Rice Genomics and Genetics 2024, Vol.15, No.4, 164-177 http://cropscipublisher.com/index.php/rgg 165 2 Structural Genomics of Oryza 2.1 Genome sequencing projects The sequencing of the rice (Oryza sativa) genome has been a pivotal milestone in plant genomics, providing a comprehensive resource for genetic studies and crop improvement. The first complete rice genome was sequenced nearly two decades ago, setting a precedent for subsequent genomic projects. Among the major sequenced genomes are Oryza sativa, Oryza rufipogon, and Oryza glaberrima. The sequencing of these genomes has provided a comprehensive view of the genetic makeup of both cultivated and wild rice species, revealing insights into their domestication, adaptation, and potential for crop improvement (Chen et al., 2019). Recent advancements have led to the development of gap-free reference genomes for two elite O. sativa varieties, 'Zhenshan 97 (ZS97)' and 'Minghui 63 (MH63)' (Figure 1), which are instrumental in studying heterosis and yield (Song et al., 2021). These high-quality reference genomes facilitate a deeper understanding of the genetic architecture and functional elements within the rice genome. Figure 1 Characterization of complete rice centromeres (Adopted from Song et al., 2021) Image caption: A: The delimiting of MH63RS3 centromeres. The layers of each chromosome graph indicate (1) the density of read mapping from CENH3 ChIP-seq with sliding windows of 10 kb and 20 kb shown in gray and blue lines, respectively; (2) the CentO satellite distribution; (3) non-TE gene distribution; and (4) TE distribution, respectively. The dotted frame represents the defined centromere region; B: Fluorescence in situ hybridization of mitotic metaphase chromosomes in MH63 and ZS97 using CENH3 ChIP-DNA as probe (red) with chromosomes counterstained with DAPI (blue); C: Coverage of HiFi, CLR, and Illumina reads and distribution of TEs in the centromere on chr1 (extended 500 kb left and right) of MH63RS3; D: The pairwise synteny visualization of chr1 centromere regions between ZS97RS3 and MH63RS3. Green lines link synteny genes between ZS97RS3 and MH63RS3. Yellow blocks are CoERs; E: Characteristics of the centromere on chr1 of MH63RS3. The 10 layers demonstrate the histone CENH3 distribution, CentOsatellite distribution, gene distribution, gene expression level (in leaf, root, and panicle), methylation distribution (of CG, CHG, and CHH), andCentOsequence similarity, respectively (Adopted from Song et al., 2021)
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