Abstract
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.
Highlights
DNA sequences of plastids have provided many important insights into plant ecology and evolution over the past three decades (Palmer 1987; Chase et al 1993; Petit & Vendramin 2007; Hollingsworth et al 2016)
Plastid sequencing can reveal the cyanobacterial origins of plastids and the genomic changes associated with endosymbiosis (McFadden 2001)
The main benefit of this approach is that de novo assembly of the enriched DNA sample is simple and will likely lead to a complete assembly even with a small number of sequence reads. This was the case in a chloroplast extraction optimization study by Shi et al (2012), where 5–10 lg of isolated plastid DNA was subject to short-read sequencing, with 50 Mb of data giving 1009 coverage and a complete assembly
Summary
DNA sequences of plastids have provided many important insights into plant ecology and evolution over the past three decades (Palmer 1987; Chase et al 1993; Petit & Vendramin 2007; Hollingsworth et al 2016). The high-copy number of plastids per cell means that genomic DNA extracts are naturally enriched for plastids (Bendich 1987) and an easier target than low-copy nuclear genes for sequencing, from small or degraded samples (Staats et al 2013). It is becoming popular to perform a ‘genome skim’ (Straub et al 2012), where gDNA is sequenced at low nuclear genome coverage (~0.1–109), and this often provides sufficient data for complete plastid assembly (Coissac et al 2016).
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