Genomics and Applied Biology 2024, Vol.15, No.1, 54-63 http://bioscipublisher.com/index.php/gab 56 phylogenetic tree illustrating the evolutionary divergence among these species over time. Key divergence events are highlighted, such as the fixation of Oryza species at 15 million years ago (mya), the divergence between AA and BB genomes at approximately 6.76 mya, and the divergence within Asian rice species around 0.55 mya (Stein et al., 2018). 1.2 History and current status of rice genome research Early genome research in rice focused on the sequencing of Oryza sativa, which has served as a model system for plant biology due to its relatively small genome size and economic importance. The completion of the rice genome sequence marked a significant milestone, enabling functional characterization and comparative genomic studies within the genus Oryza. Modern genomics technologies, such as single-molecule real-time (SMRT) sequencing, 10× Genomics, and Hi-C technologies, have further advanced our understanding of rice genomics. These technologies have facilitated high-quality de novo assemblies of wild rice genomes, revealing insights into the genomic basis of rice adaptation and domestication (Chen et al., 2019). Comparative genomic analyses have identified numerous genomic variants and structural variations that contribute to the diversity and evolution of rice species. 1.3 Current status of genomic diversity research Genomic diversity research in the Oryza genus has employed various diversity indicators, such as single nucleotide polymorphisms (SNPs), simple sequence repeats (SSRs), and linkage disequilibrium (LD) patterns. These indicators have been used to assess genetic diversity within and between different rice populations. For instance, a study using 176 SSR markers revealed significant molecular diversity and polymorphism among three groups of rice germplasm accessions, including domesticated and wild relatives. The analysis of molecular variance and principal coordinates analysis further highlighted the genetic differentiation among these groups. Additionally, the study of transposable elements has shown that these elements play a crucial role in genome size variation and structural evolution within the Oryza genus. The identification of lineage-specific gene expansions and contractions has provided insights into the adaptive evolution of rice species to diverse ecological niches (Li et al., 2020). The classification and distribution of the Oryza genus, the advancements in rice genome research, and the ongoing studies on genomic diversity collectively enhance our understanding of the evolutionary mechanisms and genetic diversity within this important genus. These insights are crucial for the continued improvement and conservation of rice as a vital global food resource. 2 The Structure and Function of the Rice Genome 2.1 Basic structure of rice genome The rice genome, particularly that of Oryza sativa, is composed of 12 chromosomes, which collectively harbor a diverse array of genes essential for various biological functions (Stein et al., 2018). The genome structure is characterized by a high degree of conservation across different species within the Oryza genus, despite the presence of lineage-specific variations and chromosomal rearrangements. Gene distribution within the rice genome is not uniform; certain regions are densely packed with genes, while others are more sparsely populated. This distribution is influenced by evolutionary processes such as gene duplication and transposon activity, which contribute to the functional diversification of the genome. The rice genome also exhibits significant polymorphism and linkage disequilibrium, which are crucial for understanding the genetic basis of traits and for crop improvement. 2.2 Genomic annotation and functional prediction Genomic annotation in rice involves the identification and characterization of genes and other functional elements within the genome. This process typically employs a combination of computational and experimental approaches. Methods such as comparative genomics, transcriptomics, and proteomics are used to predict gene functions and validate their roles. Comparative genomic analyses between different Oryza species have been particularly useful in identifying conserved and lineage-specific genes, as well as in understanding the evolutionary dynamics of
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