Montagem e caracterização do transcritoma de cana-de-açúcar (saccharum spp.) utilizando dados de sequenciamento de nova geração

• Autor(a) principal: Melo, Arthur Tavares de Oliveira
• Data de Publicação: 2015
• Tipo de documento: Tese
• Idioma: por
• Título da fonte: Repositório Institucional da UFG
• Texto Completo: http://repositorio.bc.ufg.br/tede/handle/tede/4783
• topic: Saccharum spp.; Transcritoma; Trinity; RNA-seq; Saccharum spp.; Transcriptome; RNA-seq; Trinity; CIENCIAS AGRARIAS::AGRONOMIA

The sugarcane is one of the most important crop species to provide sugar and renewable energy in the world. Due to the high amount of repetitive elements and the various polyploidization events suffer during its evolution, the Saccharum spp. genome has not yet been assembled and annotated, unlike other agronomic important species. So, the knowledge about sugarcane transcriptome become even more useful for supporting genomic analyzes studies. A draft assembly of sugarcane transcriptome was obtained from Illumina sequencing paired-ends libraries of five different plant organs, sampled from thirty elite clones. Analyzes of quality control and normalization was done in the RNA-seq data. Trinity package was used for de novo assembly. The scaffolds obtained and identified as complete ORFs were annotated according to Gene Ontology terms. The draft assembly was characterized by the identification of microsatellites and SNPs molecular markers and for assessing the contribution of different plant organs for transcriptome final assembly. The draft sugarcane transcriptome comprised 178 Mb, over 131,831 scaffolds, representing 61,225 genes. The transcripts average size was 1,350 bp and N50 value was 1,667 bp. A total of 1,250 transcripts identified as complete ORFs showed no similarity to sequences of the nr NCBI database, are considered new Transcript Active Regions (nTARs). The annotation performed using the KEGG database identified 234 transcripts coding for enzymes members of sucrose and starch metabolism, an important metabolic pathway for understanding the relationship between photosynthetic rate and sucrose accumulation in the stalk. The five plant organs used contributed equally for the draft sugarcane transcriptome. A total of 12,931 genomic regions were identified containing perfect microsatellites, with a predominance of di and tri nucleotide. On average, one SNP every 18 bp was identified, with more than four million SNPs identified with satisfactory values of haplotype and quality scores. The nucleotide diversity of thirty elite clones used in this study was high. The identification of these molecular markers, particularly SNPs markers, provides the possibility of using these polymorphisms in genomic and genetic studies of sugarcane, including the possibility of application of genome wide selection like breeding strategy. The sugarcane transcriptome draft assembly proposed in this study has data and analysis quality sufficient to be used in attempt to encompass a reference transcriptome for the species of Saccharum spp.