Transcriptome Assembly and Differentially Expressed Genes Between Males and Females in Carpotroche brasiliensis

RNA sequencing of transcriptomes is a low-cost strategy to characterize the functional component of a species genome. When applied to non-model organisms, sequencing of the transcriptome can provide insights about genes and polymorphisms that regulate relevant phenotypic characteristics. Carpotroche brasiliensis is an oleaginous species grown in agroforestry systems in Brazil, offering a range of economic and ecosystem services. Due to its dioecious nature, productive individuals can be identified as breeding stock when plants develop flowers. The main objective of this research is to develop methods for early selection of male and female C. brasiliensis seedlings. To achieve this goal we carried out a transcriptome assembly and identified genes differentially expressed between males and females in reproductive and vegetative tissue. cDNA libraries were constructed from six different tissues collected from 24 trees, to obtain RNA sequences. A total of 1,075,311 paired-end reads with average length of 345.26 bp were assembled into 986,255 unigenes. We found 19,294 putative genes matching the Arabidopsis thaliana transcriptome database, which were annotated in 33 functional Gene Ontology terms. Among these putative genes, 832 are classified as belonging to reproductive processes. The analysis from female tissue identified 4.8% of putative genes related with reproduction function, from a total of 6,638 unigenes. From male tissue we obtained 4.5% of 17,362 unigenes related with reproduction process. These genes were selected for design of sequence-capture probes that will be used for polymorphisms identification that differentiate male and female plants, to be used in a pre-breeding program of C. braziliensis.