Sequence alignments and validation of PCR primers used to detect phylogenetically diverse nrfA genes associated with dissimilatory nitrate reduction to ammonium (DNRA)
Sequence alignments and validation of PCR primers used to detect phylogenetically diverse nrfA genes associated with dissimilatory nitrate reduction to ammonium (DNRA)
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DOI：
10.1016/j.dib.2019.104016
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发表时间：
2019-08-01
期刊：
影响因子：
1.2
通讯作者：
Chee-Sanford, Joanne
中科院分区：
文献类型：
--
作者：
Cannon, Jordan;Sanford, Robert A.;Chee-Sanford, Joanne
设计了一组针对NRFA的PCR引物，该基因编码五血红素亚硝酸盐还原酶NRFA，在异化硝酸盐还原为氨(DNRA)的过程中催化亚硝酸氨化步骤。这里显示了来自代表18个不同NRFA分支的参考基因组的271个NRFA序列的引物靶区的核苷酸比对的细节，以及对基于PCR的方法的应用的验证，包括使用环境样品和选定的参考菌株的基于Illumina平台扩增的扩增片段长度多态性(AFLP)分析和测序。摘要数据表说明了正向引物nrfAF2awMOD和nrfAF2awMODgeo与新的反向引物nrfAR1MOD配对时与与18个NRFA分支成员相关的共识靶标参考序列的特异性。AFLP分析表明，新的引物对环境样品中的NRFA序列具有特异性，并获得了氨基酸翻译的扩增序列。我们还提供了全长NRFA基因的序列比对文件、PCR参考扩增序列比对、NRFA氨基酸比对和NRFA翻译的PCR扩增-氨基酸比对。完整的核苷酸和蛋白质比对包含271个参考基因组，代表了18个已识别的NRFA分支，作为一种工具，进一步帮助从业者检查与引物靶区对应的新序列，并允许在被认为与特定研究相关的情况下进行进一步的引物设计修改。对这一数据的更全面的分析可以从(优化用于检测与亚硝酸氨化相关的系统发育多样性的NRFA基因的聚合酶链式反应引物的优化)中获得(Cannon等人，2019年)。由爱思唯尔公司出版。
PCR primer sets were designed to target nrfA, the gene encoding the pentaheme nitrite reductase NrfA that catalyzes the nitrite ammonification step in the process of dissimilatory nitrate reduction to ammonium (DNRA). Details of the nucleotide alignments of the primer target regions of 271 nrfA sequences from reference genomes representing 18 distinct clades of NrfA are shown here along with validation of application to PCR-based methodology including the use of amplified fragment length polymorphism (AFLP) profiling and Illumina platform amplicon-based sequencing of environmental samples and selected reference strains. Summary data tables illustrate the specificity of forward primers nrfAF2awMOD and nrfAF2awMODgeo when paired with the new reverse primer nrfAR1MOD in relation to consensus target reference sequences associated with members of 18 NrfA clades. Specificity of the new primers to nrfA sequences in environmental samples is shown in AFLP analysis and amino acid-translated amplicon sequences obtained with the new primer sets. We also provide sequence alignment files of the full length nrfA genes, PCR reference amplicon alignment, NrfA amino-acid alignment and NrfA translated PCR amplicon-amino acid alignment. The full nucleotide and protein alignments contain 271 reference genomes that represent the 18 identified NrfA clades as a tool to further aid practitioners in examining new sequences corresponding to the primer target regions and allow further primer design modifications if deemed pertinent to specific studies. A more comprehensive analysis of this data may be obtained from ("Optimization of PCR primers to detect phylogenetically diverse nrfA genes associated with nitrite ammonification" Cannon et al., 2019). Published by Elsevier Inc.