Herbarium genomics: skimming and plastomics from archival specimens
Herbarium genomics: skimming and plastomics from archival specimens
复制标题
DOI：
10.1080/00837792.2017.1313383
复制
发表时间：
2017-01-01
期刊：
影响因子：
--
通讯作者：
Bakker, Freek T.
中科院分区：
文献类型：
--
作者：
Bakker, Freek T.
使用大规模的并行测序，也就是众所周知的第二代测序，使用标本DNA的一些经典障碍已经被克服。例如，大多数标本DNA的降解性质不再阻碍测序(因为阻碍了有效的扩增)。取而代之的是，可以在常规的基础上获得几千个碱基的基因组序列，特别是从高拷贝数的隔室，如叶绿体基因组。通过基因组浏览等方法，可以获得对重复基因组间隔(如质体)的公平覆盖，从而能够快速组装相关序列。尽管基于撇脂技术组装完整的150多个碱基的植物标记体仍然需要更多的投资，但产生跨越几个千碱基的大重叠群是直接的。它对在物种水平和物种以外的系统发育研究中使用植物标本DNA序列提出了一个重要的和具有成本效益的促进。与此同时，尽管标本DNA似乎带有古代DNA的特征，但获得的标本DNA序列的准确性似乎令人惊讶地高，因为大多数标本DNA的死后错误编码损伤被发现可以忽略不计。
Using massive parallel sequencing, which has become known as second-generation sequencing, some of the classic roadblocks to using herbarium DNA have been overcome. For instance, no longer is the degraded nature of most herbarium DNA preventing sequencing (because of blocking effective amplification). Instead, several kilobases of genomic sequence can be obtained on a routine basis, especially from high-copy number compartments such as plastomes (chloroplast genomes). With approaches such as genomic skimming a fair coverage of repetitive genome compartments (such as plastomes) can be obtained, enabling fast assembly of associated sequences. Although assembly of complete 150+kilobase herbarium plastomes based on skimming still needs more investment, the generation of large contigs spanning several kilo bases is straightforward. It presents an important and cost-effective boost to using herbarium DNA-sequences in phylogenetic studies at species-level and beyond. At the same time, although herbarium DNA appears to bear the signature of ancient DNA, the accuracy of the herbarium DNA sequences obtained appears to be surprisingly high, as post-mortem miscoding lesion damage in most herbarium DNA is found to be negligible.