PDF(Pubmed)
Abstract：
BACKGROUND: Aspergillus flavus is an important agricultural and food safety threat due to its production of carcinogenic aflatoxins. It has high level of genetic diversity that is adapted to various environments. Recently, we reported two reference genomes of A. flavus isolates, AF13 (MAT1-2 and highly aflatoxigenic isolate) and NRRL3357 (MAT1-1 and moderate aflatoxin producer). Where, an insertion of 310 kb in AF13 included an aflatoxin producing gene bZIP transcription factor, named atfC. Observations of significant genomic variants between these isolates of contrasting phenotypes prompted an investigation into variation among other agricultural isolates of A. flavus with the goal of discovering novel genes potentially associated with aflatoxin production regulation. Present study was designed with three main objectives: (1) collection of large number of A. flavus isolates from diverse sources including maize plants and field soils; (2) whole genome sequencing of collected isolates and development of a pangenome; and (3) pangenome-wide association study (Pan-GWAS) to identify novel secondary metabolite cluster genes.
RESULTS: Pangenome analysis of 346 A. flavus isolates identified a total of 17,855 unique orthologous gene clusters, with mere 41% (7,315) core genes and 59% (10,540) accessory genes indicating accumulation of high genomic diversity during domestication. 5,994 orthologous gene clusters in accessory genome not annotated in either the A. flavus AF13 or NRRL3357 reference genomes. Pan-genome wide association analysis of the genomic variations identified 391 significant associated pan-genes associated with aflatoxin production. Interestingly, most of the significantly associated pan-genes (94%; 369 associations) belonged to accessory genome indicating that genome expansion has resulted in the incorporation of new genes associated with aflatoxin and other secondary metabolites.
CONCLUSIONS: In summary, this study provides complete pangenome framework for the species of Aspergillus flavus along with associated genes for pathogen survival and aflatoxin production. The large accessory genome indicated large genome diversity in the species A. flavus, however AflaPan is a closed pangenome represents optimum diversity of species A. flavus. Most importantly, the newly identified aflatoxin producing gene clusters will be a new source for seeking aflatoxin mitigation strategies and needs new attention in research.
RESULTS: Pangenome analysis of 346 A. flavus isolates identified a total of 17,855 unique orthologous gene clusters, with mere 41% (7,315) core genes and 59% (10,540) accessory genes indicating accumulation of high genomic diversity during domestication. 5,994 orthologous gene clusters in accessory genome not annotated in either the A. flavus AF13 or NRRL3357 reference genomes. Pan-genome wide association analysis of the genomic variations identified 391 significant associated pan-genes associated with aflatoxin production. Interestingly, most of the significantly associated pan-genes (94%; 369 associations) belonged to accessory genome indicating that genome expansion has resulted in the incorporation of new genes associated with aflatoxin and other secondary metabolites.
CONCLUSIONS: In summary, this study provides complete pangenome framework for the species of Aspergillus flavus along with associated genes for pathogen survival and aflatoxin production. The large accessory genome indicated large genome diversity in the species A. flavus, however AflaPan is a closed pangenome represents optimum diversity of species A. flavus. Most importantly, the newly identified aflatoxin producing gene clusters will be a new source for seeking aflatoxin mitigation strategies and needs new attention in research.
摘要：
背景：由于黄曲霉产生致癌黄曲霉毒素，因此黄曲霉是重要的农业和食品安全威胁。它具有高度的遗传多样性，适应各种环境。最近,我们报道了黄曲霉分离株的两个参考基因组，AF13（MAT1-2和高度黄曲霉毒素分离株）和NRRL3357（MAT1-1和中度黄曲霉毒素生产者）。Where,在AF13中插入310kb包括产生黄曲霉毒素的基因bZIP转录因子，名为atfC。观察到这些具有对比表型的分离株之间的显着基因组变异，促使人们对黄曲霉的其他农业分离株之间的变异进行了研究，目的是发现可能与黄曲霉毒素生产调节相关的新基因。本研究的设计有三个主要目标：（1）从包括玉米植物和田间土壤在内的各种来源收集大量黄曲霉分离株；（2）收集的分离株的全基因组测序和pangenome的开发；（3）全基因组关联研究（Pan-GWAS）以鉴定新的次生代谢簇基因。
结果：对346个黄曲霉分离株的全基因组分析鉴定出总共17,855个独特的直系同源基因簇，只有41％（7,315）的核心基因和59％（10,540）的辅助基因表明在驯化过程中积累了高基因组多样性。美国专利5,994号附属基因组中的直向同源基因簇未在黄曲霉AF13或NRRL3357参考基因组中注释。基因组变异的全基因组关联分析确定了391个与黄曲霉毒素产生相关的显著相关的全基因。有趣的是,大多数显著相关的泛基因(94%;369个关联)属于辅助基因组,表明基因组扩增导致与黄曲霉毒素和其他次级代谢产物相关的新基因的掺入.
结论：总之，这项研究提供了完整的pangenome框架的物种黄曲霉以及相关基因的病原体生存和黄曲霉毒素的生产。大的辅助基因组表明物种A.flavus的基因组多样性很大，然而，AflaPan是一个封闭的pangenome，代表了黄曲霉物种的最佳多样性。最重要的是,新发现的黄曲霉毒素产生基因簇将成为寻求黄曲霉毒素缓解策略的新来源，需要在研究中给予新的关注。
结果：对346个黄曲霉分离株的全基因组分析鉴定出总共17,855个独特的直系同源基因簇，只有41％（7,315）的核心基因和59％（10,540）的辅助基因表明在驯化过程中积累了高基因组多样性。美国专利5,994号附属基因组中的直向同源基因簇未在黄曲霉AF13或NRRL3357参考基因组中注释。基因组变异的全基因组关联分析确定了391个与黄曲霉毒素产生相关的显著相关的全基因。有趣的是,大多数显著相关的泛基因(94%;369个关联)属于辅助基因组,表明基因组扩增导致与黄曲霉毒素和其他次级代谢产物相关的新基因的掺入.
结论：总之，这项研究提供了完整的pangenome框架的物种黄曲霉以及相关基因的病原体生存和黄曲霉毒素的生产。大的辅助基因组表明物种A.flavus的基因组多样性很大，然而，AflaPan是一个封闭的pangenome，代表了黄曲霉物种的最佳多样性。最重要的是,新发现的黄曲霉毒素产生基因簇将成为寻求黄曲霉毒素缓解策略的新来源，需要在研究中给予新的关注。
