Haplotype-resolved genome assembly of the tetraploid Youcha tree Camellia meiocarpa Hu

Camellia meiocarpa Hu, a member of <b>Youcha</b>species in the genus Camellia, is an important woody edible <b>Youcha</b> 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 <b>Youcha</b>.

小果油茶（Camellia meiocarpa Hu）是山茶属油茶（Youcha）类群的一员，为兼具极高生态与经济价值的重要木本食用油茶植物。该四倍体物种的单倍型解析基因组组装，可为解析基因组演化及亚基因组与单倍型间的功能分化提供重要参考。本研究结合PacBio HiFi、Hi-C及Illumina测序平台，完成了首个染色体级别的小果油茶单倍型解析参考基因组组装。最终获得的支架序列（scaffold）N50值分别为44.46 Mb与41.40 Mb，其被锚定至60条染色体，并进一步划分为4个各具独特转座子特征的独立单倍型。四个单倍型的基因组总长度分别为2967.25 Mb、3041.66 Mb、2946.45 Mb及3030.54 Mb。针对四个单倍型，本研究分别预测得到51336、52010、51586与52631个蛋白质编码基因，其中99.4%的基因获得了功能注释。完成注释后，我们在小果油茶的四个单倍型中鉴定出非编码RNA与重复序列元件。基因组重排与独特基因家族分析揭示了单倍型间显著的功能分化，表明它们在调控关键生命过程与表型方面发挥着独特作用。这款四倍体小果油茶的基因组资源，有望极大推动其分子与遗传层面的研究，尤其可为油茶的资源保护与开发利用提供关键支撑。