Zeng Chun-Xia, Hollingsworth Peter M, Yang Jing, He Zheng-Shan, Zhang Zhi-Rong, Li De-Zhu, Yang Jun-Bo
1Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201 Yunnan China.
2Royal Botanic Garden Edinburgh, 20A Inverleith Row, Edinburgh, EH3 5LR UK.
Plant Methods. 2018 Jun 5;14:43. doi: 10.1186/s13007-018-0300-0. eCollection 2018.
The world's herbaria contain millions of specimens, collected and named by thousands of researchers, over hundreds of years. However, this treasure has remained largely inaccessible to genetic studies, because of both generally limited success of DNA extraction and the challenges associated with PCR-amplifying highly degraded DNA. In today's next-generation sequencing world, opportunities and prospects for historical DNA have changed dramatically, as most NGS methods are actually designed for taking short fragmented DNA molecules as templates.
As a practical test of routine recovery of rDNA and plastid genome sequences from herbarium specimens, we sequenced 25 herbarium specimens up to 80 years old from 16 different Angiosperm families. Paired-end reads were generated, yielding successful plastid genome assemblies for 23 species and nuclear rDNAs for 24 species, respectively. These data showed that genome skimming can be used to generate genomic information from herbarium specimens as old as 80 years and using as little as 500 pg of degraded starting DNA.
The routine plastome sequencing from herbarium specimens is feasible and cost-effective (compare with Sanger sequencing or plastome-enrichment approaches), and can be performed with limited sample destruction.
数百年来，全球的植物标本馆收藏了由数千名研究人员采集并命名的数百万份标本。然而，由于DNA提取普遍成功率有限以及PCR扩增高度降解DNA所面临的挑战，这一宝库在很大程度上仍无法用于基因研究。在当今的新一代测序时代，历史DNA的机遇和前景发生了巨大变化，因为大多数NGS方法实际上是设计用于以短片段DNA分子为模板的。
作为从植物标本中常规回收rDNA和质体基因组序列的实际测试，我们对来自16个不同被子植物科的25份长达80年历史的植物标本进行了测序。生成了双端读数，分别成功组装了23个物种的质体基因组和24个物种的核rDNA。这些数据表明，基因组重测序可用于从长达80年历史的植物标本中生成基因组信息，并仅使用低至500 pg的降解起始DNA。
从植物标本中进行常规质体基因组测序是可行且具有成本效益的（与桑格测序或质体基因组富集方法相比），并且可以在有限的样本破坏情况下进行。
