TitleThe transcriptome of Utricularia vulgaris, a rootless plant with minimalist genome, reveals extreme alternative splicing and only moderate sequence similarity with Utricularia gibba
Publication TypeJournal Article
Year of Publication2015
AuthorsBárta, J, Stone, JD, Pech, J, Sirová, D, Adamec, L, Campbell, MA, Štorchová, H
JournalBMC Plant Biology
Volume15
Issue78
KeywordsAlternative splicing, Root-associated genes, Transcriptome, Utricularia vulgaris
Abstract

Background: The 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.
Results: We 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.
Conclusions: The 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.

DOI10.1186/s12870-015-0467-8