酿酒酵母全基因组学及其应用研究进展

文章综述了近年来对酿酒酵母在功能基因组学、比较基因组学、合成基因组学等方面的重大研究进展,并对其继续深入研究的方向及应用开发的前景进行了展望。     

一株高效降解菜籽饼粕中硫苷的枯草芽孢杆菌基因组鉴定及功能分析

为筛选可高效降解菜籽饼粕中硫苷的细菌,给硫苷降解基因工程菌的构建提供实验数据,以堆放菜籽饼粕的土壤为分离源,通过硫苷选择培养基筛选及硫苷降解率测定,获得一株硫苷降解率最大的菌株C1,采用16S rRNA基因序列进行种属鉴定,通过第3代Illumina NovaSeq PE150测序,获得其基因组完成图并进行功能注释,借助比较基因组学探究C1降解硫苷的机制。结果表明:菌株C1为枯草芽孢杆菌(Bacillus subtilis),其硫苷降解率为(68.98±4.74)%;C1菌株的基因组染色体全长为4 139 381 bp,鸟嘌呤和胞嘧啶含量为43.88%,编码区总长度占全基因组的比例为89.14%;C1菌株能编码大量的功能蛋白,主要涉及氨基酸转运与代谢;比较基因组学分析确认,C1与枯草芽孢杆菌的模式菌株(NC000964.3)共线性高,序列中未见大片段易位和倒置的区域,但C1序列中2.7 Mb处出现一个小片段的插入,2.1~2.4 Mb处出现小片段缺失,分别涵盖了2条黑芥子酶的相关基因,推测C1的硫苷降解机制为其可高效分泌黑芥子酶。C1菌株能够高效降解菜籽饼粕中的硫苷,是构建硫苷降解基因工程菌的可选材料。     

不同来源植物乳杆菌基因组的比较分析

目的 对分离自母乳、婴儿肠道的植物乳杆菌进行全基因组测序,分析菌株间亲缘关系和细菌素合成相关基因.方法 采用Illumina高通量测序平台对不同来源的植物乳杆菌进行全基因组测序,质控过滤后的数据经Unicycler组装获得基因组精细图,通过比对COG、CAZy数据库对功能基因进注释,并借助BAGEL4等生物信息学分析工...     

面向比较基因组学的可视化方法综述

利用可视分析技术对基因组学数据进行比较,能够高效地感知基因序列与属性背后的多组学功能结构,深度挖掘保守与变异对基因组亲缘关系的影响,对数据密集型的比较基因组学知识发现具有重要意义.综述近年来国内外比较基因组学可视分析的相关研究,首先简述基因组学序列及衍生信息的数据结构和分析任务,将基因组坐标空间布局分为纵向离散、横向连续和径向嵌套3类,比较归纳各类空间映射方法的研究现状和优缺点;然后针对基因组比较关系进行抽象,总结适用于交互关联和家族层次2种主要比较关系的可视化方法;最后指出面向比较基因组学的可视化方法在数据融合、交互联动、通用框架中面临的挑战和机遇.     

Silicon Era of Carbon-Based Life: Application of Genomics and Bioinformatics in Crop Stress Research

Abiotic and biotic stresses lead to massive reprogramming of different life processes and are the major limiting factors hampering crop productivity. Omics-based research platforms allow for a holistic and comprehensive survey on crop stress responses and hence may bring forth better crop improvement strategies. Since high-throughput approaches generate considerable amounts of data, bioinformatics tools will play an essential role in storing, retrieving, sharing, processing, and analyzing them. Genomic and functional genomic studies in crops still lag far behind similar studies in humans and other animals. In this review, we summarize some useful genomics and bioinformatics resources available to crop scientists. In addition, we also discuss the major challenges and advancements in the “-omics” studies, with an emphasis on their possible impacts on crop stress research and crop improvement.     

Increased single-nucleotide discrimination of PCR by primer probes bearing hydrophobic 4'C modifications

We report on significantly increased selectivity of real-time PCR through employment of primer probes that bear hydrophobic 4'C modifications at the 3'-terminal nucleotide. The primer probes were designed to bind the target sequences in such a way that the 3'-terminal nucleotide defines whether a matched or a single mismatched basepair is present depending on the respective target sequence. Several commercially available thermostable DNA polymerases belonging to different DNA polymerase families were tested for their efficacy in discriminating between PCR amplification of matched substrates and duplexes that contain a single mismatch. It turned out that, depending on the 4'C modification and the employed DNA polymerase, significantly increased differentiation between single matches and mismatches could be observed with real-time PCR. The degrees of the observed effects varied with the employed 4'C modification and the sequence context studied. The system is robust enough to work faithfully under several buffer conditions. Our approach should be useful for the direct diagnosis of single nucleotide variations within genes, like single nucleotide polymorphisms or mutations, by PCR without the need for further time- and cost-intensive post-PCR analysis.