中文摘要：

新一代测序技术已经广泛应用于转录组的研究（即RNA－seq），其数据几乎涵盖了特定组织和特定时期的所有转录本。由于其高通量和低成本的优势，RNA－seq越来越受到研究者的青睐，特别是在那些缺乏基因组信息的物种上。在此综述中，讨论了RNA－seq的测序策略，包括物种遗传背景的考量，测序平台和数据拼接软件的选择。RNA－seq数据对于ssR和sNP等分子标记的开发是非常有用的，由于这些标记在相关物种中有很高的通用性，因此在比较作图中有其不可替代的优势。

英文摘要：

The next-generation sequencing （NGS） has been extensively applied in transcriptomics, called RNA-seq, which characterizes transcriptional events occurring in a specific tissue and a given period. RNA-seq has the advantages of high-throughput and low cost, and becomes the first choice for researchers to carry out biological researches. It has been proven very useful in non-model species, which often lack the resources of sequenced genome. In this review, we discussed about some strategies of RNA-seq, including genetic background consideration, platform selection for sequencing and bioinformatics tools selection for reads assembly. RNA-seq data are also valuable resource for markers development, including microsattelite （SSR）, single nucleotide polymorphism （SNP） and so on. This kind of marker has a high transferability between related species and is a powerful tool in comparative mapping.