Chromosome-level genome assembly of Zizania latifolia provides insights into its seed shattering and phytocassane biosynthesis

Abstract

Chinese wild rice (Zizania latifolia; family: Gramineae) is a valuable medicinal homologous grain in East and Southeast Asia. Here, using Nanopore sequencing and Hi-C scaffolding, we generated a 547.38 Mb chromosome-level genome assembly comprising 332 contigs and 164 scaffolds (contig N50 = 4.48 Mb; scaffold N50 = 32.79 Mb). The genome harbors 38,852 genes, with 52.89% of the genome comprising repetitive sequences. Phylogenetic analyses revealed close relation of Z. latifolia to Leersia perrieri and Oryza species, with a divergence time of 19.7-31.0 million years. Collinearity and transcriptome analyses revealed candidate genes related to seed shattering, providing basic information on abscission layer formation and degradation in Z. latifolia. Moreover, two genomic blocks in the Z. latifolia genome showed good synteny with the rice phytocassane biosynthetic gene cluster. The updated genome will support future studies on the genetic improvement of Chinese wild rice and comparative analyses between Z. latifolia and other plants.

Fig. 1. Photographs of Chinese wild rice plants and inflorescence with seeds.

a Chinese wild rice plants growing in a paddy field. b Inflorescence and seed morphology of Chinese wild rice. The pictures were taken by Ning Yan from Tobacco Research Institute of Chinese Academy of Agricultural Sciences.

Fig. 2. Chinese wild rice genome information.

a Hi-C contact data mapped on the updated Chinese wild rice genome showing genome-wide all-by-all interactions. b Overview of the Chinese wild rice genome. Ring A: distribution of GC content (green); ring B: gene density (blue); ring C: density of repeat sequences (purple); and ring D: syntenic blocks within the genome.

Fig. 3. Comparative genomic analyses of Chinese wild rice genome.

a Distribution of gene copy number in Chinese wild rice and nine other species. b Venn diagram of shared orthologous gene families in Chinese wild rice and other four related gramineous species (Brachypodium distachyon, Leersia perrieri, Oryza brachyantha, and O. sativa). c Phylogenetic tree of Chinese wild rice and nine other species. “+” represents the number of gene families expanded on the node and “-” represents the number of gene families contracted on the node. The pie chart shows the proportion of the corresponding branch contraction and expansion gene families. d, KEGG enrichment analyses for the expanded genes in the Chinese wild rice genome. e Ks distribution in Chinese wild rice and other representative species.

Fig. 4. Histologic and transcriptome analyses of abscission layer formation (ALF) and degradation (ALD) in Chinese wild rice.

a ALF and b, ALD as revealed by staining with the cell-permeant dye Acridine Orange (green fluorescence: dye bound to dsDNA; red fluorescence: dye bound to ssDNA or RNA). The white arrows indicate the abscission layer. Scale bar = 200 μm. c Volcano plot of differentially expressed genes between ALF and ALD. In this figure, green, red, and black dots represent genes with a low expression, high expression, and non-differentially expressed genes, respectively. d Expression levels of genes related to seed shattering between ALF and ALD. e KEGG enrichment bubble plot of differentially expressed genes between ALF and ALD.

Fig. 5. Characterization of the phytocassane biosynthetic gene cluster in Zizania latifolia genome.

a, Genomic synteny between chromosome 2 of O. sativa and chromosomes 8 and 10 of Z. latifolia. Syntenic genomic blocks are illustrated by the grey lines. The homologous genomic regions of phytocassane biosynthetic gene clusters between O. sativa and Z. latifolia are highlighted in red. b Gene-level synteny between phytocassane biosynthetic gene cluster of O. sativa and Z. latifolia; CYP450 genes are colored dark yellow; genes coding terpene synthases are colored dark blue. The genes unrelated to the cluster are in grey. c Gene co-expression pattern for the genes in the two sub-gene clusters in chromosomes 8 and 10. d, Proposed evolutionary history of the phytocassane biosynthetic gene cluster in the Z. latifolia, L. perrieri, and Oryza species.