Čeština
EnglishThe transcriptome of Utricularia vulgaris, a rootless plant with minimalist genome, reveals extreme alternative splicing and only moderate sequence similarity with Utricularia gibba
Barta J., Stone J.D., Pech J., Sirová D., Adamec L., Campbell M.A., Štorchová H.*
BMC PLANT BIOLOGY 15: 78, 2015
Klíčová slova: Transcriptome, root-associated genes, alternative splicing, Utricularia vulgaris
Abstrakt: Abstract Background: The species of Utricularia attract attention not only owing to their carnivorous lifestyle, but also owing to an elevated subtitution rate and a dynamic evolution of genome size leading to its dramatic reduction. To better understand genomic dynamics and 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, the species 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 a 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 have also found a strong correspondence in 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 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.
DOI:
Autoři z ÚEB: Helena Štorchová
BMC PLANT BIOLOGY 15: 78, 2015
Klíčová slova: Transcriptome, root-associated genes, alternative splicing, Utricularia vulgaris
Abstrakt: Abstract Background: The species of Utricularia attract attention not only owing to their carnivorous lifestyle, but also owing to an elevated subtitution rate and a dynamic evolution of genome size leading to its dramatic reduction. To better understand genomic dynamics and 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, the species 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 a 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 have also found a strong correspondence in 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 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.
DOI:
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