PDF(Pubmed)
Abstract：
Date palm (Phoenixdactylifera) is the most significant crop across North Africa and the Middle East. However, the crop faces a severe threat from Bayoud disease caused by the fungal pathogen Fusarium oxysporum f. sp. albedinis (FOA). FOA is a soil-borne fungus that infects the roots and vascular system of date palms, leading to widespread destruction of date palm plantations in North Africa over the last century. This is considered the most devastating pathogen of oasis agriculture in North Africa and responsible for loss of 13 million trees in Algeria and Morocco alone. In this study, we present a chromosome-scale high-quality genome assembly of the virulent isolate Foa 44, which provides valuable insights into understanding the genetic basis of Bayoud disease. The genome assembly consists of 11 chromosomes and 40 unplaced contigs, totalling 65,971,825 base pairs in size. It exhibits a GC ratio of 47.77% and a TE (transposable element) content of 17.30%. Through prediction and annotation, we identified 20,416 protein-coding genes. By combining gene and repeat densities analysis with alignment to Fusarium oxysporum f. sp. lycopersici (FOL) 4287 isolate genome sequence, we determined the core and lineage-specific compartments in Foa 44, shedding light on the genome structure of this pathogen. Furthermore, a phylogenomic analysis based on the 3,292 BUSCOs core genome revealed a distinct clade of FOA isolates within the Fusarium oxysporum species complex (FOSC). Notably, the genealogies of the five identified Secreted In Xylem (SIX) genes (1, 6, 9, 11 and 14) in FOA displayed a polyphyletic pattern, suggesting a horizontal inheritance of these effectors. These findings provide a valuable genomics toolbox for further research aimed at combatting the serious biotic constraints posed by FOA to date palm. This will pave the way for a deeper understanding of Bayoud disease and facilitate the development of effective diagnostic tools and control measures.
摘要：
椰枣（Phoenixdactylifera）是北非和中东最重要的作物。然而,该作物面临由真菌病原体尖孢镰刀菌引起的Bayoud病的严重威胁。阿尔贝迪尼斯（FOA）。FOA是一种土源性真菌，感染枣树的根部和血管系统，导致了上个世纪北非枣树种植园的广泛破坏。这被认为是北非绿洲农业最具破坏性的病原体，仅在阿尔及利亚和摩洛哥就造成了1300万棵树的损失。在这项研究中,我们提出了毒力分离株Foa44的染色体级高质量基因组组装,这为理解Bayoud病的遗传基础提供了有价值的见解.基因组组装由11个染色体和40个未放置的重叠群组成，总计65,971,825个碱基对。它表现出47.77%的GC比率和17.30%的TE(转座元素)含量。通过预测和注释，我们确定了20,416个蛋白质编码基因。通过将基因和重复密度分析与尖孢镰刀菌f.sp.lycopersici（FOL）4287分离基因组序列，我们确定了Foa44中的核心和谱系特异性区室，从而揭示了该病原体的基因组结构。此外，基于3,292BUSCOs核心基因组的系统基因组分析揭示了尖孢镰刀菌物种复合体（FOSC）中FOA分离株的独特进化枝。值得注意的是,在FOA中确定的五个分泌的木质部（六个）基因（1、6、9、11和14）的家谱显示出多系模式，暗示了这些效应器的水平继承。这些发现为进一步研究提供了一个有价值的基因组学工具箱，旨在对抗FOA对棕榈的严重生物限制。这将为更深入地了解Bayoud病铺平道路，并促进开发有效的诊断工具和控制措施。
