First chromosome-scale genome assembly for holly reported

Ilex (Aquifoliaceae), the hollies, is one of the largest and most characteristic woody dioecious genera in tropical and subtropical southwest China. Many species throughout the range of the genus have been used as sources of beverages and medicines, ornamentals, honey plants, dyes, timber, and other minor uses. Subspecific variation has been utilized in horticulture for the development of new cultivars and hybrids, but not yet in the huge market for holly beverages and medicines.

In a study published in Horticulture Research, scientists from the Xishuangbanna Tropical Botanical Garden (XTBG) of the Chinese Academy of Sciences investigated the subspecific variation and local adaptation in Ilex polyneura, a widespread diploid member of the deciduous East Asian clade. Using a combination of Illumina short reads, PacBio single-molecule real-time sequencing technology, and Hi-C techniques, they assembled the whole genome of Ilex polyneura.

Using the high-quality genome as a reference, they conducted a population genomics study of 112 individuals collected from 21 populations across the whole elevation range of the species using restriction site-associated DNA sequencing (RADseq).

The assembled genome was approximately 727.10 Mb. A BUSCO analysis produced 97.6 percent universal single-copy orthologs, indicating high contiguity and completeness of the assembly, and 98.9 percent of the genome assembly was anchored to 20 pseudochromosomes.

"This is the first published genome at chromosome-scale in the huge genus Ilex as well as in the order Aquifoliales. It is also the only genome available for a woody member of the campanulids," said Yao Xin of XTBG.

Population genetic analyses revealed evidence of divergent selection leading to genomic adaptation of Ilex polyneura to different elevations. Populations at low and high elevations had simpler genetic structures, while populations at medium elevations had mixed ancestry from both low and high elevations.

The study thus provides evidence for genetic divergence and significant local adaptation in the face of the expected high levels of gene flow between populations in Ilex.