Evolution of intraspecific transcriptomic landscapes in yeasts.
Evolution of intraspecific transcriptomic landscapes in yeasts.
复制标题
酵母中种内转录组内景观的演变。
DOI：
10.1093/nar/gkv363
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发表时间：
2015-05-19
影响因子：
14.9
通讯作者：
Schacherer J
中科院分区：
文献类型：
--
作者：
Brion C;Pflieger D;Friedrich A;Schacherer J
基因表达的变化已被广泛探讨，以获得一个准确的概述的变化，在监管网络的基础表型多样性。许多研究已经表征了大量模式生物如酿酒酵母（Saccharomyces cerevisiae）个体之间基因组表达的差异。为了更广泛地调查物种间转录组景观的演变，我们使用RNAseq测量了另一种酵母物种的大量集合中的全基因组表达：Lachancea kluyveri（以前的Saccharomyces kluyveri）。有趣的是，这个物种从S。在其祖先的全基因组复制之前的酿酒酵母谱系。此外，L. kluyveri窝藏一个染色体规模的组成异质性，由于1-Mb的祖先渗入区，以及一个独特的未注释的基因的大集合。在这种情况下，我们的比较转录组学分析清楚地表明了基因进化历史和表达行为之间的联系。事实上，最近获得或功能松弛的基因往往较少转录，表现出较高的种内变异（可塑性），较少参与网络（连通性）。此外，利用这种方法在L。kluyveri还强调了有氧呼吸、氨基酸生物合成和糖基化中的特定调控网络特征，这可能是由于其不同的生活方式。我们的数据集揭示了一个重要的光在远距离物种的种内转录组变异的演变。
Variations in gene expression have been widely explored in order to obtain an accurate overview of the changes in regulatory networks that underlie phenotypic diversity. Numerous studies have characterized differences in genomic expression between large numbers of individuals of model organisms such as Saccharomyces cerevisiae. To more broadly survey the evolution of the transcriptomic landscape across species, we measured whole-genome expression in a large collection of another yeast species: Lachancea kluyveri (formerly Saccharomyces kluyveri), using RNAseq. Interestingly, this species diverged from the S. cerevisiae lineage prior to its ancestral whole genome duplication. Moreover, L. kluyveri harbors a chromosome-scale compositional heterogeneity due to a 1-Mb ancestral introgressed region as well as a large set of unique unannotated genes. In this context, our comparative transcriptomic analysis clearly showed a link between gene evolutionary history and expression behavior. Indeed, genes that have been recently acquired or under function relaxation tend to be less transcribed show a higher intraspecific variation (plasticity) and are less involved in network (connectivity). Moreover, utilizing this approach in L. kluyveri also highlighted specific regulatory network signatures in aerobic respiration, amino-acid biosynthesis and glycosylation, presumably due to its different lifestyle. Our data set sheds an important light on the evolution of intraspecific transcriptomic variation across distant species.
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DOI：
10.1093/bioinformatics/btu638
发表时间：
2015-01-15
期刊：
Bioinformatics (Oxford, England)
影响因子：
--
作者：
Anders S;Pyl PT;Huber W
通讯作者：
Huber W
影响因子：
12.3
作者：
Capra JA;Pollard KS;Singh M
通讯作者：
Singh M
影响因子：
7
作者：
Roy, Sushmita;Wapinski, Ilan;Regev, Aviv
通讯作者：
Regev, Aviv
影响因子：
64.8
作者：
Schacherer J;Shapiro JA;Ruderfer DM;Kruglyak L
通讯作者：
Kruglyak L
影响因子：
4.3
作者：
Kim WK;Marcotte EM
通讯作者：
Marcotte EM