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.

Encyclia Hook. is a tropical orchid known for its delightful fragrance and distinctive flower shapes, which have been widely used as superior parents for inter and intrageneric breeding. In this study, karyotype analysis shows that the number of chromosomes in diploid plants of Encyclia is 40, with all species exhibiting mesial and central filamentous chromosomes. The karyotype of diploid plants is primarily 2B. Among the three detected intergeneric hybrids, both Enanthleya Circus Lady ‘Coastal Star’ and Guaricyclia Kyoguchi ‘Fumi’ are triploid, while Robertsara ‘Green Wonder’ is tetraploid. By evaluating various lysates and tissues, a flow cytometry system (FCM) is developed with Galbraith’s buffer (GLB) and tender leaves. By using Dendrobium officinale as an external reference, the genome size of the Encyclia species and its intra and intergeneric hybrids are assessed, which ranges from 1.07 Gb to 3.23 Gb. These results will establish a foundation for high-throughput identification of germplasms, advance crossbreeding efforts, and enhance the understanding of the genome in Encyclia.