The NBS disease-related gene family coordinates the inherent immune system in plants in response to pathogen infections. Previous studies have identified NBS-encoding genes in Pyrus bretschneideri (‘Dangshansuli’, an Asian pear) and Pyrus communis (‘Bartlett’, a European pear) genomes, but the patterns of genetic variation and selection pressure on these genes during pear domestication have remained unsolved. In this study, 338 and 412 NBS-encoding genes were identified from Asian and European pear genomes. This difference between the two pear species was the result of proximal duplications. About 15.79% orthologous gene pairs had Ka/Ks ratio more than one, indicating two pear species undergo strong positive selection after the divergence of Asian and European pear. We identified 21 and 15 NBS-encoding genes under fire blight and black spot disease-related QTL, respectively, suggesting their importance in disease resistance. Domestication caused decreased nucleotide diversity across NBS genes in Asian cultivars (cultivated 6.23E-03; wild 6.47E-03), but opposite trend (cultivated 6.48E-03; wild 5.91E-03) appeared in European pears. Many NBS-encoding coding regions showed Ka/Ks ratio of greater than 1, indicating the role of positive selection in shaping diversity of NBS-encoding genes in pear. Furthermore, we detected 295 and 122 significantly different SNPs between wild and domesticated accessions in Asian and European pear populations. Two NBS genes (Pbr025269.1 and Pbr019876.1) with significantly different SNPs showed >5x upregulation between wild and cultivated pear accessions, and > 2x upregulation in Pyrus calleryana after inoculation with Alternaria alternata. We propose that positively selected and significantly different SNPs of an NBS-encoding gene (Pbr025269.1) regulate gene expression differences in the wild and cultivated groups, which may affect resistance in pear against A. alternata. Proximal duplication mainly led to the different number of NBS-encoding genes in P. bretschneideri and P. communis genomes. The patterns of genetic diversity and positive selection pressure differed between Asian and European pear populations, most likely due to their independent domestication events. This analysis helps us understand the evolution, diversity, and selection pressure in the NBS-encoding gene family in Asian and European populations, and provides opportunities to study mechanisms of disease resistance in pear.

中文翻译：

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亚洲和欧洲梨的NBS编码基因差异后，相反的遗传变异和阳性选择

NBS疾病相关基因家族协调植物对病原体感染的内在免疫系统。先前的研究已经在梨梨（Pyrus bretschneideri）（“ Dangshansuli”，亚洲梨）和梨梨（Pyrus communis）（“ Bartlett”，欧洲梨）的基因组中鉴定了NBS编码基因，但是在梨驯化期间这些基因的遗传变异和选择压力存在仍未解决。在这项研究中，从亚洲和欧洲梨基因组中鉴定出338个和412个NBS编码基因。两种梨之间的差异是近端重复的结果。大约15.79％的直系同源基因对的Ka / Ks比大于1，表明在亚洲和欧洲梨分化之后，两个梨种经历了强正选择。我们分别在火疫病和与黑斑病相关的QTL下鉴定了21和15个NBS编码基因，表明它们在抗病性中的重要性。驯化导致亚洲品种（栽培的6.23E-03；野生的6.47E-03）中NBS基因之间核苷酸多样性降低，但欧洲梨出现相反的趋势（栽培的6.48E-03；野生的5.91E-03）。许多编码NBS的编码区的Ka / Ks比大于1，表明正选择在塑造梨NBS编码基因多样性中的作用。此外，我们在亚洲和欧洲梨种群的野生和驯养品系中检测到295和122个显着不同的SNP。两个NBS基因（Pbr025269.1和Pbr019876.1）的SNP明显不同，显示野生和栽培梨种之间的> 5倍上调，并且> 交替链格孢菌接种后，Pyrus calleryana的表达上调2倍。我们建议积极选择和显着不同的NBS编码基因（Pbr025269.1）的SNP调节野生和耕作组中的基因表达差异，这可能会影响梨对交链杆菌的抗性。近端复制主要导致B.schreideideri和P. communis基因组中NBS编码基因的数量不同。亚洲和欧洲梨种群之间的遗传多样性和正选择压力的模式不同，这很可能是由于它们独立的驯化事件。该分析有助于我们了解亚洲和欧洲人群中NBS编码基因家族的进化，多样性和选择压力，并为研究梨的抗病机制提供了机会。