and a comprehensive survey of allelic variation in the transcriptome. By aligning the sequencing reads from multiple genotypes we detected 23,742 SNPs, 83% of which were validated in a sample. Genome-wide nucleotide diversity was estimated for 2,392 contigs using a modified theta () parameter, adapted for measuring genetic diversity from polymorphisms detected by randomly sequencing a multigenotype cDNA pool. Diversity estimates in non-synonymous nucleotides were on average 4x smaller than in synonymous, suggesting purifying selection. Non-synonymous to synonymous substitutions (Ka/Ks) among 2,001 contigs averaged 0.30 and was skewed to the right, further supporting that most genes are under purifying selection. Comparison of these estimates among contigs identified major functional classes of genes under purifying and diversifying selection in agreement with previous researches.