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RNAseq‐based transcriptome assembly of Clostridium acetobutylicum for functional genome annotation and discovery
AIChE Journal ( IF 3.7 ) Pub Date : 2018-10-02 , DOI: 10.1002/aic.16396
Matthew T. Ralston 1, 2 , Eleftherios T. Papoutsakis 1, 3
Affiliation  

Accurate genome annotations are essential in modern biology and biotechnology, yet they are still largely based on genome sequencing and comparative analyses. We show that the Clostridium acetobutylicum genome annotation can be markedly improved by integrating bioinformatic predictions with RNA sequencing (RNAseq) data. Samples were acquired under butanol, butyrate, and unstressed treatments across various growth conditions. Analysis of an initial assembly revealed errors due to background signals and limitations of assembly algorithms. Hurdles for RNAseq transcriptome mapping include optimizing library complexity and sequencing depth, yet most studies report low sequencing depth and ignore the effect of ribosomal RNA abundance. An integrative analysis was developed to combine motif predictions, single‐nucleotide resolution sequencing depth, and library complexity to resolve difficulties in assembly curation. This minimized false positive error and determined gene boundaries, in some cases, to the exact base‐pair of prior studies. This is the first strand‐specific transcriptome assembly in a Clostridium organism. © 2018 American Institute of Chemical Engineers AIChE J, 64: 4271–4280, 2018

中文翻译:

丙酮丁醇梭菌基于RNAseq的转录组组装,用于功能基因组注释和发现

准确的基因组注释在现代生物学和生物技术中必不可少,但它们仍主要基于基因组测序和比较分析。我们表明丙酮丁醇梭菌通过将生物信息学预测与RNA测序(RNAseq)数据整合在一起,可以显着改善基因组注释。在各种生长条件下,在丁醇,丁酸和未经压力的处理下采集样品。初始装配的分析揭示了由于背景信号和装配算法的限制而引起的错误。RNAseq转录组作图的障碍包括优化文库复杂性和测序深度,但是大多数研究报告测序深度较低,并且忽略了核糖体RNA丰度的影响。进行了综合分析,以结合基序预测,单核苷酸分辨率测序深度和文库复杂性,以解决装配管理中的困难。在某些情况下,这可以最大程度地减少假阳性错误并确定基因边界,以达到先前研究的确切碱基对。梭菌生物。©2018美国化学工程师学会AIChE J,64:4271–4280,2018
更新日期:2018-10-02
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