High-throughput transcriptome analysis and marker discovery in four tropical tree species.
The Amazonian rainforest is predicted to be deeply impacted by ongoing environmental changes. While evaluating the impact of such changes on tropical trees genetic diversity is being crucial, a serious lack of genetic resources need to be overridden.  In this study, we analyze the transcriptome of four widespread tropical tree genera (Carapa, Eperua, Symphonia and Virola) exhibiting contrasted ecological features. We sequenced cDNA libraries from three organs (leaves, stems, and roots) using 454-pyrosequencing.  We followed a comprehensive bioinformatic procedure including de novo assembly, gene identification, and marker discovery (SSRs and SNPs). From 17103 (for Symphonia globulifera) to 23390 (for Eperua falcata) contigs involved in various biological processes were assembled. Transcriptome profiles show strong divergence between genera while little variation is depicted between organs. We highlight from1837 (for Symphonia globulifera) to 3696 (for Carapa guianensis) high quality SNPs and from 448 (for Eperua falcata) and 1793 SSRs (for Virola surinamensis). The resulting SNP density calculated around 2.10-3 is consistent with those observed in other tree species.  Some of those thousands of newly identified genes become available to accurately investigate the drivers of populations’ evolution and fill in the lack of indispensable genomic data in tropical trees.