Institute of Evolutionary Biology, Ashworth Laboratories, University of Edinburgh, Edinburgh, EH9 3FL, UK.
Department of Biology, University of Toronto Mississauga, Mississauga, ON, Canada.
Mol Ecol Resour. 2017 Sep;17(5):858-868. doi: 10.1111/1755-0998.12626. Epub 2016 Nov 28.
Plastid sequencing is an essential tool in the study of plant evolution. This high-copy organelle is one of the most technically accessible regions of the genome, and its sequence conservation makes it a valuable region for comparative genome evolution, phylogenetic analysis and population studies. Here, we discuss recent innovations and approaches for de novo plastid assembly that harness genomic tools. We focus on technical developments including low-cost sequence library preparation approaches for genome skimming, enrichment via hybrid baits and methylation-sensitive capture, sequence platforms with higher read outputs and longer read lengths, and automated tools for assembly. These developments allow for a much more streamlined assembly than via conventional short-range PCR. Although newer methods make complete plastid sequencing possible for any land plant or green alga, there are still challenges for producing finished plastomes particularly from herbarium material or from structurally divergent plastids such as those of parasitic plants.
质体测序是研究植物进化的重要工具。这种高拷贝细胞器是基因组中最具技术可及性的区域之一，其序列保守性使其成为比较基因组进化、系统发育分析和群体研究的有价值区域。在这里，我们讨论了利用基因组工具进行从头质体组装的最新创新和方法。我们专注于技术发展，包括用于基因组刮擦的低成本序列文库制备方法、通过杂交诱饵和甲基化敏感捕获进行的富集、具有更高读取输出和更长读取长度的序列平台，以及用于组装的自动化工具。这些发展比传统的短距离 PCR 允许更流畅的组装。尽管更新的方法使任何陆地植物或绿藻都有可能进行完整的质体测序，但从标本材料或结构上不同的质体（如寄生植物的质体）中产生完整质体仍然存在挑战。
