Structural characterization and comparative analysis of the chloroplast genome of Ginkgo biloba and other gymnosperms

Ginkgo biloba is a famous living “fossil” and has played an important role in the evolution of the Plant Kingdom. Here, the complete chloroplast genome of G. biloba was sequenced and analysed. The chloroplast genome was 156,990 bp long and predicted to encode 134 genes including 85 protein-coding genes, 41 tRNA genes and 8 rRNA genes. The chloroplast genome has a typical quadripartite structure with a pair of inverted repeat regions (IRa and IRb, 17,732 bp), a large (LSC, 99,259 bp) and small single (SSC, 22,267 bp) copy region. After an extensive comparison to previously published gymnosperm plastomes, the gene content and organisation of G. biloba showed high divergence, although part was relatively conserved. The two typical IR regions in the G. biloba chloroplast genome were relatively shorter because it the ycf2 gene. In addition, it was obvious that the IR regions and gene loss were responsible for changes in chloroplast genome size and structure stability, which influenced plastome evolution in different gymnosperms. Phylogenetic analysis revealed that G. biloba is sister to cycads rather than to gnetophytes, cupressophytes, and Pinaceae. Overall, the study showed that the genomic characteristics of G. biloba would be of great help in the further research on the taxonomy, species identification and evolutionary history of gymnosperms, especially for their position in plant systematics and evolution.