Abstract
BackgroundThe species of Utricularia attract attention not only owing to their carnivorous lifestyle, but also due to an elevated substitution rate and a dynamic evolution of genome size leading to its dramatic reduction. To better understand the evolutionary dynamics of genome size and content as well as the great physiological plasticity in this mostly aquatic carnivorous genus, we analyzed the transcriptome of Utricularia vulgaris, a temperate species with well characterized physiology and ecology. We compared its transcriptome, namely gene content and overall transcript profile, with a previously described transcriptome of Utricularia gibba, a congener possessing one of the smallest angiosperm genomes.ResultsWe sequenced a normalized cDNA library prepared from total RNA extracted from shoots of U. vulgaris including leaves and traps, cultivated under sterile or outdoor conditions. 454 pyrosequencing resulted in more than 1,400,000 reads which were assembled into 41,407 isotigs in 19,522 isogroups. We observed high transcript variation in several isogroups explained by multiple loci and/or alternative splicing. The comparison of U. vulgaris and U. gibba transcriptomes revealed a similar distribution of GO categories among expressed genes, despite the differences in transcriptome preparation. We also found a strong correspondence in the presence or absence of root-associated genes between the U. vulgaris transcriptome and U. gibba genome, which indicated that the loss of some root-specific genes had occurred before the divergence of the two rootless species.ConclusionsThe species-rich genus Utricularia offers a unique opportunity to study adaptations related to the environment and carnivorous habit and also evolutionary processes responsible for considerable genome reduction. We show that a transcriptome may approximate the genome for gene content or gene duplication estimation. Our study is the first comparison of two global sequence data sets in Utricularia.Electronic supplementary materialThe online version of this article (doi:10.1186/s12870-015-0467-8) contains supplementary material, which is available to authorized users.
Highlights
The species of Utricularia attract attention owing to their carnivorous lifestyle, and due to an elevated substitution rate and a dynamic evolution of genome size leading to its dramatic reduction
To facilitate the comparison between our data and the U. gibba transcriptome published by [12], raw reads of U. gibba were downloaded from DNA Data Bank of Japan (DDBJ) under the submission SRA029151 and assembled by Newbler 2.7 using the same parameters as adopted for the U. vulgaris transcriptome (UT_U.gibba)
Our study is the first example of comparative transcriptomics in the species-rich genus Utricularia
Summary
The species of Utricularia attract attention owing to their carnivorous lifestyle, and due to an elevated substitution rate and a dynamic evolution of genome size leading to its dramatic reduction. To better understand the evolutionary dynamics of genome size and content as well as the great physiological plasticity in this mostly aquatic carnivorous genus, we analyzed the transcriptome of Utricularia vulgaris, a temperate species with well characterized physiology and ecology. U. gibba was the subject of the first broad survey of nuclear gene transcripts in Utricularia species [11,12], revealing several interesting aspects of their physiology and morphology. Utricularia spp. have since been identified as prime candidates for further research on the complexities of plant ecophysiology associated with carnivory, metagenomic surveys of trap microbial communities, novel plant nitrogen/nutrient utilization pathways, the ecology of prey attraction, whole-plant and trap comparative development, and the evolution of a minimalist angiosperm genome [3,5,14,15,16,17,18,19,20]. Its ecophysiology is subtly but meaningfully distinct from that of U. gibba, offering the possibility for a comprehensive comparison of genome-wide expression patterns between the two species
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