Huang Yiting, Luo Yingfeng, Lin Xiao
Department of Agri-microbiomics and Biotechnology, State Key Laboratory of Microbial Diversity and Innovative Utilization, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China.
University of the Chinese Academy of Sciences, Beijing 100049, China.
iScience. 2025 Jun 10;28(7):112869. doi: 10.1016/j.isci.2025.112869. eCollection 2025 Jul 18.
Sugarcane ( spp. hybrids) is an important crop for sugar and biofuel production. However, pathogens cause significant yield losses. Most plant resistance (R) proteins are nucleotide-binding leucine-rich repeat (NLR) proteins, which detect pathogen effectors and activate immune responses. Recent advances in polyploid sugarcane genomes will accelerate sugarcane resistance breeding, however, gene prediction in the complex polyploid genomes remains challenging. To address this, we developed a diploidy-assisted annotation of polyploid NLRs (DaapNLRSeek) pipeline to accurately predict and annotate genes from the complex polyploid sugarcane genomes. Using DaapNLRSeek, we annotated genes in and five sugarcane cultivars (R570, ZZ1, XTT22, Np-X, and AP85-441), analyzing their architecture, collinearity, and evolution. We also identified paired NLRs, TIR-only, and genes from these sugarcane genomes. Intriguingly, two sugarcane-paired s induce immune responses in . DaapNLRSeek bridges polyploid genome assembly with functional genomics and will accelerate sugarcane resistance breeding.
甘蔗（杂交种）是用于制糖和生物燃料生产的重要作物。然而，病原体导致产量大幅损失。大多数植物抗性（R）蛋白是核苷酸结合富含亮氨酸重复序列（NLR）蛋白，其可检测病原体效应子并激活免疫反应。多倍体甘蔗基因组的最新进展将加速甘蔗抗性育种，然而，在复杂的多倍体基因组中进行基因预测仍然具有挑战性。为解决这一问题，我们开发了一种多倍体NLRs的二倍体辅助注释（DaapNLRSeek）流程，以准确预测和注释来自复杂多倍体甘蔗基因组的基因。使用DaapNLRSeek，我们注释了[具体品种]和五个甘蔗品种（R570、ZZ1、XTT22、Np-X和AP85-441）中的基因，分析了它们的结构、共线性和进化。我们还从这些甘蔗基因组中鉴定出成对的NLRs、仅含TIR的基因以及[具体基因类型]基因。有趣的是，两个甘蔗成对的[具体基因名称]在[具体植物]中诱导免疫反应。DaapNLRSeek将多倍体基因组组装与功能基因组学联系起来，并将加速甘蔗抗性育种。
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