Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, 97331, USA.
Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, MI, 48824, USA.
New Phytol. 2019 Apr;222(1):511-525. doi: 10.1111/nph.15613. Epub 2019 Jan 12.
Endogonales (Mucoromycotina), composed of Endogonaceae and Densosporaceae, is the only known non-Dikarya order with ectomycorrhizal members. They also form mycorrhizal-like association with some nonspermatophyte plants. It has been recently proposed that Endogonales were among the earliest mycorrhizal partners with land plants. It remains unknown whether Endogonales possess genomes with mycorrhizal-lifestyle signatures and whether Endogonales originated around the same time as land plants did. We sampled sporocarp tissue from four Endogonaceae collections and performed shotgun genome sequencing. After binning the metagenome data, we assembled and annotated the Endogonaceae genomes. We performed comparative analysis on plant-cell-wall-degrading enzymes (PCWDEs) and small secreted proteins (SSPs). We inferred phylogenetic placement of Endogonaceae and estimated the ages of Endogonaceae and Endogonales with expanded taxon sampling. Endogonaceae have large genomes with high repeat content, low diversity of PCWDEs, but without elevated SSP/secretome ratios. Dating analysis estimated that Endogonaceae originated in the Permian-Triassic boundary and Endogonales originated in the mid-late Silurian. Mycoplasma-related endobacterium sequences were identified in three Endogonaceae genomes. Endogonaceae genomes possess typical signatures of mycorrhizal lifestyle. The early origin of Endogonales suggests that the mycorrhizal association between Endogonales and plants might have played an important role during the colonization of land by plants.
内囊霉目（Mucoromycotina）由内囊霉科和丛赤壳科组成，是唯一已知具有外生菌根成员的非双囊菌目。它们还与一些非种子植物形成类似菌根的共生关系。最近有人提出，内囊霉目是最早与陆地植物形成菌根共生关系的真菌之一。目前尚不清楚内囊霉目是否具有菌根生活方式特征的基因组，以及内囊霉目是否与陆地植物同时起源。我们从四个内囊霉科的标本中采集了孢子组织，并进行了鸟枪法基因组测序。在对宏基因组数据进行分类后，我们组装并注释了内囊霉科的基因组。我们对内囊霉科的植物细胞壁降解酶（PCWDEs）和小分泌蛋白（SSPs）进行了比较分析。我们推断了内囊霉科的系统发育位置，并通过扩大分类群采样估计了内囊霉科和内囊霉目的起源时间。内囊霉科的基因组较大，重复含量高，PCWDE 多样性低，但 SSP/分泌组比例没有升高。定年分析估计内囊霉科起源于二叠纪-三叠纪之交，内囊霉目起源于中-晚志留世。在三个内囊霉科的基因组中鉴定到了与支原体相关的内共生菌序列。内囊霉科的基因组具有典型的菌根生活方式特征。内囊霉目的早期起源表明，内囊霉目与植物之间的菌根共生关系可能在植物向陆地的殖民过程中发挥了重要作用。
