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A plant pathology perspective of fungal genome sequencing.
IMA Fungus ( IF 5.4 ) Pub Date : 2017-08-22 , DOI: 10.5598/imafungus.2017.08.01.01
Janneke Aylward 1 , Emma T Steenkamp 2 , Léanne L Dreyer 1 , Francois Roets 3 , Brenda D Wingfield 4 , Michael J Wingfield 2
Affiliation  

The majority of plant pathogens are fungi and many of these adversely affect food security. This mini-review aims to provide an analysis of the plant pathogenic fungi for which genome sequences are publically available, to assess their general genome characteristics, and to consider how genomics has impacted plant pathology. A list of sequenced fungal species was assembled, the taxonomy of all species verified, and the potential reason for sequencing each of the species considered. The genomes of 1090 fungal species are currently (October 2016) in the public domain and this number is rapidly rising. Pathogenic species comprised the largest category (35.5 %) and, amongst these, plant pathogens are predominant. Of the 191 plant pathogenic fungal species with available genomes, 61.3 % cause diseases on food crops, more than half of which are staple crops. The genomes of plant pathogens are slightly larger than those of other fungal species sequenced to date and they contain fewer coding sequences in relation to their genome size. Both of these factors can be attributed to the expansion of repeat elements. Sequenced genomes of plant pathogens provide blueprints from which potential virulence factors were identified and from which genes associated with different pathogenic strategies could be predicted. Genome sequences have also made it possible to evaluate adaptability of pathogen genomes and genomic regions that experience selection pressures. Some genomic patterns, however, remain poorly understood and plant pathogen genomes alone are not sufficient to unravel complex pathogen-host interactions. Genomes, therefore, cannot replace experimental studies that can be complex and tedious. Ultimately, the most promising application lies in using fungal plant pathogen genomics to inform disease management and risk assessment strategies. This will ultimately minimize the risks of future disease outbreaks and assist in preparation for emerging pathogen outbreaks.

中文翻译:

真菌基因组测序的植物病理学观点。

大多数植物病原体是真菌,其中许多对食品安全有不利影响。这份小型综述旨在提供可公开获得其基因组序列的植物病原真菌的分析,评估其总体基因组特征,并考虑基因组学如何影响植物病理。列出了已测序的真菌物种的清单,验证了所有物种的分类学,并对所考虑的每个物种进行测序的潜在原因。目前(2016年10月)有1090种真菌物种的基因组处于公共领域,并且这一数字正在迅速增加。致病物种占最大类别(35.5%),其中植物病原体占主导地位。在191种具有可用基因组的植物病原性真菌物种中,有61.3%的原因是粮食作物上的疾病,其中一半以上是主食。植物病原体的基因组比迄今测序的其他真菌物种的基因组稍大,并且相对于其基因组大小,它们包含的编码序列更少。这两个因素都可以归因于重复元件的扩展。植物病原体的测序基因组提供了蓝图,可以从中识别出潜在的毒力因子,并可以预测与不同病原性策略相关的基因。基因组序列也使得评估病原体基因组和经历选择压力的基因组区域的适应性成为可能。然而,一些基因组模式仍然知之甚少,仅植物病原体基因组还不足以阐明复杂的病原体与宿主之间的相互作用。因此,基因组 无法取代可能繁琐而繁琐的实验研究。最终,最有希望的应用在于使用真菌植物病原体基因组学为疾病管理和风险评估策略提供信息。这最终将使未来疾病暴发的风险最小化,并有助于为新出现的病原体暴发做好准备。
更新日期:2019-11-01
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