The telomere‐to‐telomere gap‐free genome of four rice parents reveals SV and PAV patterns in hybrid rice breeding

作者：Yilin Zhang, Jun Fu, Kai Wang, Xue Han, Tianze Yan, Yanning Su, Yanfeng Li, Zechuan Lin, Peng Qin, Chenjian Fu, Xing Wang Deng, Degui Zhou, Yuanzhu Yang, Hang He · 发表于：Plant Biotechnology Journal · 年份：2022 · DOI：10.1111/pbi.13880 · 被引用次数：66 · 研究领域：Chromosomal and Genetic Variations、Silicon Effects in Agriculture、Genomics and Phylogenetic Studies

Xiangling628S (XL628S), Longke638S (LK638S), and Jing4155S (J4155S) are excellent two-line sterile lines, and Huazhan (HZ) and Wu-Shan-Si-Miao (WSSM) are both two-line and three-line restorers. LK638S and J4155S are derived from XL628S, belonging to the same pedigree, while WSSM is derived from HZ, belonging to another pedigree. Between 2018 and 2020, the planting area of JLYHZ, JLY534, and LLYHZ ranked among top 3 of China's hybrid rice (Figure 1a). In the published genomes, 82 and 129 gaps remained for J4155S and Huazhan assemblies, respectively, while no assemblies for LK638S and XL628S were observed (Qin et al., 2021; Zhang et al., 2021). To analyze the genomic basis of modern elite hybrid rice heterosis, high-quality genome reference of core restorer lines and sterile lines is necessary. We adopted an assembly strategy that integrated Pacbio HiFi and Oxford Nanopore Technology (ONT) ultra-long reads and then generated four gap-free genomes. The estimated genome size was 400 Mb by K-mer analysis. For HiFi, the assembly of contigs by hifiasm realized the gapless assembly by utilizing the gap-filling method PGA (Li et al., 2021). For ONT, the ultra-long reads directly assembled 12 gapless contigs by Nextdenovo which could be entirely anchored to chromosomes completely. Finally, the HiFi and short reads were combined to polish the ONT assembly. The Illumina mapping rates were from 98.83% to 99.66% and the coverage rates were more than 99.97%. The completeness of the genomes ...