DataSheet_1_Genome-wide analysis of NBS-LRR genes revealed contribution of disease resistance from Saccharum spontaneum to modern sugarcane cultivar.docx

IntroductionDuring plant evolution, nucleotide-binding sites (NBS) and leucine-rich repeat (LRR) genes have made significant contributions to plant disease resistance. With many high-quality plant genomes sequenced, identification and comprehensive analyses of NBS-LRR genes at whole genome level are of great importance to understand and utilize them.
MethodsIn this study, we identified the NBS-LRR genes of 23 representative species at whole genome level, and researches on NBS-LRR genes of four monocotyledonous grass species, Saccharum spontaneum, Saccharum officinarum, Sorghum bicolor and Miscanthus sinensis, were focused.
Results and discussionWe found that whole genome duplication, gene expansion, and allele loss could be factors affecting the number of NBS-LRR genes in the species, and whole genome duplication is likely to be the main cause of the number of NBS-LRR genes in sugarcane. Meanwhile, we also found a progressive trend of positive selection on NBS-LRR genes. These studies further elucidated the evolutionary pattern of NBS-LRR genes in plants. Transcriptome data from multiple sugarcane diseases revealed that more differentially expressed NBS-LRR genes were derived from S. spontaneum than from S. officinarum in modern sugarcane cultivars, and the proportion was significantly higher than the expected. This finding reveals that S. spontaneum has a greater contribution to disease resistance for modern sugarcane cultivars. In addition, we observed allelespecific expression of seven NBS-LRR genes under leaf scald, and 125 NBS-LRR genes responding to multiple diseases were identified. Finally, we built a plant NBS-LRR gene database to facilitate subsequent analysis and use of NBSLRR genes obtained here. In conclusion, this study complemented and completed the research of plant NBS-LRR genes, and discussed how NBS-LRR genes responding to sugarcane diseases, which provided a guide and genetic resources for further research and utilization of NBS-LRR genes.

引言：在植物演化进程中，核苷酸结合位点（nucleotide-binding sites, NBS）与富亮氨酸重复序列（leucine-rich repeat, LRR）类基因在植物抗病性方面发挥了重要作用。随着大量高质量植物基因组被测序完成，在全基因组层面开展核苷酸结合位点-富亮氨酸重复序列（NBS-LRR）基因的鉴定与综合分析，对于深入理解并利用这类基因具有重要意义。
方法：本研究首先在全基因组层面完成了23个代表性物种的NBS-LRR基因鉴定，并重点针对4种单子叶禾本科物种——斑茅（*Saccharum spontaneum*）、热带甘蔗（*Saccharum officinarum*）、高粱（*Sorghum bicolor*）以及芒草（*Miscanthus sinensis*）的NBS-LRR基因开展了深入研究。
结果与讨论：研究发现，全基因组复制、基因扩张以及等位基因丢失均可能是影响物种内NBS-LRR基因数量的因素，其中全基因组复制很可能是调控甘蔗NBS-LRR基因数量的核心原因。同时，本研究还发现NBS-LRR基因存在正向选择的渐进演化趋势。上述结果进一步阐明了植物NBS-LRR基因的演化模式。通过对多种甘蔗病害的转录组数据分析可知，在现代栽培甘蔗品种中，源自斑茅的差异表达NBS-LRR基因数量多于热带甘蔗，且该比例显著高于预期。该结果表明斑茅对现代栽培甘蔗的抗病性贡献更大。此外，本研究还观察到7个NBS-LRR基因在甘蔗叶灼病胁迫下呈现等位基因特异性表达，并筛选得到125个可响应多种病害的NBS-LRR基因。最后，本研究构建了植物NBS-LRR基因数据库，以方便后续对本研究获得的NBS-LRR基因开展分析与利用。
综上，本研究完善并拓展了植物NBS-LRR基因的相关研究，同时探讨了NBS-LRR基因响应甘蔗病害的机制，为后续NBS-LRR基因的研究与利用提供了理论指导与遗传资源。