The chromosome-level holly (Ilex latifolia) genome reveals key enzymes in triterpenoid saponin biosynthesis and fruit color change

Abstract

The Ilex L. (hollies) genus of Aquifoliaceae shows high species diversity in tropical and subtropical regions of Asia and South America. Throughout the range of the genus, Ilex species have been widely used in beverage and medicine production and as ornamentals. Here, we assembled a high-quality, chromosome-level genome of Ilex latifolia, which has extremely high economic value because of its useful secondary metabolite production and the high ornamental value of its decorative red berries. The 99.8% genome sequence was anchored to 20 pseudochromosomes, with a total length of 766.02 Mb and a scaffold N50 of 33.45 Mb. Based on the comparative genomic analysis of 14 angiosperm species, we recovered I. latifolia as the sister group to all other campanulids. Two whole-genome duplication (WGD) events were identified in hollies: one shared ancient WGD in the ancestor of all eudicots and a recent and independent WGD in hollies. We performed a genome-wide search to screen candidate genes involved in the biosynthesis of pentacyclic triterpenoid saponins in I. latifolia. Three subfamilies of CYP450 (CYP71A, CYP72A, and CYP716A) appear to have expanded. The transcriptomic analysis of I. latifolia leaves at five developmental stages revealed that two CYP716A genes and one CYP72A gene probably play important roles in this biosynthetic pathway. In addition, we totally identified 12 genes in the biosynthesis pathways of pelargonidin and cyanidin and observed their differential expression in green and red fruit pericarps, suggesting an association between pelargonidin and cyanidin biosynthesis and fruit pericarp color change. The accumulation of pelargonidin and cyanidin is expected to play an important role in the ornamental value of I. latifolia. Altogether, this study elucidated the molecular basis of the medicinal and ornamental value of I. latifolia, providing a data basis and promising clues for further applications.

Yerba mate (Ilex paraguariensis) genome provides new insights into convergent evolution of caffeine biosynthesis

“…1). This confirms the lineage-specific polyploidization event (Ip-α) previously reported in Ilex 9, 11, 36, 37 , in addition to the shared ancestral WGT-γ which is indicated by a median K s value of ∼1.4 (Fig. 2b).…”

“…Recent transcriptome-based analyses 36, 37 reported an ancient polyploidization event in the Ilex lineage around 60 Ma (Cretaceous–Paleogene boundary), based on phylogenomic and synonymous substitution rate (K s ) evidence. Evolutionary analyses of Ilex polyneura 9 and Ilex latifolia 11 genomes also provided evidence of a shared Ilex -specific whole genome duplication (WGD). As YM is the first American holly to have its genome sequenced, we performed synteny-based analyses of its genome to deepen our understanding of Aquifoliales evolution (Fig.…”

Genome Survey Sequencing and Genetic Background Characterization of Ilex chinensis Sims (Aquifoliaceae) Based on Next-Generation Sequencing

“…In this study, the genome size of I. chinensis determined by flow cytometry was approximately 660 Mb, and our k-mer analysis using genome survey data suggested a genome size of around 618 Mb, which was close to the results derived from flow cytometry. Together, these data provide robust evidence that the genome size of I. chinensis is 618–660 Mb, a value that was slightly smaller than those of other members of the Ilex genus family reported previously [ 9 , 10 , 11 ]. I. chinensis , with its small genome size, can often be given priority in performing whole-genome sequencing projects for economic reasons [ 34 ].…”

“…The current research on I. chinensis mainly focuses on the chemical composition and pharmacological effects, while the genetic information of I. chinensis has remained largely unknown [ 4 , 5 , 6 ], although some studies have performed transcriptome analysis [ 7 ], genetic diversity analysis based on SSR markers [ 2 ], and complete chloroplast genome sequencing [ 8 ]. Thus far, most genomic research on the Ilex genus is focused on very few commercially important species, including I. latifolia [ 9 ], I. asprella [ 10 ], and I. polyneura [ 11 ], whereas few studies have been reported for I. chinensis . The lack of a reference genome for I. chinensis leads to limited enhancement in molecular biology and breeding programs.…”

Application of third-generation sequencing to herbal genomics

“…According to previous studies ( Supplementary Table 1 ), nuclear genomes of medicinal plants are usually diploids or polyploids with large genome sizes, high heterozygosity, and high repeat sequences proportion. It is also demonstrated that the GC content of nuclear genomes of many medicinal plants is generally lower than 50% on average and unevenly distributed in different chromosomes ( Shang et al., 2020 ; Sun et al., 2020 ; Wu et al., 2021b ; Li et al., 2022a ; Xu et al., 2022a ). These features have brought traditional short reads methods under challenge.…”