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.

中文翻译：

---

完整质体基因组测序的策略。

质体测序是植物进化研究的重要工具。这种高拷贝细胞器是基因组中技术上最容易接近的区域之一，其序列保守性使其成为比较基因组进化、系统发育分析和种群研究的宝贵区域。在这里，我们讨论利用基因组工具进行质体从头组装的最新创新和方法。我们专注于技术开发，包括用于基因组撇取的低成本序列文库制备方法、通过混合诱饵和甲基化敏感捕获进行富集、具有更高读取输出和更长读取长度的序列平台以及自动化组装工具。这些进展使得组装比传统的短程 PCR 更加简化。尽管较新的方法使得对任何陆地植物或绿藻进行完整的质体测序成为可能，但生产成品质体仍然存在挑战，特别是从植物标本或结构不同的质体（例如寄生植物的质体）中产生。