Gapless Genome Assembly of ZH8015 and Preliminary Multi-Omics Analysis to Investigate ZH8015’s Responses Against Brown Planthopper Infestation

doi:10.1016/j.rsci.2024.02.001

Abstract

Abstract:

Accurate genomic information is essential for advancing genetic breeding research in specific rice varieties. This study presented a gapless genome assembly of the indica rice cultivar Zhonghui 8015 (ZH8015) using PacBio HiFi, Hi-C, and ONT (Oxford Nanopore Technologies) ultra-long sequencing technologies, annotating 43 037 gene structures. Subsequently, utilizing this genome along with transcriptomic and metabolomic techniques, we explored ZH8015’s response to brown planthopper (BPH) infestation. Continuous transcriptomic sampling indicated significant changes in gene expression levels around 48 h after BPH feeding. Enrichment analysis revealed particularly significant alterations in genes related to reactive oxygen species scavenging and cell wall formation. Metabolomic results demonstrated marked increases in levels of several monosaccharides, which are components of the cell wall and dramatic changes in flavonoid contents. Omics association analysis identified differentially expressed genes associated with key metabolites, shedding light on ZH8015’s response to BPH infestation. In summary, this study constructed a reliable genome sequence resource for ZH8015, and the preliminary multi-omics results will guide future insect-resistant breeding research.

Key words: brown planthopper, gapless genome, genome assembly, multi-omics, Nilaparvata lugens, rice

Li Dian, Duan Wenjing, Liu Qun’en, Wu Weixun, Zhan Xiaodeng, Sun Lianping, Zhang Yingxin, Cheng Shihua. Gapless Genome Assembly of ZH8015 and Preliminary Multi-Omics Analysis to Investigate ZH8015’s Responses Against Brown Planthopper Infestation[J]. Rice Science, 2024, 31(3): 317-327.

Figures/Tables 4

Fig. 1. Genomic landscape of rice Zhonghui 8015. From inside to outside: Distribution of the genome (1st), GC skew of the whole genome (2nd) (i.e. the offset of GC content in single-stranded DNA), gene density (3rd), chromosome length (4th, orange ticks represent predicted centromere regions, and purple triangles represent 5′- and 3′-telomeres), the light green region is a significant nucleotide-binding leucine-rich repeat (NLR) gene enriched region at the telomeric end of chromosome 11 (5th), and distribution of identified NLR genes in the genome (6th).

Fig. 2. Differentially expressed genes (DEGs) in brown planthopper (BPH) infestation groups compared with control group. A, Venn plot for number of DEGs. B, Volcano plot for DEGs. Each point represents a DEG. The green points represent genes with up-regulated expression compared with the control RNA-seq (with none BPH infestation), the blue points represent down-regulated genes, and the gray points are genes without significant difference in expression. ER, Early stage RNA-seq; MR, Middle stage RNA-seq; LR, Late stage RNA-seq; FC, Fold change.

Fig. 3. Enrichment results of differentially expressed genes (DEGs) in three brown planthopper (BPH) infestation groups. A, Gene Ontology (GO) enrichment of ER vs CR. B, GO enrichment of MR vs CR. C, GO enrichment of LR vs CR. D, Kyoto Encyclopedia of Genes and Genomes enrichment results of three groups vs CR. CR, Control RNA-seq, with no BPH infestation; ER, Early stage RNA-seq, 12 h after BPH infestation; MR, Middle stage RNA-seq, 48 h after BPH infestation; LR, Late stage RNA-seq, 96 h after BPH infestation; BP, Biological process; CC, Cell component; MF, Molecular function. The size of the bubbles reflects the number of genes enriched in the KEGG pathway/GO term, while color reflects the significance of the enrichment.

Fig. 4. Integrated analysis of metabolomics data (at the middle stage, 48 h brown planthopper infestation). A, Orthogonal Partial Least Squares Discrimination Analysis for discriminating between different brown planthopper infestation groups. CM, Control metabolism; MM, Middle stage metabolism, 48 h brown planthopper infestation. B, Categorization of differentially abundant metabolites. C, Heatmap of Spearman correlation coefficients between differentially abundant metabolite and differentially expressed gene levels. Each row represents a gene, and each column represents a metabolite.

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