Revealing Genomic Traits and Evolutionary Insights of Oryza officinalis from Southern China Through Genome Assembly and Transcriptome Analysis

Can Chen; Haifei Hu; Hui Guo; Xiuzhong Xia; Zongqiong Zhang; Baoxuan Nong; Rui Feng; Shuhui Liang; Boheng Liu; Jianhui Liu; Danting Li; Junliang Zhao; Xinghai Yang

Revealing Genomic Traits and Evolutionary Insights of Oryza officinalis from Southern China Through Genome Assembly and Transcriptome Analysis

2025

Abstract Wild rice, as the ancestor of cultivated rice, has accumulated a wide range of beneficial traits through prolonged natural selection and evolution. Oryza officinalis, belonging to the CC genome, differs significantly from the AA genome. In this study, we utilized second- and third-generation sequencing, along with Hi-C technology, to assemble the genome of MT10 (O. officinalis). The assembled genome is 552.58 Mb, with contigs and scaffold N50 values of 40.04 and 44.48 Mb, respectively, and 96.73% of the sequences anchored to 12 chromosomes. A total of 33,813 genes were annotated, and repetitive sequences account for 54.24% of the MT10 genome. The number of unique genes in MT10 exceeds that in the O. officinalis genome from Thailand, and their divergence time is estimated at 1.6 million years ago. The MT10 genome exhibits fewer expanded gene families compared to contracted ones, with the expanded families predominantly associated with disease and pest resistance. Comparative genomic analysis of MT10 and Nipponbare reveals sequence variations in biotic and abiotic resistance-related genes. In particular, the presence of R genes and cystatin gene families in MT10 may contribute to its unique insect resistance. Transcriptome analyses indicate that flavonoid biosynthesis and MAPK-related genes are expressed in response to brown planthopper infestation. This study represents the first chromosome-level genome assembly of MT10, providing a reference sequence for the efficient cloning of beneficial genes from O. officinalis, which holds significant potential for the genetic improvement of cultivated rice.

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