Sedaghatjoo Somayyeh, Mishra Bagdevi, Forster Monika K, Becker Yvonne, Keilwagen Jens, Killermann Berta, Thines Marco, Karlovsky Petr, Maier Wolfgang
Institute for Epidemiology and Pathogen Diagnostics, Julius Kühn Institute (JKI) - Federal Research Centre for Cultivated Plants, Messeweg 11-12, 38104, Brunswick, Germany.
Senckenberg Biodiversity and Climate Research Centre, Senckenberganlage 25, 60325, Frankfurt am Main, Germany.
IMA Fungus. 2022 Jun 7;13(1):11. doi: 10.1186/s43008-022-00098-y.
Tilletia caries and T. laevis, which are the causal agents of common bunt, as well as T. controversa, which causes dwarf bunt of wheat, threaten especially organic wheat farming. The three closely related fungal species differ in their teliospore morphology and partially in their physiology and infection biology. The gene content as well as intraspecies variation in these species and the genetic basis of their separation is unknown. We sequenced the genome of four T. caries, five T. controversa, and two T. laevis and extended this dataset with five publicly available ones. The genomes of the three species displayed microsynteny with up to 94.3% pairwise aligned regions excluding repetitive regions. The majority of functionally characterized genes involved in pathogenicity, life cycle, and infection of corn smut, Ustilago maydis, were found to be absent or poorly conserved in the draft genomes and the biosynthetic pathway for trimethylamine in Tilletia spp. could be different from bacteria. Overall, 75% of the identified protein-coding genes comprising 84% of the total predicted carbohydrate utilizing enzymes, 72.5% putatively secreted proteins, and 47.4% of effector-like proteins were conserved and shared across all 16 isolates. We predicted nine highly identical secondary metabolite biosynthesis gene clusters comprising in total 62 genes in all species and none were species-specific. Less than 0.1% of the protein-coding genes were species-specific and their function remained mostly unknown. Tilletia controversa had the highest intraspecies genetic variation, followed by T. caries and the lowest in T. laevis. Although the genomes of the three species are very similar, employing 241 single copy genes T. controversa was phylogenetically distinct from T. caries and T. laevis, however these two could not be resolved as individual monophyletic groups. This was in line with the genome-wide number of single nucleotide polymorphisms and small insertions and deletions. Despite the conspicuously different teliospore ornamentation of T. caries and T. laevis, a high degree of genomic identity and scarcity of species-specific genes indicate that the two species could be conspecific.
引起小麦腥黑穗病的小麦光腥黑粉菌（Tilletia caries）和网腥黑粉菌（T. laevis），以及导致小麦矮腥黑穗病的小麦矮腥黑粉菌（T. controversa），对有机小麦种植构成了特别的威胁。这三种密切相关的真菌物种在冬孢子形态上有所不同，在生理和侵染生物学方面也存在部分差异。这些物种的基因含量、种内变异以及它们分化的遗传基础尚不清楚。我们对4个小麦光腥黑粉菌、5个小麦矮腥黑粉菌和2个网腥黑粉菌的基因组进行了测序，并将这个数据集与5个公开可用的数据集进行了扩展。这三个物种的基因组显示出微共线性，排除重复区域后，成对排列区域高达94.3%。在玉米黑粉菌（Ustilago maydis）中参与致病性、生命周期和侵染的大多数功能已明确的基因，在草图基因组中要么缺失，要么保守性较差，并且小麦腥黑粉菌属中三甲胺的生物合成途径可能与细菌不同。总体而言，在所有16个分离株中，75%的已鉴定蛋白质编码基因是保守且共有的，这些基因占预测的总碳水化合物利用酶的84%、推测的分泌蛋白的72.5%以及效应样蛋白的47.4%。我们预测了9个高度相同的次生代谢物生物合成基因簇，所有物种中总共包含62个基因，且没有一个是物种特异性的。蛋白质编码基因中不到0.1%是物种特异性的，其功能大多仍不清楚。小麦矮腥黑粉菌的种内遗传变异最高，其次是小麦光腥黑粉菌，网腥黑粉菌的种内遗传变异最低。尽管小麦光腥黑粉菌和网腥黑粉菌的冬孢子纹饰明显不同，但高度的基因组同一性和物种特异性基因的稀缺表明这两个物种可能是同种的。
