Advances in Phylogenomics Based on Complete Chloroplast Genomes

Phylogenomics is a new synthesized discipline which combines genomics with phylogenetics. Phylogenomics based on chloroplast genomes has shown many great advantages in plant phylogenetic research in recent years, providing resolutions for phylogeny of some taxonomically difficult groups of plants. However, there are some problems coming along with chloroplast phylogenomics as well. In this review, the application prospects and potential problems of chloroplast phylogenomics in plant phylogenetic reconstruction were discussed based on recent phylogenomic case studies. The influence of next-generation sequencing on chloroplast phylogenomics was also discussed.