High-throughput sequencing of amplicons has been widely used to precisely and efficiently identify species compositions and analyze community structures,greatly promoting biological studies involving large amounts of ...High-throughput sequencing of amplicons has been widely used to precisely and efficiently identify species compositions and analyze community structures,greatly promoting biological studies involving large amounts of complex samples,especially those involving environmental and pathogen-monitoring ones.Commercial library preparation kits for amplicon sequencing,which generally require multiple steps,including adapter ligation and indexing,are expensive and time-consuming,especially for applications at a large scale.To overcome these limitations,a“one-step PCR approach”has been previously proposed for constructions of amplicon libraries using long fusion primers.However,efficient amplifications of target genes and accurate demultiplexing of pooled sequencing data remain to be addressed.To tackle these,we present an integrative protocol for one-step PCR amplicon library construction(OSPALC).High-quality reads have been generated by this approach to reliably identify species compositions of mock bacterial communities and environmental samples.With this protocol,the amplicon library is constructed through one regular PCR with long primers,and the total cost per DNA/cDNA sample decreases to just 7%of the typical cost via the multi-step PCR approach.Empirically tested primers and optimized PCR conditions to construct OSPALC libraries for 16S rDNA V4 regions are demonstrated as a case study.Tools to design primers targeting at any genomic regions are also presented.In principle,OSPALC can be readily applied to construct amplicon libraries of any target genes using DNA or RNA samples,and will facilitate research in numerous fields.展开更多
Many modern biology studies require deep, whole-genome sequencing of hundreds to thousands of samples. Although persamplecosts have dramatically decreased, the total budget for such massive genome sequencing constitut...Many modern biology studies require deep, whole-genome sequencing of hundreds to thousands of samples. Although persamplecosts have dramatically decreased, the total budget for such massive genome sequencing constitutes a significantbarrier for poorly funded labs. The costly lab tools required for genomics experiments further hinder such studies. Here, weshare two strategies for extensively reducing the costs of massive genomics experiments, including miniaturization of theNEBNext Ultra II FS DNA Library Prep Kit for Illumina (reducing the per-sample total costs to ~ 1/6 of that charged byservice providers) and in-lab 3D model-designing of genomics tools. These strategies not only dramatically release fundingpressure for labs, but also provide students with additional training in hands-on genomics and 3D-model-designing skills,demonstrating the high potential for their application in genomics experiments and science education.展开更多
基金supported by the National Natural Science Foundation of China(31961123002,31872228)the Fundamental Research Funds for the Central Universities of China(202041001)+1 种基金the Young Taishan Scholars Program of Shandong Province(tsqn201812024)the National Science Foundation(DEB-1927159).
文摘High-throughput sequencing of amplicons has been widely used to precisely and efficiently identify species compositions and analyze community structures,greatly promoting biological studies involving large amounts of complex samples,especially those involving environmental and pathogen-monitoring ones.Commercial library preparation kits for amplicon sequencing,which generally require multiple steps,including adapter ligation and indexing,are expensive and time-consuming,especially for applications at a large scale.To overcome these limitations,a“one-step PCR approach”has been previously proposed for constructions of amplicon libraries using long fusion primers.However,efficient amplifications of target genes and accurate demultiplexing of pooled sequencing data remain to be addressed.To tackle these,we present an integrative protocol for one-step PCR amplicon library construction(OSPALC).High-quality reads have been generated by this approach to reliably identify species compositions of mock bacterial communities and environmental samples.With this protocol,the amplicon library is constructed through one regular PCR with long primers,and the total cost per DNA/cDNA sample decreases to just 7%of the typical cost via the multi-step PCR approach.Empirically tested primers and optimized PCR conditions to construct OSPALC libraries for 16S rDNA V4 regions are demonstrated as a case study.Tools to design primers targeting at any genomic regions are also presented.In principle,OSPALC can be readily applied to construct amplicon libraries of any target genes using DNA or RNA samples,and will facilitate research in numerous fields.
基金by the National NaturalScience Foundation of China (3187222& 31961123002)DistinguishedScholars Support Program of Laboratory for Marine Biology and Biotechnology,Qingdao Pilot National Laboratory for Marine Scienceand Technology (YJ2019N004)+1 种基金the Taishan Scholars Program forEarly Career Experts of Shandong Province (tsqn201812024)theFundamental Research Funds for the Central Universities of China(201822020).
文摘Many modern biology studies require deep, whole-genome sequencing of hundreds to thousands of samples. Although persamplecosts have dramatically decreased, the total budget for such massive genome sequencing constitutes a significantbarrier for poorly funded labs. The costly lab tools required for genomics experiments further hinder such studies. Here, weshare two strategies for extensively reducing the costs of massive genomics experiments, including miniaturization of theNEBNext Ultra II FS DNA Library Prep Kit for Illumina (reducing the per-sample total costs to ~ 1/6 of that charged byservice providers) and in-lab 3D model-designing of genomics tools. These strategies not only dramatically release fundingpressure for labs, but also provide students with additional training in hands-on genomics and 3D-model-designing skills,demonstrating the high potential for their application in genomics experiments and science education.