Ilex, in the monogeneric family Aquifoliaceae, is the largest woody dioecious genus in the angiosperms with approximately 600 species. The genus is widespread in mesic habitats but the global diversity centers are in East Asia and South America. In China, several species of Ilex are used to produce a popular medicinal tea, kuding cha. Ilex species are also widely grown as ornamental plants because of their persistent red fruits and often distinctive leaves. However, the taxonomy and evolutionary history of the genus remain unclear due to the lack of a robust species-level phylogeny.

Researchers from Xishuangbanna Tropical Botanical Garden (XTBG) presented the complete chloroplast genomes of seven Ilex species through Illumina sequencing and reference-guided assembly of de novo contigs. They then tested the feasibility of phylogeny reconstruction using chloroplast genomes in Ilex. A new chloroplast genome for Helwingia himalaica, from the most closely related family, Helwingiaceae, was used as the outgroup.

The researchers compared topologies of the phylogenies constructed from different molecular datasets, including the whole cp genome, the coding regions, and single-copy region (LSC), inverted repeat (IR), small single-copy region (SSC), and introns and spacers. Eleven divergent regions were identified, which can be used to develop phylogenetic markers.

A total of 144 genes were identified, including 96 protein-coding genes, 40 tRNA and 8 rRNA. Thirty-four repetitive sequences were identified in Ilex pubescens, with lengths >14 bp and identity >90%, and 11 divergence hotspot regions that could be targeted for phylogenetic markers.

Their results will be useful for identification at the species level and for helping to resolve the deeper branches of the phylogeny.

The study entitled “Chloroplast genome structure in Ilex (Aquifoliaceae)” has been published in Scientific Reports.