US Department of Agriculture, Arid Land Agricultural Research Center, Tucson, AZ 85701, USA.
US Department of Agriculture, Food and Feed Safety Research Unit, New Orleans, LA 70124, USA.
G3 (Bethesda). 2023 Aug 30;13(9). doi: 10.1093/g3journal/jkad150.
Fungi can synthesize a broad array of secondary metabolite chemicals. The genes underpinning their biosynthesis are typically arranged in tightly linked clusters in the genome. For example, ∼25 genes responsible for the biosynthesis of carcinogenic aflatoxins by Aspergillus section Flavi species are grouped in a ∼70 Kb cluster. Assembly fragmentation prevents assessment of the role of structural genomic variation in secondary metabolite evolution in this clade. More comprehensive analyses of secondary metabolite evolution will be possible by working with more complete and accurate genomes of taxonomically diverse Aspergillus species. Here, we combined short- and long-read DNA sequencing to generate a highly contiguous genome of the aflatoxigenic fungus, Aspergillus pseudotamarii (isolate NRRL 25517 = CBS 766.97; scaffold N50 = 5.5 Mb). The nuclear genome is 39.4 Mb, encompassing 12,639 putative protein-encoding genes and 74-97 candidate secondary metabolite biosynthesis gene clusters. The circular mitogenome is 29.7 Kb and contains 14 protein-encoding genes that are highly conserved across the genus. This highly contiguous A. pseudotamarii genome assembly enables comparisons of genomic rearrangements between Aspergillus section Flavi series Kitamyces and series Flavi. Although the aflatoxin biosynthesis gene cluster of A. pseudotamarii is conserved with Aspergillus flavus, the cluster has an inverted orientation relative to the telomere and occurs on a different chromosome.
真菌可以合成广泛的次生代谢物化学物质。支持其生物合成的基因通常在基因组中紧密连锁成簇。例如，负责黄曲霉属物种产生致癌黄曲霉毒素的约 25 个基因聚集在一个约 70 Kb 的簇中。组装片段化阻止了对结构基因组变异在这个进化枝中次生代谢物进化中的作用的评估。通过使用分类学上多样化的曲霉属物种更完整和准确的基因组，对次生代谢物进化进行更全面的分析将成为可能。在这里，我们结合了短读和长读 DNA 测序，生成了产黄曲霉毒素真菌 Aspergillus pseudotamarii（分离物 NRRL 25517=CBS 766.97；支架 N50=5.5 Mb）的高度连续基因组。核基因组为 39.4 Mb，包含 12639 个推定的蛋白质编码基因和 74-97 个候选次生代谢产物生物合成基因簇。圆形线粒体基因组为 29.7 Kb，包含 14 个在属内高度保守的蛋白质编码基因。这个高度连续的 A. pseudotamarii 基因组组装使我们能够比较 Kitamyces 和 Flavi 系列黄曲霉属节的基因组重排。尽管 A. pseudotamarii 的黄曲霉毒素生物合成基因簇与 Aspergillus flavus 保守，但该簇相对于端粒呈倒置取向，并且发生在不同的染色体上。
