Haplotype-resolved genome assembly of the tetraploid Youcha tree Camellia meiocarpa Hu
Camellia meiocarpa Hu, a member of Youchaspecies in the genus Camellia, is an important woody edible Youcha plant with high ecological and economic value. The haplotype-resolved genome assembly of this tetraploid species can shed light on genomic evolution and the functional divergence among subgenomes and haplotypes. In this study, we assembled the first haplotype-resolved reference genome of C. meiocarpa at the chromosome level, utilizing a combination of sequencing technologies: PacBio HiFi, Hi-C, and Illumina platforms. The resulting scaffolds, with an N50 of 44.46 Mb and 41.40 Mb, were anchored to 60 chromosomes and further assigned to four distinct haplotypes, each with unique transposon characteristics. The lengths of four hyplotypes are 2967.25Mb, 3041.66Mb, 2946.45Mb and 3030.54Mb. A total of 51336, 52010, 51586, and 52631 protein-coding genes were predicted for each of the four haplotypes, of which 99.4% were functionally annotated. Following annotation, we identified non-coding RNAs and repetitive elements within the four haplotypes of C. meiocarpa. Genome rearrangements and unique gene families revealed significant functional divergence among the haplotypes, suggesting their distinct roles in controlling vital processes and phenotypes. This genomic resource of the tetraploid C. meiocarpa is expected to greatly facilitate research at the molecular and genetic levels, particularly for the conservation and utilization of the Youcha.