数字农科院2.0

A near-complete genome assembly for northern wild rice (Zizania palustris L.)

文献类型： 外文期刊

作者： Ma, Qing;Gu, Lei;Xie, Yanning;Li, Wanhong;Wang, Lixia;Qiu, Jie;Zhang, Zhongfeng;Yan, Ning

作者机构：

关键词： Northern wild rice;Genome assembly;Long terminal repeat;Phytocassane biosynthetic gene cluster

期刊名称： CROP JOURNAL

ISSN： 2095-5421

年卷期： 2025 年 13 卷 6 期

页码：

收录情况： SCIE（2025版） ; ; CSCD（2025-2026年度） ; ; 科技核心（2024版） ; ; 农林核心（2024版）

摘要： Northern wild rice (NWR; Zizania palustris L.), an annual aquatic plant in the Poaceae family, has high economic importance due to its nutrient-rich grains. However, the existing NWR genome assembly for this species has severe fragmentation and incomplete gene representation. A near-complete genome was assembled in this study to provide a high-quality genomic reference for NWR-associated research. The assembled genome exhibited a total contig length of 1.41 Gb and a contig N50 of 109.22 Mb. Overall, a 73.60% repetitive sequence content was identified and 47,804 genes predicted. Phylogenetic analysis indicated that Z. palustris was most closely related to Zizania latifolia, with an estimated divergence time of 4.57-8.15 Mya. Meanwhile, Z. palustris underwent a recent, species-specific long terminal repeat (LTR) expansion, associated with its larger genome size. We identified two genomic blocks in the Z. palustris and Z. latifolia genomes that exhibit strong synteny with the rice phytocassane biosynthetic gene cluster. The centromeric satellite repeats in Z. palustris identified in this study primarily comprised a 145 bp repetitive unit. The findings also revealed centromere homogenisation and rearrangement accompanied by LTR invasion in NWR. Among the genes missing in the previous NWR genome, we observed LTR insertion events that resulted in expanded gene lengths in our updated NWR genome. The present updated NWR genome provides a valuable resource for crop genetic improvement, functional gene discovery, and research on critical biological processes. (c) 2025 Crop Science Society of China and Institute of Crop Science, CAAS. Production and hosting by Elsevier B.V. on behalf of KeAi Communications Co., Ltd. This is an open access article under the CC BY-NCND license (http://creativecommons.org/licenses/by-nc-nd/4.0/).

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