Beijing Key Laboratory for Agriculture Application and New Technique, College of Plant Science and Technology, Beijing University of Agriculture, Beijing, 102206, China.
Bioinformatics Center, Beijing University of Agriculture, Beijing, 102206, China.
Sci Data. 2024 May 29;11(1):552. doi: 10.1038/s41597-024-03405-x.
Malus hybrid 'SH6' (M. honanensis × M. domestica)is a commonly used apple interstock in China, known for its excellent dwarfing characteristics and cold tolerance. In this study, a combined strategy utilizing PacBio HiFi, Hi-C and parental resequencing data were employed to assemble two haploid genomes for 'SH6'. After chromosome anchoring, the final hapH genome size was 596.63 Mb, with a contig N50 of 34.38 Mb. The hapR genome was 649.37 Mb, with a contig N50 of 36.84 Mb. Further analysis predicted that repeated sequences made up 59.69% and 62.52% of the entire genome, respectively. Gene annotations revealed 45,435 genes for hapH and 48,261 genes for hapR. Combined with genomic synteny we suggest that the hapR genome originates from its maternal parent M. domestica cv. Ralls Janet, while the hapH genome comes from its paternal parent, M. honanensis. The assembled genome significantly contributes to the discovery of genes associated with apple dwarfing and the molecular mechanisms governing them.
“SH6”苹果（蜜脆×富士）杂种是中国常用的苹果矮化砧木，具有优良的矮化特性和耐寒性。本研究采用 PacBio HiFi、Hi-C 和双亲重测序数据的联合策略，组装了“SH6”的两个单体基因组。染色体锚定后，最终的 hap H 基因组大小为 596.63 Mb，contig N50 为 34.38 Mb。hap R 基因组大小为 649.37 Mb，contig N50 为 36.84 Mb。进一步分析预测，重复序列分别占整个基因组的 59.69%和 62.52%。基因注释表明，hap H 基因组有 45435 个基因，hap R 基因组有 48261 个基因。结合基因组共线性，我们推测 hap R 基因组来源于其母本红肉苹果，而 hap H 基因组来源于其父本蜜脆。组装的基因组为发现与苹果矮化相关的基因及其调控机制提供了重要资源。
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