Montagem e análise do transcritoma do mogno africano (Khaya grandifoliola C. DC.)

• Autor(a) principal: Soares, Sabrina Delgado
• Data de Publicação: 2019
• Tipo de documento: Tese
• Idioma: por
• Título da fonte: Repositório Institucional da UFG
• Texto Completo: http://repositorio.bc.ufg.br/tede/handle/tede/13002
• topic: Montagem de novo; RNA-seq; Bioinformática; Madeira nobre; De novo assembly; RNA-seq; Bioinformatics; High-value wood; CIENCIAS BIOLOGICAS::GENETICA

Khaya grandifoliola C. DC. is a tropical species with high value wood in international markets. Despite the high interest for reforestation and timber production, virtually nothing is known about the genetic and genomic aspects of the species. With the development of next-generation sequencing platforms (NGS), the characterization of transcriptomes can be performed on a large scale and at affordable cost. In this context, the objective of the work was to discover K. grandifoliola genes by using RNA-Seq technique and to identify those differentially expressed between the leaf and the xylem K. grandifoliola tissues. Total RNA was extracted from leaf and xylem samples of four trees planted in the experimental area of the UFG. mRNA samples were sequenced on the Illumina HiSeq 2000 platform, in paired-end mode 2 × 100 bp. Sequencing resulted in a total of 857 million sequences which, after quality control, decreased to 808 million with an average size of 24 to 85 bp. Trinity program was used to reassemble the transcriptome, obtaining 116,289 transcripts for a total of 36,271 genes. Transcripts ranged from 524 to 12,031 bp with a mean of 1,366 bp and N50 of 1,657 bp. Analyses of gene expression identified 13,626 differentially expressed genes (DEGs) (FDR <0.05) between the two tissues. Of these, 5,438 had higher expression in leaves and 8,188 in xylem. A functional enrichment analysis of Gene Ontology categories among the DEGs was performed by the Blast2GO program. This analysis identified 26 GO terms enriched among the most active DEGs in xylem. Among genes up-regulated in leaves, 48 enriched terms were found. As expected, the categories identified as enriched between DGEs point to biological processes and cellular components specific of each tissue. For example, among the most active genes in leaf tissue, terms associated with thylakoids (GO:0009579), plastids (GO:0009536) and photosynthesis (GO:0015979) were identified. On the other hand, for the xylem, terms related to carbohydrate metabolism (GO:0005975), cell wall (GO:0071554) and cytoskeletal proteins (GO:0008092) were significantly enriched. To the best of our knowledge, this is the first report of large-scale gene sequences for K. grandifoliola. Differential expression analysis allowed us to identify which genes are most active in leaf and xylem. Analysis in iPath3 identified the metabolic routes activated in leaf and xylem tissues. A BlastX search against the orange proteome (Citrus sinensis) revealed the presence of 95 DEGs annotated for the enzymes of the limonoid, a secondary metabolite with medicinal properties.