Wheat Christopher W
Department of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland.
Methods Mol Biol. 2012;888:33-53. doi: 10.1007/978-1-61779-870-2_3.
Roche 454 sequencing of the transcriptome has become a standard approach for efficiently obtaining single nucleotide polymorphisms (SNPs) in non-model species. In this chapter, the primary issues facing the development of SNPs from the transcriptome in non-model species are presented: tissue and sampling choices, mRNA preparation, considerations of normalization, pooling and barcoding, how much to sequence, how to assemble the data and assess the assembly, calling transcriptome SNPs, developing these into genomic SNPs, and publishing the work. Discussion also covers the comparison of this approach to RAD-tag sequencing and the potential of using other sequencing platforms for SNP development.
罗氏454转录组测序已成为在非模式生物中高效获取单核苷酸多态性（SNP）的标准方法。在本章中，介绍了在非模式生物中从转录组开发SNP所面临的主要问题：组织和样本选择、mRNA制备、标准化、混合和条形码的考虑因素、测序量、如何组装数据和评估组装结果、鉴定转录组SNP、将其开发为基因组SNP以及发表研究成果。讨论还涵盖了这种方法与RAD标签测序的比较以及使用其他测序平台进行SNP开发的潜力。
