PDF(Pubmed)
Abstract：
To explore the connection between chloroplast and coffee resistance factors, designated as SH1 to SH9, whole genomic DNA of 42 coffee genotypes was sequenced, and entire chloroplast genomes were de novo assembled. The chloroplast phylogenetic haplotype network clustered individuals per species instead of SH factors. However, for the first time, it allowed the molecular validation of Coffea arabica as the maternal parent of the spontaneous hybrid \"Híbrido de Timor\". Individual reads were also aligned on the C. arabica reference genome to relate SH factors with chloroplast metabolism, and an in-silico analysis of selected nuclear-encoded chloroplast proteins (132 proteins) was performed. The nuclear-encoded thioredoxin-like membrane protein HCF164 enabled the discrimination of individuals with and without the SH9 factor, due to specific DNA variants linked to chromosome 7c (from C. canephora-derived sub-genome). The absence of both the thioredoxin domain and redox-active disulphide center in the HCF164 protein, observed in SH9 individuals, raises the possibility of potential implications on redox regulation. For the first time, the identification of specific DNA variants of chloroplast proteins allows discriminating individuals according to the SH profile. This study introduces an unexplored strategy for identifying protein/genes associated with SH factors and candidate targets of H. vastatrix effectors, thereby creating new perspectives for coffee breeding programs.
摘要：
探讨叶绿体与咖啡抗性因子的关系,命名为SH1至SH9，对42种咖啡基因型的全基因组DNA进行测序，整个叶绿体基因组从头组装。叶绿体系统发育单倍型网络聚集了每个物种的个体，而不是SH因子。然而,第一次,它允许阿拉伯咖啡作为自发杂种“HíbridodeTimor”的母本进行分子验证。还在阿拉伯C.arabica参考基因组上比对个体读数，以将SH因子与叶绿体代谢联系起来，并对选定的核编码叶绿体蛋白（132种蛋白）进行了计算机分析。核编码的硫氧还蛋白样膜蛋白HCF164能够区分有和没有SH9因子的个体，由于与染色体7c相关的特定DNA变体（来自C.canephora衍生的亚基因组）。在HCF164蛋白中不存在硫氧还蛋白结构域和氧化还原活性二硫化物中心，在SH9个体中观察到，提高了对氧化还原调节的潜在影响的可能性。第一次,通过鉴定叶绿体蛋白的特定DNA变体,可以根据SH谱区分个体.本研究引入了一种尚未探索的策略，用于鉴定与SH因子相关的蛋白质/基因和H.vastatrix效应子的候选靶标，从而为咖啡育种计划创造了新的视角。
