Assembly, annotation and analysis of chloroplast genomes

Chloroplast genome data is useful for phylogenetic analyses, for species identification and for tracing evolutionary adaptations. Current sequencing technology enables us to obtain complete plastome on a large scale. The aim of this study was to develop robust computational plastome assembly and annotation tools and databases. In particular, a novel annotation algorithm was developed to address challenges in plastome annotation. The annotation software Chloe (https://chloe.plantenergy.edu.au) was used to re-annotate the ~4000 available plastomes of land plants in GenBank, and annotate the newly assembled plastomes. These newly developed tools and databases are valuable resources for future studies in chloroplast genomics.