Abstract
BackgroundThe Amazonian rainforest is predicted to suffer from ongoing environmental changes. Despite the need to evaluate the impact of such changes on tree genetic diversity, we almost entirely lack genomic resources.ResultsIn this study, we analysed the transcriptome of four tropical tree species (Carapa guianensis, Eperua falcata, Symphonia globulifera and Virola michelii) with contrasting ecological features, belonging to four widespread botanical families (respectively Meliaceae, Fabaceae, Clusiaceae and Myristicaceae). We sequenced cDNA libraries from three organs (leaves, stems, and roots) using 454 pyrosequencing. We have developed an R and bioperl-based bioinformatic procedure for de novo assembly, gene functional annotation and marker discovery. Mismatch identification takes into account single-base quality values as well as the likelihood of false variants as a function of contig depth and number of sequenced chromosomes. Between 17103 (for Symphonia globulifera) and 23390 (for Eperua falcata) contigs were assembled. Organs varied in the numbers of unigenes they apparently express, with higher number in roots. Patterns of gene expression were similar across species, with metabolism of aromatic compounds standing out as an overrepresented gene function. Transcripts corresponding to several gene functions were found to be over- or underrepresented in each organ. We identified between 4434 (for Symphonia globulifera) and 9076 (for Virola surinamensis) well-supported mismatches. The resulting overall mismatch density was comprised between 0.89 (S. globulifera) and 1.05 (V. surinamensis) mismatches/100 bp in variation-containing contigs.ConclusionThe relative representation of gene functions in the four transcriptomes suggests that secondary metabolism may be particularly important in tropical trees. The differential representation of transcripts among tissues suggests differential gene expression, which opens the way to functional studies in these non-model, ecologically important species. We found substantial amounts of mismatches in the four species. These newly identified putative variants are a first step towards acquiring much needed genomic resources for tropical tree species.Electronic supplementary materialThe online version of this article (doi:10.1186/1471-2164-15-238) contains supplementary material, which is available to authorized users.
Highlights
The Amazonian rainforest is predicted to suffer from ongoing environmental changes
Sequence data were obtained from all tissues and species except S. globulifera, for which root cDNA sequencing failed
More reads were associated with roots than with stems or leaves (Table 2). This is in agreement with the higher levels of gene expression which were found in the roots compared to other organs in model species such as Arabidopsis thaliana [58]
Summary
The Amazonian rainforest is predicted to suffer from ongoing environmental changes. The Amazonian rainforest hosts one of the greatest pools of terrestrial biodiversity, including very large tree species diversity [1,2,3]. While ongoing anthropogenic climate change is suspected to deeply affect the stability of Neotropical rainforests [4], tropical tree species genetic resources and adaptive potential are. A thorough assessment of tropical tree species’ genetic diversity requires large amounts of genomic data and informative molecular markers [11,12]. High-throughput sequencing and genotyping methods have paved the way to genomic studies in non-model species [14,18,19], by permitting cost-effective sequencing and the generation of very large genetic data collections. Transcriptomes include a large number of loci with known or predictable functions [22,23] and have been applied to comparative genomics [24], marker discovery [25], and population genomic studies [26]
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