Engelbrecht Juanita, Duong Tuan A, Prabhu S Ashok, Seedat Mohamed, van den Berg Noëlani
Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute, University of Pretoria, Pretoria, South Africa.
BMC Genomics. 2021 Apr 26;22(1):302. doi: 10.1186/s12864-021-07552-y.
Phytophthora cinnamomi is an oomycete pathogen of global relevance. It is considered as one of the most invasive species, which has caused irreversible damage to natural ecosystems and horticultural crops. There is currently a lack of a high-quality reference genome for this species despite several attempts that have been made towards sequencing its genome. The lack of a good quality genome sequence has been a setback for various genetic and genomic research to be done on this species. As a consequence, little is known regarding its genome characteristics and how these contribute to its pathogenicity and invasiveness.
In this work we generated a high-quality genome sequence and annotation for P. cinnamomi using a combination of Oxford Nanopore and Illumina sequencing technologies. The annotation was done using RNA-Seq data as supporting gene evidence. The final assembly consisted of 133 scaffolds, with an estimated genome size of 109.7 Mb, N50 of 1.18 Mb, and BUSCO completeness score of 97.5%. Genome partitioning analysis revealed that P. cinnamomi has a two-speed genome characteristic, similar to that of other oomycetes and fungal plant pathogens. In planta gene expression analysis revealed up-regulation of pathogenicity-related genes, suggesting their important roles during infection and host degradation.
This study has provided a high-quality reference genome and annotation for P. cinnamomi. This is among the best assembled genomes for any Phytophthora species assembled to date and thus resulted in improved identification and characterization of pathogenicity-related genes, some of which were undetected in previous versions of genome assemblies. Phytophthora cinnamomi harbours a large number of effector genes which are located in the gene-poor regions of the genome. This unique genomic partitioning provides P. cinnamomi with a high level of adaptability and could contribute to its success as a highly invasive species. Finally, the genome sequence, its annotation and the pathogenicity effectors identified in this study will serve as an important resource that will enable future studies to better understand and mitigate the impact of this important pathogen.
樟疫霉是一种具有全球影响力的卵菌病原体。它被认为是最具入侵性的物种之一，已对自然生态系统和园艺作物造成了不可逆转的损害。尽管已经多次尝试对其基因组进行测序，但目前该物种仍缺乏高质量的参考基因组。缺乏高质量的基因组序列阻碍了对该物种进行各种遗传和基因组研究。因此，人们对其基因组特征以及这些特征如何影响其致病性和入侵性知之甚少。
在这项工作中，我们结合牛津纳米孔测序技术和Illumina测序技术，为樟疫霉生成了高质量的基因组序列和注释。注释使用RNA-Seq数据作为支持基因证据。最终组装结果由133个支架组成，估计基因组大小为109.7 Mb，N50为1.18 Mb，BUSCO完整性得分97.5%。基因组分区分析表明，樟疫霉具有双速基因组特征，与其他卵菌和真菌植物病原体类似。植物体内基因表达分析显示与致病性相关的基因上调，表明它们在感染和宿主降解过程中发挥重要作用。
本研究为樟疫霉提供了高质量的参考基因组和注释。这是迄今为止组装的任何疫霉物种中最好的基因组之一，从而改进了与致病性相关基因的鉴定和表征，其中一些基因在以前版本的基因组组装中未被检测到。樟疫霉含有大量效应子基因，这些基因位于基因组中基因贫乏的区域。这种独特的基因组分区为樟疫霉提供了高度的适应性，并可能有助于其成为高度入侵性物种。最后，本研究中鉴定的基因组序列、其注释和致病性效应子将作为重要资源，使未来的研究能够更好地理解和减轻这种重要病原体的影响。
