Max Planck Institute for Evolutionary Biology, Department of Evolutionary Genetics, August-Thienemannstr, 2, 24306 Plön, Germany.
BMC Genomics. 2011 Feb 1;12:91. doi: 10.1186/1471-2164-12-91.
Species with heteromorphic sex chromosomes face the challenge of large-scale imbalance in gene dose. Microarray-based studies in several independent male heterogametic XX/XY systems suggest that dosage compensation mechanisms are in place to mitigate the detrimental effects of gene dose differences. However, recent genomic research on female heterogametic ZZ/ZW systems has generated surprising results. In two bird species and one lepidopteran no evidence for a global dosage compensating mechanism has been found. The recent advent of massively parallel RNA sequencing now opens up the possibility to gauge the generality of this observation with a broader phylogenetic sampling. It further allows assessing the validity of microarray-based inference on dosage compensation with a novel technology.
We here exemplify this approach using massively parallel sequencing on barcoded individuals of a bird species, the European crow (Corvus corone), where previously no genetic resources were available. Testing for Z-linkage with quantitative PCR (qPCR,) we first establish that orthology with distantly related species (chicken, zebra finch) can be used as a good predictor for chromosomal affiliation of a gene. We then use a digital measure of gene expression (RNA-seq) on brain transcriptome and confirm a global lack of dosage compensation on the Z chromosome. RNA-seq estimates of male-to-female (m:f) expression difference on the Z compare well to previous microarray-based estimates in birds and lepidopterans. The data further lends support that an up-regulation of female Z-linked genes conveys partial compensation and suggest a relationship between sex-bias and absolute expression level of a gene. Correlation of sex-biased gene expression on the Z chromosome across all three bird species further suggests that the degree of compensation has been partly conserved across 100 million years of avian evolution.
This work demonstrates that the study of dosage compensation has become amenable to species where previously no genetic resources were available. Massively parallele transcriptome sequencing allows re-assessing the degree of dosage compensation with a novel tool in well-studies species and, in addition, gain valuable insights into the generality of mechanisms across independent taxonomic group for both the XX/XY and ZZ/ZW system.
具有异型性染色体的物种面临着基因剂量大规模失衡的挑战。在几个独立的雄性异型性 XX/XY 系统中基于微阵列的研究表明，存在剂量补偿机制来减轻基因剂量差异的不利影响。然而，最近对雌性异型性 ZZ/ZW 系统的基因组研究产生了令人惊讶的结果。在两种鸟类和一种鳞翅目动物中，没有发现全局剂量补偿机制的证据。最近大规模平行 RNA 测序的出现为更广泛的系统发育采样提供了评估这种观察结果的普遍性的可能性。它还可以使用一种新技术来评估基于微阵列的剂量补偿推断的有效性。
我们在这里使用大规模平行测序来研究一种鸟类物种，即欧洲乌鸦（Corvus corone），在这种鸟类中，以前没有遗传资源。通过定量 PCR(qPCR) 测试 Z 连锁，我们首先确定与远缘物种（鸡、斑胸草雀）的同源性可以作为预测基因染色体归属的良好指标。然后，我们使用大脑转录组的数字基因表达（RNA-seq）测量来确认 Z 染色体上缺乏全局剂量补偿。Z 染色体上雄性到雌性（m:f）表达差异的 RNA-seq 估计与鸟类和鳞翅目动物中以前的微阵列估计值非常吻合。这些数据进一步表明，雌性 Z 连锁基因的上调表达提供了部分补偿，并表明性别偏向与基因的绝对表达水平之间存在关系。所有三种鸟类中 Z 染色体上性别偏向基因表达的相关性进一步表明，补偿程度在 1 亿年的鸟类进化过程中部分得到了保留。
这项工作表明，在以前没有遗传资源的物种中，剂量补偿的研究已经变得可行。大规模平行转录组测序允许使用一种新工具在研究充分的物种中重新评估剂量补偿的程度，此外，还可以深入了解 XX/XY 和 ZZ/ZW 系统中独立分类群的机制的普遍性。
