Biosystematics Group, Wageningen University, Wageningen, The Netherlands.
PLoS One. 2013 Jul 29;8(7):e69189. doi: 10.1371/journal.pone.0069189. Print 2013.
Unlocking the vast genomic diversity stored in natural history collections would create unprecedented opportunities for genome-scale evolutionary, phylogenetic, domestication and population genomic studies. Many researchers have been discouraged from using historical specimens in molecular 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 (NGS) 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. Here we show that using a standard multiplex and paired-end Illumina sequencing approach, genome-scale sequence data can be generated reliably from dry-preserved plant, fungal and insect specimens collected up to 115 years ago, and with minimal destructive sampling. Using a reference-based assembly approach, we were able to produce the entire nuclear genome of a 43-year-old Arabidopsis thaliana (Brassicaceae) herbarium specimen with high and uniform sequence coverage. Nuclear genome sequences of three fungal specimens of 22-82 years of age (Agaricus bisporus, Laccaria bicolor, Pleurotus ostreatus) were generated with 81.4-97.9% exome coverage. Complete organellar genome sequences were assembled for all specimens. Using de novo assembly we retrieved between 16.2-71.0% of coding sequence regions, and hence remain somewhat cautious about prospects for de novo genome assembly from historical specimens. Non-target sequence contaminations were observed in 2 of our insect museum specimens. We anticipate that future museum genomics projects will perhaps not generate entire genome sequences in all cases (our specimens contained relatively small and low-complexity genomes), but at least generating vital comparative genomic data for testing (phylo)genetic, demographic and genetic hypotheses, that become increasingly more horizontal. Furthermore, NGS of historical DNA enables recovering crucial genetic information from old type specimens that to date have remained mostly unutilized and, thus, opens up a new frontier for taxonomic research as well.
unlocking the vast genomic diversity stored in natural history collections would create unprecedented opportunities for genome-scale evolutionary, phylogenetic, domestication and population genomic studies. 解锁自然历史收藏中存储的巨大基因组多样性，将为全基因组进化、系统发育、驯化和群体基因组研究创造前所未有的机会。
Many researchers have been discouraged from using historical specimens in molecular studies because of both generally limited success of DNA extraction and the challenges associated with PCR-amplifying highly degraded DNA. 由于 DNA 提取的普遍成功率有限，以及与高度降解 DNA 的 PCR 扩增相关的挑战，许多研究人员在分子研究中都对使用历史标本感到气馁。
In today's next-generation sequencing (NGS) 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. 在当今的下一代测序（NGS）世界中，历史 DNA 的机会和前景发生了巨大变化，因为大多数 NGS 方法实际上是为将短的碎片化 DNA 分子作为模板而设计的。
Here we show that using a standard multiplex and paired-end Illumina sequencing approach, genome-scale sequence data can be generated reliably from dry-preserved plant, fungal and insect specimens collected up to 115 years ago, and with minimal destructive sampling. 在这里，我们展示了使用标准多重和配对末端 Illumina 测序方法，可以从 115 年前采集的干燥保存的植物、真菌和昆虫标本中可靠地生成全基因组序列数据，并且采样破坏性最小。
Using a reference-based assembly approach, we were able to produce the entire nuclear genome of a 43-year-old Arabidopsis thaliana (Brassicaceae) herbarium specimen with high and uniform sequence coverage. 使用基于参考的组装方法，我们能够生成一个 43 岁的拟南芥（十字花科）标本的整个核基因组，具有高且均匀的序列覆盖度。
Nuclear genome sequences of three fungal specimens of 22-82 years of age (Agaricus bisporus, Laccaria bicolor, Pleurotus ostreatus) were generated with 81.4-97.9% exome coverage. 对三个年龄在 22-82 岁的真菌标本（双孢蘑菇、双色鹅膏菌、糙皮侧耳）的核基因组序列进行了生成，外显子覆盖率为 81.4-97.9%。
Complete organellar genome sequences were assembled for all specimens. 所有标本的完整细胞器基因组序列都被组装。
Using de novo assembly we retrieved between 16.2-71.0% of coding sequence regions, and hence remain somewhat cautious about prospects for de novo genome assembly from historical specimens. 使用从头组装，我们检索到了 16.2-71.0%的编码序列区域，因此对于从历史标本中进行从头组装基因组的前景仍然有些谨慎。
Non-target sequence contaminations were observed in 2 of our insect museum specimens. 我们的两个昆虫博物馆标本中观察到了非目标序列污染。
We anticipate that future museum genomics projects will perhaps not generate entire genome sequences in all cases (our specimens contained relatively small and low-complexity genomes), but at least generating vital comparative genomic data for testing (phylo)genetic, demographic and genetic hypotheses, that become increasingly more horizontal. 我们预计，未来的博物馆基因组学项目可能不会在所有情况下都生成整个基因组序列（我们的标本包含相对较小且低复杂度的基因组），但至少会生成重要的比较基因组数据，用于测试（系统发育）遗传、人口和遗传假设，这些假设变得越来越横向。
Furthermore, NGS of historical DNA enables recovering crucial genetic information from old type specimens that to date have remained mostly unutilized and, thus, opens up a new frontier for taxonomic research as well. 此外，历史 DNA 的 NGS 能够从迄今为止大部分未被利用的旧型标本中恢复关键的遗传信息，因此也为分类学研究开辟了一个新的前沿。
