Department of Plant Biology, Cornell University, Ithaca, New York 14853, USA.
Am J Bot. 2012 Feb;99(2):383-96. doi: 10.3732/ajb.1100312. Epub 2012 Feb 1.
RNA-seq analysis of plant transcriptomes poses unique challenges due to the highly duplicated nature of plant genomes. We address these challenges in the context of recently formed polyploid species and detail an RNA-seq experiment comparing the leaf transcriptome profile of an allopolyploid relative of soybean with the diploid species that contributed its homoeologous genomes.
RNA-seq reads were obtained from the three species and were aligned against the genome sequence of Glycine max. Transcript levels were estimated for each gene, relative contributions of polyploidy-duplicated loci (homoeologues) in the tetraploid were identified, and comparisons of transcript profiles and individual genes were used to analyze the regulation of transcript levels.
We present a novel metric developed to address issues arising from high degrees of gene space duplication and a method for dissecting a gene's measured transcript level in a polyploid species into the relative contribution of its homoeologues. We identify the gene family likely contributing to differences in photosynthetic rate between the allotetraploid and its progenitors and show that the tetraploid appears to be using the "redundant" gene copies in novel ways.
Given the prevalence of polyploidy events in plants, we believe many of the approaches developed here to be applicable, and often necessary, in most plant RNA-seq experiments. The deep sampling provided by RNA-seq allows us to dissect the genetic underpinnings of specific phenotypes as well as examine complex interactions within polyploid genomes.
由于植物基因组高度重复的性质，对植物转录组进行 RNA-seq 分析带来了独特的挑战。我们在最近形成的多倍体物种的背景下解决这些挑战，并详细介绍了一个比较大豆的异源多倍体近缘种和贡献其同源基因组的二倍体物种的叶片转录组图谱的 RNA-seq 实验。
从三个物种中获得 RNA-seq 读数，并将其与 Glycine max 的基因组序列进行比对。估计每个基因的转录水平，确定四倍体中多倍体复制基因座（同源物）的相对贡献，并比较转录谱和单个基因，以分析转录水平的调节。
我们提出了一种新的指标，用于解决由于基因空间高度重复而产生的问题，并提出了一种在多倍体物种中将基因的测量转录水平分解为其同源物相对贡献的方法。我们确定了可能导致异源四倍体与其祖先在光合速率上差异的基因家族，并表明四倍体似乎正在以新的方式利用“冗余”基因拷贝。
鉴于多倍体事件在植物中的普遍性，我们认为这里开发的许多方法在大多数植物 RNA-seq 实验中是适用的，而且通常是必要的。RNA-seq 的深度采样使我们能够剖析特定表型的遗传基础，并研究多倍体基因组内的复杂相互作用。
