A telomere-to-telomere genome assembly of Camellia nitidissima

Abstract

Camellia nitidissima is the model species of the Camellia sect. Chrysantha Chang, the only lineage within the genus Camellia known to produce golden-yellow flowers. This species holds high aesthetic, germplasm and medical value. Unfortunately, due to excessive collection and habitat loss, C. nitidissima is classified as a critically endangered plant. In this study, we assembled a telomere-to-telomere (T2T) genome of C. nitidissima by incorporating PacBio HiFi and Hi-C data. The assembled genome consisted of 15 pseudo-chromosomes, with a total size estimated to be 2.72 Gb. The GC content and repetitive sequences occupied 38.05% and 84.38% of the assembled genome, respectively. In total, 35,701 protein-coding genes were annotated. Multiple evaluation methods confirmed the contiguity (contig N50: 81.74 Mb), completeness (BUSCOs: 98.80%) and high LTR Assembly Index (LAI: 14.57) of the genome. This high-quality T2T genome will provide valuable insights into the genomic characteristics of C. nitidissima and facilitate conservation efforts as well as functional genomic studies in Camellia sect. Chrysantha species.

Fig. 1

Example photo captions for different blooming stages of Camellia nitidissima. (a) flower bud initiation stage, at the onset of bud development, newly emerging flower buds are green. (b) early flower bud stage, the bud transitions to a yellow hue. (c) flower bud enlargement stage, the bud continues to grow and enlarge, turning a golden yellow as it approaches anthesis. (d) early flowering stage, the petals gradually unfurl as the flower begins to open. (e) blooming stage, the petals are fully expanded, marking the full anthesis.

Fig. 2

Features of the Camellia nitidissima genome. (a–g) Circular tracks represent, from outer to inner, 15 chromosomal-level scaffolds (Chr01-Chr15), percentage of repeats (0%–100%), Gypsy (0%–99.96%), Copia (0%–99.80%), gene density (0–26), GC content (23.39%–61.69%) and the spectrum of collinear analysis (each line connects one pair of homologous genes and a cluster of such lines represents one collinear block). All statistics are calculated in 200-Kb windows. (h) The Hi-C heatmap of the Camellia nitidissima genome. Each box represents a pseudo-chromosome. (i) Long-read mapping coverage of all pseudo-chromosomes. (j) Short-read mapping coverage of all pseudo-chromosomes.