Chromosome-level and haplotype-resolved genome assembly of Bougainvillea glabra

Abstract

Bougainvillea glabra Choisy, a common perennial shrub or climbing vine in tropical and subtropical areas, has significant ornamental and ecological value due to its showy floriferous blooms and adaptability to multiple environmental stresses. In this study, based on PacBio and Hi-C sequencing data, we presented the haplotype-resolved, and chromosome-level assembled genomes for B. glabra (2n = 34). We obtained two haplotypes with genome size of 2,855,692,602 bp and 2,889,511,499 bp, N50 of 165 Mbp and 167 Mbp, and both anchored to 17 chromosomes with anchor ratio of 97.07% and 97.55%, respectively. Through the BUSCO evaluation process, the two assembled haplotypes both exhibited the high score of 96%. By combining the high-confidence different evidence of genome structure annotation pipeline we annotated each haplotype containing ~33,000 predicted genes, of which 86% were functionally annotated by different databases. These high-quality haplotypes assembly and annotation results will serve as a great genomic resource to explore the ornamental traits and environmental adaptability and accelerate improvement in future.

Fig. 1

The overview features of the B. glabra Choisy. (a) Morphological characters of floral organs in B. glabra plants. The blooming shoots are densely arranged with inflorescences arise as terminal or axillary cymose. The inflorescences show asynchronous flowering, with some differences in timing among individuals. The flower is salver-shaped, with tubular perianths constricted in the middle, its pedicel is attached to the central midrib of bract. Axillary thorns can become hard through lignification during vegetative growth stage, or differentiate into inflorescences during reproductive growth stage. (b) The genome survey results based on the kmer size of 51. (c) and (d) exhibited the Hi-C heatmap of Hap1 and Hap2 respectively. The darker colours indicate that contigs in the region have more interactions with each other. (e and f) exhibited the kmer spectrum analysis performed by KAT, the black region represents the proportion of kmers present in the HiFi reads but missing in the assemblies. Other colours indicate how many times the specific kmer occurred in the assembled genome.

Fig. 2

The assembly and assessment results of two different haplotypes in B. glabra Choisy. (a) The circos plot for Hap1 and Hap2 assembled results, the same chromosome numbers indicated that the homologous chromosome. From the outside to the inside, each circos represents the chromosome, GC ratio, the gene density and the repeat content density. (b) The BUSCO evaluation results of the assembly and annotation results. (c) The ratio of different variation type in the total genome size between the Hap1 and Hap2.