Die Jose V, Castro Patricia, Millán Teresa, Gil Juan
Department of Genetics, ETSIAM, University of Córdoba, 14071 Córdoba, Spain.
Genes (Basel). 2018 Nov 23;9(12):568. doi: 10.3390/genes9120568.
Garden asparagus is an important horticultural plant worldwide. It is, however, susceptible to a variety of diseases, which can affect the potential yield, spear quality, and lifespan of production fields. Screening studies have identified resistant germplasm. The genetic resistance is usually complex, and the genes underlying that resistance are still unknown. Most often, disease resistance is determined by resistance genes (). The most predominant -genes contain nucleotide binding site and leucine-rich repeat (NBS-LRR) domains. Using bioinformatics and data mining approaches, we identified and characterized 68 NBS predicted proteins encoded by 49 different loci in the asparagus genome. The NBS-encoding genes were grouped into seven distinct classes based on their domain architecture. The genes are unevenly distributed through the genome and nearly 50% of the genes are present in clusters. Chromosome 6 is significantly NBS-enriched and one single cluster hosts 10% of the genes. Phylogenetic analysis points to their diversification into three families during their evolution. Recent duplications are likely to have dominated the expansion with both tandem genes and duplication events across multiple chromosomes. Transcriptome sequencing data provided evidence for their transcription and tissue-specific expression. The total number of -regulatory elements as well as their relative positions within the NBS promoters suggests a complex transcriptional network regulating defense responses. Our study provides a strong groundwork for the isolation of candidate -genes in garden asparagus.
石刁柏是一种在全球范围内重要的园艺植物。然而，它易受多种病害影响，这些病害会影响潜在产量、嫩茎品质以及生产田的寿命。筛选研究已鉴定出抗性种质。遗传抗性通常较为复杂，其抗性背后的基因仍不清楚。大多数情况下，抗病性由抗性基因决定。最主要的抗性基因包含核苷酸结合位点和富含亮氨酸重复序列（NBS-LRR）结构域。利用生物信息学和数据挖掘方法，我们在石刁柏基因组中鉴定并表征了由49个不同位点编码的68个NBS预测蛋白。基于其结构域结构，编码NBS的基因被分为七个不同类别。这些基因在基因组中分布不均，近50%的基因成簇存在。第6号染色体显著富含NBS，一个单一的簇包含10%的基因。系统发育分析表明它们在进化过程中分化为三个家族。近期的复制可能主导了NBS的扩增，既有串联基因复制，也有跨多条染色体的复制事件。转录组测序数据为它们的转录和组织特异性表达提供了证据。NBS启动子内调控元件的总数及其相对位置表明存在一个复杂的转录网络调控防御反应。我们的研究为石刁柏中候选抗性基因的分离提供了坚实的基础。
