ARDEP, a Rapid Degenerate Primer Design Pipeline Based on k -mers for Amplicon Microbiome Studies

Yueni Wu, Kai Feng, Ziyan Wei, Zhujun Wang and Ye Deng
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Yueni Wu: Key Laboratory for Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
Kai Feng: Key Laboratory for Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
Ziyan Wei: Institute of Marine Science and Technology, Shandong University, Qingdao 266237, China
Zhujun Wang: Key Laboratory for Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
Ye Deng: Key Laboratory for Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China

IJERPH, 2020, vol. 17, issue 16, 1-12

Abstract: The survey of microbial diversity in various environments has relied upon the widespread use of well-evaluated amplification primers for taxonomic marker genes (e.g., prokaryotic 16S and fungal ITS). However, it is urgent to develop a fast and accurate bioinformatic program to design primers for microbial functional genes to explore more mechanisms in the microbial community. Here, we provide a rapid degenerate primer design pipeline (ARDEP) based on the k -mer algorithm, which can bypass the time-consuming step of sequence alignment to greatly reduce run times while ensuring accuracy. In addition, we developed an open-access platform for the implementation of primer design projects that could also calculate the amplification product length, GC content, Annealing Temperature (Tm), and ΔG of primer self-folding, and identify covered species and functional groups. Using this new platform, we designed primers for several functional genes in the nitrogen cycle, including napA and amoA . Our newly designed primers achieved higher coverage than the commonly used primers for all tested genes. The program and the associated platform that applied the k -mer algorithm could greatly enhance the design and evaluation of primers for environmental microbiome studies.

Keywords: bioinformatic program; primer design; k -mer; analysis platform; primer assessment (search for similar items in EconPapers)
JEL-codes: I I1 I3 Q Q5 (search for similar items in EconPapers)
Date: 2020
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