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The transcriptome of Utricularia vulgaris, a rootless plant with minimalist genome, reveals extreme alternative splicing and only moderate sequence similarity with Utricularia gibba.

Bárta J, Stone JD, Pech J, Sirová D, Adamec L, Campbell MA, Štorchová H - BMC Plant Biol. (2015)

Bottom Line: 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.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.Our study is the first comparison of two global sequence data sets in Utricularia.

View Article: PubMed Central - PubMed

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.

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Ortholog similarity distribution. The distribution of putative orthologous pairs between U. gibba and U. vulgaris according to their sequence similarity. Each bar represents the number of pairs of a given similarity spanning 1% interval. Blue–all orthologous pairs, orange–pairs with U. vulgaris isotigs, grey–pairs with U. vulgaris singletons.
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Fig5: Ortholog similarity distribution. The distribution of putative orthologous pairs between U. gibba and U. vulgaris according to their sequence similarity. Each bar represents the number of pairs of a given similarity spanning 1% interval. Blue–all orthologous pairs, orange–pairs with U. vulgaris isotigs, grey–pairs with U. vulgaris singletons.

Mentions: We identified 12,267 putative orthologous pairs, 10,600 of them contained U. vulgaris isotigs and the remaining 1,667 pairs contained U. vulgaris singletons. The orthologs represented about 42.9% of all genes annotated in the U. gibba genomic draft. We ordered putative orthologous pairs between U. gibba and U. vulgaris according to the sequence similarity of the regions aligned by BLAST. The distribution of orthologs assigned to individual similarity classes is shown in Figure 5. Most orthologous pairs exhibited a sequence similarity of 85%-90%, whether or not they included U. vulgaris isotigs or singletons. Singletons are much shorter than an average isotig (1,514 bp; Table 1), thus they often represent incomplete transcripts. Their sequence similarity depends on whether they are derived from a more or less conserved part of the gene, it does not reflect the similarity across an entire gene. For this reason, we performed the following analyses of the most conserved orthologs with the pairs containing only U. vulgaris isotigs, not singletons.Figure 5


The transcriptome of Utricularia vulgaris, a rootless plant with minimalist genome, reveals extreme alternative splicing and only moderate sequence similarity with Utricularia gibba.

Bárta J, Stone JD, Pech J, Sirová D, Adamec L, Campbell MA, Štorchová H - BMC Plant Biol. (2015)

Ortholog similarity distribution. The distribution of putative orthologous pairs between U. gibba and U. vulgaris according to their sequence similarity. Each bar represents the number of pairs of a given similarity spanning 1% interval. Blue–all orthologous pairs, orange–pairs with U. vulgaris isotigs, grey–pairs with U. vulgaris singletons.
© Copyright Policy - open-access
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC4358910&req=5

Fig5: Ortholog similarity distribution. The distribution of putative orthologous pairs between U. gibba and U. vulgaris according to their sequence similarity. Each bar represents the number of pairs of a given similarity spanning 1% interval. Blue–all orthologous pairs, orange–pairs with U. vulgaris isotigs, grey–pairs with U. vulgaris singletons.
Mentions: We identified 12,267 putative orthologous pairs, 10,600 of them contained U. vulgaris isotigs and the remaining 1,667 pairs contained U. vulgaris singletons. The orthologs represented about 42.9% of all genes annotated in the U. gibba genomic draft. We ordered putative orthologous pairs between U. gibba and U. vulgaris according to the sequence similarity of the regions aligned by BLAST. The distribution of orthologs assigned to individual similarity classes is shown in Figure 5. Most orthologous pairs exhibited a sequence similarity of 85%-90%, whether or not they included U. vulgaris isotigs or singletons. Singletons are much shorter than an average isotig (1,514 bp; Table 1), thus they often represent incomplete transcripts. Their sequence similarity depends on whether they are derived from a more or less conserved part of the gene, it does not reflect the similarity across an entire gene. For this reason, we performed the following analyses of the most conserved orthologs with the pairs containing only U. vulgaris isotigs, not singletons.Figure 5

Bottom Line: 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.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.Our study is the first comparison of two global sequence data sets in Utricularia.

View Article: PubMed Central - PubMed

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.

Show MeSH
Related in: MedlinePlus