Bárta Jiří, Stone James D, Pech Jiří, Sirová Dagmara, Adamec Lubomír, Campbell Matthew A, Štorchová Helena
BMC Plant Biol. 2015 Mar 7;15:78. doi: 10.1186/s12870-015-0467-8.
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.
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.
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.
狸藻属植物不仅因其食虫的生活方式而受到关注，还因其较高的替代率以及基因组大小的动态进化导致其显著减小而备受瞩目。为了更好地理解该主要水生食虫属植物基因组大小和内容的进化动态以及巨大的生理可塑性，我们分析了普通狸藻的转录组，这是一种具有特征明确的生理学和生态学的温带物种。我们将其转录组，即基因内容和整体转录谱，与之前描述的一种拥有最小被子植物基因组之一的同属植物——奇异狸藻的转录组进行了比较。
我们对从普通狸藻包括叶片和捕虫囊的茎中提取的总RNA制备的标准化cDNA文库进行了测序，这些样本在无菌或室外条件下培养。454焦磷酸测序产生了超过140万个读段，这些读段被组装成19522个同组基因中的41407个重叠群。我们在几个同组基因中观察到了由多个位点和/或可变剪接解释的高转录变异。普通狸藻和奇异狸藻转录组的比较显示，尽管转录组制备存在差异，但在表达基因中GO类别分布相似。我们还发现普通狸藻转录组和奇异狸藻基因组中与根相关基因的有无存在强烈对应关系，这表明在这两个无根物种分化之前，一些根特异性基因已经丢失。
物种丰富的狸藻属为研究与环境和食虫习性相关的适应性以及导致基因组大幅减少的进化过程提供了独特的机会。我们表明转录组可以在基因内容或基因复制估计方面近似基因组。我们的研究是狸藻属中两个全局序列数据集的首次比较。
