Next Generation Sequencing Facilitates Comparative Transcriptomes Analysis for different Yarrowia lipolytica strains synthesizing different levels of β-carotene as end products.. Next Generation Sequencing Facilitates Comparative Transcriptomes Analysis for different Yarrowia lipolytica strains synthesizing different levels of β-carotene as end products.

Purpose: According to comparative transcriptomes data, the differentially expressed genes within these selected Y. lipolytica strains can be digged out and further analyzed, seeking potential targets that were tuned drastically and might improve β-carotene production when modified. Methods: mRNA profiles of three Y. lipolytica strains ctrl, Y5_2, Y5_3 (each named as Yl_5_1, Yl_5_2, Yl_5_3 in related manuscript) were generated in triplicate using illumina. Sequencing libraries were generated using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (NEB, USA) and index codes were added to each sample. The library preparations were sequenced on an Illumina Hiseq 4000 platform. 150 bp paired-end reads were generated as raw data. The read counts for each gene in the genome were summarized as processed data. Results: In all strain samples, the transcriptome data for all 6145 genes throughout genome were detected. The results showed that the expression levels of nearly half of the total genes were tuned to a higher or a lower value. Conclusions: There were 2848 differentially expressed genes between strain ctrl and Y5-2 and this number was 2889 for ctrl vs. Y5_3. The GO and KEGG enrichment of these differentially expressed genes would be further operated for exploring drastically regulated functions and pathways. Overall design: The transcirptomes of different Yarrowia lipolytica strains were sequenced by Illumina, giving both unchanged genes and differentially expressed genes that would affect β-carotene production.

研究目的：基于比较转录组数据，挖掘所选解脂耶氏酵母（Yarrowia lipolytica，常缩写为Y. lipolytica）菌株中的差异表达基因并开展后续分析，以期筛选出经修饰后可显著调控并提升β-胡萝卜素产量的潜在靶点。
实验方法：采用Illumina测序平台对3株解脂耶氏酵母菌株（对照株ctrl、Y5_2、Y5_3，相关文献中分别命名为Yl_5_1、Yl_5_2、Yl_5_3）设置3次生物学重复，获取其mRNA表达谱。测序文库构建采用NEBNext® Ultra™ RNA文库制备试剂盒（适配Illumina®平台，美国NEB公司），并为每个样本添加索引条码。随后在Illumina HiSeq 4000平台上完成文库测序，获得150 bp双端原始测序读段。对基因组中每个基因的读段计数进行汇总，得到处理后的数据。
实验结果：在所有菌株样本中，均检测到全基因组6145个基因的转录组数据。结果显示，近半数基因的表达水平发生了上调或下调。
研究结论：对照株ctrl与Y5_2之间存在2848个差异表达基因，对照株ctrl与Y5_3之间的差异表达基因数量为2889个。后续将对上述差异表达基因进行GO（Gene Ontology）富集分析与KEGG（Kyoto Encyclopedia of Genes and Genomes）富集分析，以探究受显著调控的生物学功能与通路。
整体实验设计：采用Illumina测序平台对不同解脂耶氏酵母菌株的转录组进行测序，获取可影响β-胡萝卜素产量的未差异表达基因与差异表达基因数据。