Strategies for complete plastid genome sequencing

Research output: Contribution to journalArticlepeer-review

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.

Original languageEnglish
Pages (from-to)858-868
Number of pages11
JournalMolecular Ecology Resources
Volume17
Issue number5
Early online date28 Nov 2016
DOIs
Publication statusPublished - 1 Sep 2017

Keywords

  • plastid
  • chloroplast
  • genomic
  • next-generation sequencing
  • plant evolution

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