DaapNLRSeek, prediction, and evolution of resistance genes in polyploid sugarcane genomes

IF 4.6 2区综合性期刊 Q1 MULTIDISCIPLINARY SCIENCES

iScience Pub Date : 2025-06-10 DOI:10.1016/j.isci.2025.112869

Yiting Huang , Yingfeng Luo , Xiao Lin

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引用次数: 0

Abstract

Sugarcane (Saccharum 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, NLR 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 NLR genes from the complex polyploid sugarcane genomes. Using DaapNLRSeek, we annotated NLR genes in Erianthus rufipilus 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 TPK genes from these sugarcane genomes. Intriguingly, two sugarcane-paired NLRs induce immune responses in Nicotiana benthamiana. DaapNLRSeek bridges polyploid genome assembly with functional genomics and will accelerate sugarcane resistance breeding.

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多倍体甘蔗基因组中抗性基因的寻找、预测和进化

甘蔗（Saccharum spp.杂种）是制糖和生物燃料生产的重要作物。然而，病原体会造成重大的产量损失。大多数植物抗性(R)蛋白是核苷酸结合的富含亮氨酸重复序列（NLR）蛋白，其检测病原体效应物并激活免疫反应。甘蔗多倍体基因组的最新研究进展将加速甘蔗抗性育种，然而，复杂多倍体基因组中NLR基因的预测仍然具有挑战性。为了解决这个问题，我们开发了一个多倍体NLR的二倍体辅助注释（DaapNLRSeek）管道，以准确预测和注释复杂多倍体甘蔗基因组中的NLR基因。利用DaapNLRSeek软件，对5个甘蔗品种（R570、ZZ1、XTT22、Np-X和AP85-441）的NLR基因进行了标记，分析了NLR基因的结构、共线性和进化特征。我们还从这些甘蔗基因组中鉴定了成对的NLRs、TIR-only和TPK基因。有趣的是，两种甘蔗配对的nlr诱导了烟叶的免疫反应。DaapNLRSeek将多倍体基因组组装与功能基因组学连接起来，将加速甘蔗抗性育种。

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来源期刊

iScience Multidisciplinary-Multidisciplinary

CiteScore

7.20

自引率

1.70%

发文量

1972

审稿时长

6 weeks

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