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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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Phylogenetic analyses ofEIN2. MP and ML tree constructed from the alignment of partial EIN2 sequences across angiosperms exhibited the same topology. Bootstrap supports calculated from 1000 pseudoreplicates are shown above branches (MP) or below branches in parentheses (ML).
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Fig4: Phylogenetic analyses ofEIN2. MP and ML tree constructed from the alignment of partial EIN2 sequences across angiosperms exhibited the same topology. Bootstrap supports calculated from 1000 pseudoreplicates are shown above branches (MP) or below branches in parentheses (ML).

Mentions: To achieve the correct assembly of alternative transcripts in a species without reference genome is very difficult. It becomes even more challenging if multiple similar paralogous genes are transcribed and alternatively spliced. In such cases, chimeric misassembled contigs are frequently generated [28]. The isogroup 00006 homologous to the ETHYLENE INSENSITIVE 2 EIN2 gene (At5g03280) in Arabidopsis is an example of the mixture of alternatively spliced transcripts derived from at least two loci. We identified contigs corresponding to the exons and introns of the EIN2 gene. Several putative exons existed in two sequence variants and occurred in chimeric isotigs. We confirmed the occurrence of two EIN2 gene copies by direct sequencing of U. vulgaris genomic DNA. We designed two primer pairs UV304_F1, R1 and UV308_F1, R1 (Additional file 4) and amplified and sequenced a part of exon 7 from both EIN2 paralogs. The alignment (1,360 bp) of U. vulgaris sequences with EIN2 homologs across angiosperms was used in phylogenetic analysis to generate MP and ML trees (Figure 4). The trees constructed by both methods showed the same topology and confirmed a relatively recent duplication of EIN2, preceding the divergence of U. vulgaris and U. gibba. We found only one EIN2 homolog in the U. gibba genome (CoGe-id36222).Figure 4


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)

Phylogenetic analyses ofEIN2. MP and ML tree constructed from the alignment of partial EIN2 sequences across angiosperms exhibited the same topology. Bootstrap supports calculated from 1000 pseudoreplicates are shown above branches (MP) or below branches in parentheses (ML).
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Fig4: Phylogenetic analyses ofEIN2. MP and ML tree constructed from the alignment of partial EIN2 sequences across angiosperms exhibited the same topology. Bootstrap supports calculated from 1000 pseudoreplicates are shown above branches (MP) or below branches in parentheses (ML).
Mentions: To achieve the correct assembly of alternative transcripts in a species without reference genome is very difficult. It becomes even more challenging if multiple similar paralogous genes are transcribed and alternatively spliced. In such cases, chimeric misassembled contigs are frequently generated [28]. The isogroup 00006 homologous to the ETHYLENE INSENSITIVE 2 EIN2 gene (At5g03280) in Arabidopsis is an example of the mixture of alternatively spliced transcripts derived from at least two loci. We identified contigs corresponding to the exons and introns of the EIN2 gene. Several putative exons existed in two sequence variants and occurred in chimeric isotigs. We confirmed the occurrence of two EIN2 gene copies by direct sequencing of U. vulgaris genomic DNA. We designed two primer pairs UV304_F1, R1 and UV308_F1, R1 (Additional file 4) and amplified and sequenced a part of exon 7 from both EIN2 paralogs. The alignment (1,360 bp) of U. vulgaris sequences with EIN2 homologs across angiosperms was used in phylogenetic analysis to generate MP and ML trees (Figure 4). The trees constructed by both methods showed the same topology and confirmed a relatively recent duplication of EIN2, preceding the divergence of U. vulgaris and U. gibba. We found only one EIN2 homolog in the U. gibba genome (CoGe-id36222).Figure 4

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