Fungal OTU Table and Taxonomic Assignments Generated via SEED2

This dataset contains original bioinformatically processed data from fungal sequencing library using the SEED2 (v2.0.4) pipeline (Větrovský et al., 2018). The data were processed as described in Řezáčová et al. (2019) and Řezáč et al. (2021, 2025). Paired-end reads were assembled, low-quality sequences and reads shorter than 250 bp were removed, and the target regions were extracted. The sequences were then clustered into Operational Taxonomic Units (OTUs) at a 97% similarity threshold. Chimera detection was performed using USEARCH 8.1.1861. A representative sequence (most abundant in the cluster) was selected for each OTU and taxonomically assigned using BLASTn (v2.5.0+) against curated fungal reference databases. The dataset includes: OTU table: An abundance matrix of OTUs across samples. Taxonomy table: Taxonomic assignments of representative OTUs including higher-rank classification and trophic mode assignments (saprotrophic, symbiotic, pathogenic), where available. Note: This dataset represents a part of the data analyzed in the manuscript:Řezáčová, V., Šimon, T., Némethová, E., Saska, P., Mayerová, M. (2025). Soil cultivation methods rather than catch crop species enhance bacterial diversity in soil over a three-year experiment. Scientific Reports (under revision after peer review).本数据集包含采用SEED2（v2.0.4）分析流程（Větrovský等，2018）处理的真菌测序文库原始生物信息学数据。数据处理严格遵循Řezáčová等人（2019）及Řezáč等人（2021、2025）的方法学方案。 对双端测序读段进行拼接后，剔除低质量序列与长度不足250 bp的读段，并提取目标测序区域。随后以97%的相似性阈值将序列聚类为操作分类单元（Operational Taxonomic Units，OTUs）。使用USEARCH 8.1.1861完成嵌合体检测。为每个OTU选取聚类内丰度最高的序列作为代表性序列，并基于经过人工整理的真菌参考数据库，使用BLASTn（v2.5.0+）进行分类学归属注释。 本数据集包含以下内容： 1. OTU表：跨样本的OTU丰度矩阵。 2. 分类学表：OTU代表性序列的分类学注释结果，涵盖高阶分类层级及营养模式注释（腐生型、共生型、致病型），若可获取相关信息则一并提供。 注意：本数据集为下述手稿中分析数据的一部分：Řezáčová, V., Šimon, T., Némethová, E., Saska, P., Mayerová, M. (2025). 《三年田间试验表明土壤耕作方式而非覆盖作物物种可提升土壤细菌多样性》. 《科学报告（Scientific Reports）》（同行评审后修订中）。