Rice Genomics and Genetics 2025, Vol.16, No.3, 159-179 http://cropscipublisher.com/index.php/rgg 163 chromosome-level assemblies for each rice genome. This approach ensures that each assembled genome is of reference quality, facilitating accurate detection of large inversions or translocations. In addition, optical mapping and Bionano genome maps have sometimes been employed to resolve complex repeats or structural ambiguities. An emerging strategy is to use hybrid assembly pipelines that integrate Illumina, PacBio/Nanopore, and Hi-C data to maximize accuracy. In summary, the state-of-the-art in rice pan-genome sequencing is to generate high-depth long reads for each accession, polish the assemblies with short reads, and scaffold them with Hi-C, yielding multiple high-quality genomes for comparative analysis. Figure 1 A syntelog-based pangenome of rice. a Consensus quality values and number of homozygous SNPs based on self-mapping for genomes in four pan-genome projects. b Phylogeny of rice genomes used in this study and their pairwise synteny kinship. c The relationship among rice genomes measured by genetic distance (IBD, identity-by-descent) based on SNPs and synteny based on gene orders. d Number of syntelog groups (SGs) represented in all 74 rice genomes versus the number of genomes. The subspecies pan-genome compositions for GJ and XI were extracted from the whole rice pan-genome. The numbers of core (present in the genomes of all accessions), soft-core (present in the genomes of > 90% accessions), dispensable (present in the genomes of less than 90% of all but at least two accessions), private (only present in a single genome), and absent SGs (identified by using all populations but absent in sub-population) were counted (Adopted from Wu et al., 2023)
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