Can Agroforestry Reproduce the Diversity of a Natural Forest? a Comparative Transcriptome Analysis of a Non-Model Tree from Brazilian Atlantic Forest

Agroforestry systems offer a possible solution for the responsible use of the environment by agricultural crop cultivation in natural forests. Such systems favor crop diversification, soil nutrients recycling, maintenance of ecological corridors and biodiversity preservation. However, understanding the impact of agronomic activities on natural forest species is critical to manage the two components of agroforestry systems efficiently. Here we investigated the transcriptome variation in populations of the economically and ecologically important tree Carpotroche brasiliensis, established in an agroforestry system and a natural forest. This non-model tree species is a nutritional resource for mammals due to its large rich-oilseeds fruits, but it also important for pharmaceutical and cosmetic industries due to the therapeutic properties of its oil. We developed six cDNA libraries from leaves of C. brasiliensis grown in a natural forest, and in an agroforestry system. A de novo transcriptome assembly was performed by high throughput RNA sequencing using the MiSeq Illumina Plataform (2x250bp), followed by analysis in the Trinity pipeline. A total of 126.455.482 bases were assembled into 186.722 unigenes, with a mean length of 359 bases. The comparative analysis of gene expression between C. brasiliensis populations from natural forests or agroforestry was performed using edgeR, and resulted in the detection of 153 unigenes differentially represented. These results contribute to our understanding of the impact of agroforestry to the genome of native, non-model tree species. Moreover our findings are strategic for the comprehension that under transcriptome analysis the agroforestry is not significantly differently from that of natural population.