Telomere-to-Telomere assembly and annotation of Prunus salicina 'Fengtangli'

We generated a total of 26.84 Gb (~100× coverage, reads N50 of 17,471 bp) sequence coverage of raw PacBio high-fidelity long reads (HiFi) data and 30 Gb (∼120× coverage) of chromosome conformation capture sequencing (Hi-C) data for assembling the Prunus salicina ‘Fengtangli’ genome. For the initial assembly, the N50 value of contig-level for haplotype 1 and haplotype 2 were 20,111,805 bp and 19,658,610 bp, respectively, about 14 times that of the ‘Sanyueli’ contig-level assembly, with the largest contig reaching a length of 52,178,471bp. After anchoring and ordering, the scaffold N50 sizes reached 28.08 Mb and 28.37 Mb.24 of the expected 32 telomeres (8 chromosomes of two haplotypes) were identified, and 11 and 13 telomeres were found in PS_T2T_hap1 and PS_T2T_hap2. For gene annotation, 28,775 and 28,139 protein-coding genes were predicted for two haplotypes. BUSCOs assessment using the longest transcribed proteins revealed that two haplotypes captured 96.6% and 94.0% of a BUSCOs reference gene set, respectively. An Extensive de novo TE Annotator (EDTA) was used to generate a high-quality repetitive sequence library, and identified 119,630,196 bp and 121,705,710 bp of repetitive sequences in the two haplotypes, accounting for 45.41% and 46.19% of PS_T2T_hap1 and PS_T2T_hap2, respectively.本研究为组装李属（Prunus salicina）‘蜂糖李’基因组，共获取了26.84 Gb（约100×测序深度，读长N50为17471 bp）的原始PacBio高保真长读长（HiFi）测序数据，以及30 Gb（约120×测序深度）的染色体构象捕获测序（Hi-C）数据。 初始组装结果显示，单倍型1与单倍型2的重叠群（contig）水平N50值分别为20111805 bp与19658610 bp，约为‘三月李’重叠群水平组装结果的14倍；最大重叠群长度达52178471 bp。经过锚定与排序后，支架序列（scaffold）的N50长度分别达到28.08 Mb与28.37 Mb。本研究共鉴定到预期32个端粒（两个单倍型共8条染色体）中的24个，其中PS_T2T_hap1与PS_T2T_hap2分别包含11个与13个端粒。 基因注释阶段，本研究为两个单倍型分别预测得到28775个与28139个蛋白质编码基因。采用最长转录本进行BUSCO（Benchmarking Universal Single-Copy Orthologs）评估，结果显示两个单倍型分别覆盖了BUSCO参考基因集的96.6%与94.0%。 本研究使用从头转座子注释器（Extensive de novo TE Annotator，EDTA）构建了高质量的重复序列文库，并在两个单倍型中分别鉴定到119630196 bp与121705710 bp的重复序列，分别占PS_T2T_hap1与PS_T2T_hap2基因组总长度的45.41%与46.19%。