Cox Murray P, Guo Yanan, Winter David J, Sen Diya, Cauldron Nicholas C, Shiller Jason, Bradley Ellie L, Ganley Austen R, Gerth Monica L, Lacey Randy F, McDougal Rebecca L, Panda Preeti, Williams Nari M, Grunwald Niklaus J, Mesarich Carl H, Bradshaw Rosie E
Laboratory of Molecular Plant Pathology/Bioprotection Aotearoa, School of Natural Sciences, Massey University, Palmerston North, New Zealand.
Institute of Environmental Science and Research (ESR), Porirua, New Zealand.
Front Microbiol. 2022 Nov 2;13:1038444. doi: 10.3389/fmicb.2022.1038444. eCollection 2022.
species are notorious plant pathogens, with some causing devastating tree diseases that threaten the survival of their host species. One such example is , the causal agent of kauri dieback - a root and trunk rot disease that kills the ancient, iconic and culturally significant tree species, (New Zealand kauri). A deeper understanding of how pathogens infect their hosts and cause disease is critical for the development of effective treatments. Such an understanding can be gained by interrogating pathogen genomes for effector genes, which are involved in virulence or pathogenicity. Although genome sequencing has become more affordable, the complete assembly of genomes has been problematic, particularly for those with a high abundance of repetitive sequences. Therefore, effector genes located in repetitive regions could be truncated or missed in a fragmented genome assembly. Using a combination of long-read PacBio sequences, chromatin conformation capture (Hi-C) and Illumina short reads, we assembled the genome into ten complete chromosomes, with a genome size of 57 Mb including 34% repeats. This is the first genome assembled to chromosome level and it reveals a high level of syntenic conservation with the complete genome of , the only other completely assembled genome sequence of an oomycete. All chromosomes have clearly defined centromeres and contain candidate effector genes such as RXLRs and CRNs, but in different proportions, reflecting the presence of gene family clusters. Candidate effector genes are predominantly found in gene-poor, repeat-rich regions of the genome, and in some cases showed a high degree of duplication. Analysis of candidate RXLR effector genes that occur in multicopy gene families indicated half of them were not expressed . Candidate CRN effector gene families showed evidence of transposon-mediated recombination leading to new combinations of protein domains, both within and between chromosomes. Further analysis of this complete genome assembly will help inform new methods of disease control against and other species, ultimately helping decipher how pathogens have evolved to shape their effector repertoires and how they might adapt in the future.
卵菌纲物种是臭名昭著的植物病原体，其中一些会引发毁灭性的树木疾病，威胁宿主物种的生存。一个这样的例子是引起贝壳杉凋萎病的病菌，这是一种根部和树干腐烂病，会杀死古老、标志性且具有文化意义的贝壳杉树种（新西兰贝壳杉）。深入了解卵菌纲病原体如何感染宿主并引发疾病对于开发有效的治疗方法至关重要。通过在病原体基因组中探寻效应子基因可以获得这样的认识，这些基因与毒力或致病性有关。尽管基因组测序的成本已经降低，但卵菌纲基因组的完整组装一直存在问题，尤其是对于那些具有大量重复序列的基因组。因此，位于重复区域的效应子基因在碎片化的基因组组装中可能会被截断或遗漏。我们结合长读长的PacBio序列、染色质构象捕获技术（Hi-C）和Illumina短读长序列，将该卵菌纲基因组组装成了十条完整的染色体，基因组大小为57兆碱基，其中34%为重复序列。这是首个组装到染色体水平的卵菌纲基因组，它揭示了与另一种卵菌纲物种的完整基因组高度的共线性保守性，后者是唯一另一个完全组装好的卵菌纲基因组序列。所有染色体都有明确界定的着丝粒，并包含诸如RXLR和CRN等候选效应子基因，但比例不同，这反映了基因家族簇的存在。候选效应子基因主要存在于基因组中基因贫乏、富含重复序列的区域，并且在某些情况下显示出高度的重复。对多拷贝基因家族中出现的候选RXLR效应子基因的分析表明，其中一半没有表达。候选CRN效应子基因家族显示出转座子介导的重组证据，导致染色体内部和染色体之间蛋白质结构域的新组合。对这个完整基因组组装的进一步分析将有助于为针对该卵菌纲物种和其他卵菌纲物种的疾病控制新方法提供信息，最终有助于解读卵菌纲病原体如何进化以形成其效应子库以及它们未来可能如何适应。
