The genus Phoebe Nees in the family Lauraceae includes around 100 tree species distributed in tropical and subtropical Asia. It is an economically important genus. However, systematics of the genus is unclear, and currently there is no species-level phylogeny.Researchers thus wondered if there are other molecular markers from chloroplast genomes of Phoebe useful to reconstruct the phylogeny of the genus.
Researchers from Xishuangbanna Tropical Botanical Garden (XTBG) sampled two species of Phoebe (Lauraceae) for sequencing the complete chloroplast genomes. They determined the complete chloroplast genome sequences of the two species with long-range PCR and next genome sequencing technologies, and identified mutation sites and highly variable regions
The researchers present two complete chloroplast genomes for rare woody plants in the genus Phoebe obtained by using Illumina high-throughput sequencing technology. Both genomes are very similar in structure and size, but the IR regions of P. omeiensis are 17 and 38 bp shorter than those of P. sheareri and C. kanehirae, while they are 2 bp larger than those of M. balansae and M. yunnanensis.
Comparative analysis indicated that the length of the truncated ycf1 gene differed among the chloroplast genomes from six species in the Laurales. The length of the truncated ycf1 gene of P. omeiensis is 17 and 27 bp shorter than those of P. sheareri and C. kanehirae, and 1 bp longer than those of M. balansae and M. yunnanensis.
It confirms that the cause of the IR contraction in the Laurales is the truncation of the ycf1 gene at the IR boundary.