Vuyisich Momchilo, Arefin Ayesha, Davenport Karen, Feng Shihai, Gleasner Cheryl, McMurry Kim, Parson-Quintana Beverly, Price Jennifer, Scholz Matthew, Chain Patrick
Los Alamos National Laboratory, P.O. Box 1663, MS M888, Los Alamos, NM 87545, USA.
Parkview Medical Center School for Medical Laboratory Science, 400 West 16th Street, Pueblo, CO 81003, USA.
Int J Genomics. 2014;2014:434575. doi: 10.1155/2014/434575. Epub 2014 Nov 13.
Sequencing bacterial genomes has traditionally required large amounts of genomic DNA (~1 μg). There have been few studies to determine the effects of the input DNA amount or library preparation method on the quality of sequencing data. Several new commercially available library preparation methods enable shotgun sequencing from as little as 1 ng of input DNA. In this study, we evaluated the NEBNext Ultra library preparation reagents for sequencing bacterial genomes. We have evaluated the utility of NEBNext Ultra for resequencing and de novo assembly of four bacterial genomes and compared its performance with the TruSeq library preparation kit. The NEBNext Ultra reagents enable high quality resequencing and de novo assembly of a variety of bacterial genomes when using 100 ng of input genomic DNA. For the two most challenging genomes (Burkholderia spp.), which have the highest GC content and are the longest, we also show that the quality of both resequencing and de novo assembly is not decreased when only 10 ng of input genomic DNA is used.
传统上，对细菌基因组进行测序需要大量的基因组DNA（约1μg）。很少有研究来确定输入DNA量或文库制备方法对测序数据质量的影响。几种新的市售文库制备方法能够从低至1ng的输入DNA进行鸟枪法测序。在本研究中，我们评估了用于细菌基因组测序的NEBNext Ultra文库制备试剂。我们评估了NEBNext Ultra在四个细菌基因组重测序和从头组装中的效用，并将其性能与TruSeq文库制备试剂盒进行了比较。当使用100ng输入基因组DNA时，NEBNext Ultra试剂能够对各种细菌基因组进行高质量的重测序和从头组装。对于两个最具挑战性的基因组（伯克霍尔德菌属），它们具有最高的GC含量且最长，我们还表明，当仅使用10ng输入基因组DNA时，重测序和从头组装的质量均未降低。
