本文应用有参考基因组组装策略对一株提取自啤酒中的乳杆菌的两种生理状态进行转录组学分析。利用基因组测序技术得到此株乳杆菌的全部基因组信息之后，把此株乳杆菌用低温诱导至VBNC状态，对正常状态和VBNC状态乳杆菌提取总RNA。对RNA质量进行验证，将符合要求的RNA进行逆转录形成cDNA，之后进行文库构建和Solexa测序。通过相关指标对测序结果进行评估，之后以此前获得的全基因组序列为对照，进行转录组与基因组的序列比对和基因表的达差异分析。结果显示比对率大于95%，表达上调的基因有21个，表达下降的基因有7个。本文所应用的基因组De novo组装结合比较RNA-Seq策略与常规De novo RNA-Seq策略相比，省却De novo拼接与组装的繁琐步骤，具有更高的准确性，为今后食品微生物在不同生理状态中分子调控机制的研究提供重要基础。

A new reference-based assembly strategy was applied for the transcriptome analysis of a Lactobacillus strain in two physiological states, isolated from beer. First, the genomic information was collected using the Illumina HiSeq 2500 sequencing system and de novo assembly. Next, this Lactobacillus strain was induced into the viable but nonculturable (VBNC) state and total RNA were extracted in the normal and VBNC states. The quality of total RNA was evaluated and RNA with acceptable quality was reverse-transcribed into cDNA. A library was constructed and Solexa sequencing was performed. Based on five relevant indices, the sequencing quality was evaluated. Subsequently, the whole genome sequence obtained previously was used as a control for sequence alignment between the transcriptome and genome, as well as to analyze differences in gene expression. The results showed that the total mapping ratio was greater than 95% after sequence comparison, and 21 significantly up-regulated and seven down-regulated genes were detected. Compared to conventional de novo RNA-Seq technology, this application of genome de novo assembly and reference-based transcriptome assembly strategy can help avoid the tedious steps required in de novo assembly, shows high accuracy, and provides an important foundation for studying the molecular regulation mechanisms of food microorganisms in different physiological states.

国家973计划项目“食品加工过程安全控制理论与技术的基础研究”（2012CB720800）；国家自然科学基金青年基金项目“食品加工过程中金黄色葡萄球菌生物被膜行为的分子机制研究”（31201362）；广东省优秀博士学位论文作者资助项目“食品体系中典型病原微生物关键致毒与有害因子监控平台研究”（K3140030）；中国博士后科学基金面上项目（2014M552204）