MOESM1 of Transcriptomic characterization of Caecomyces churrovis: a novel, non-rhizoid-forming lignocellulolytic anaerobic fungus

Additional file 1: Table S1. Alignment results for transcriptomes of A. robustus, N. californiae, and P. finnis [5]. Shown are # of transcripts (% of transcriptome) in the transcriptome of the fungus listed on the left side successfully aligned to the transcriptome of the fungus listed across the top row using blastn analysis. Table S2. Alignment of scaffoldin amino acid sequences from P. finnis [13] to the transcriptome of C. churrovis by tblastn identifies scaffoldin transcripts. Only results with an alignment E value of 0 are shown. Figure S1. ITS1 Phylogeny of Caecomyces strains shows C. churrovis is significantly different compared to other strains. ITS1 phylogeny of only Caecomyces fungal strains identified a clear separation of C. churrovis from other isolated strains. Figure S2. Full ITS Phylogeny confirms observations about C. churrovis. Phylogeny of ITS1-5.8S-ITS2 regions confirmed the observations that C. churrovis represents a new species in the Caecomyces genus. Figure S3. Catabolic pathways for biomass derived sugars were reconstructed using transcriptome annotations. Enzyme commission numbers and BLAST alignments were used to identify complete sugar pathways present in the transcriptome of C. churrovis. This analysis revealed catabolic routes for glucose, xylose, and fructose, but not mannose, sucrose, and arabinose. Catabolism of Îą-d-galactose was identified using BLAST annotations, but not EC numbers. Figure S4. The secretomes of anaerobic gut fungi display free enzymes and multi enzymes complexes (cellulosomes). The same amount of secreted proteins (determined by BCA assay) of P. finnis (F), N. californiae (G1), A. robustus (S4) and C. churrovis (C) were loaded on Native (A) and SDS (B) PAGE. While the Native PAGE (stained by silver staining) shows strong bands indicative of cellulosomes around 1200Â kDa, the SDS PAGE (stained by SYPRO Ruby) shows many bands in dissociated cellulosome complexes.附加文件1：表S1。健壮厌氧真菌（A. robustus）、加州新美鞭菌（N. californiae）与芬尼斯厌氧真菌（P. finnis）的转录组比对结果[5]。结果展示左侧所列真菌转录组中，经BLASTn分析成功与顶行所列真菌转录组比对的转录本数量及其占总转录组的百分比。表S2。通过TBLASTN将芬尼斯厌氧真菌（P. finnis）的支架蛋白氨基酸序列[13]比对至查罗假囊酵母（C. churrovis）转录组，以此鉴定支架蛋白转录本，仅展示比对E值为0的结果。图S1。假囊酵母属（Caecomyces）菌株的ITS1系统发育分析显示，查罗假囊酵母（C. churrovis）与其他菌株存在显著差异；仅针对假囊酵母属真菌菌株的ITS1系统发育分析结果明确区分了查罗假囊酵母与其他分离菌株。图S2。完整ITS系统发育分析验证了查罗假囊酵母的相关结论。通过ITS1-5.8S-ITS2区域构建的系统发育树证实，查罗假囊酵母为假囊酵母属内的全新物种。图S3。利用转录组注释重构生物质来源糖类的分解代谢通路。通过酶委员会（EC）编号与BLAST比对结果，鉴定查罗假囊酵母转录组中完整的糖类代谢通路：本分析揭示了葡萄糖、木糖与果糖的分解代谢途径，但未发现甘露糖、蔗糖与阿拉伯糖的代谢通路；α-D-半乳糖的分解代谢途径可通过BLAST注释鉴定，但未匹配到对应的EC编号。图S4。厌氧肠道真菌的分泌组包含游离酶与多酶复合体（纤维小体，cellulosome）。将等量的芬尼斯厌氧真菌（F）、加州新美鞭菌（G1）、健壮厌氧真菌（S4）与查罗假囊酵母（C）的分泌蛋白（经BCA蛋白定量法测定）分别上样至标记为A的非变性聚丙烯酰胺凝胶电泳（Native PAGE）与标记为B的十二烷基硫酸钠-聚丙烯酰胺凝胶电泳（SDS-PAGE）。银染后的非变性PAGE可见约1200 kDa处存在代表纤维小体的强条带；而经SYPRO Ruby染料染色的SDS-PAGE则在解离的纤维小体复合体中显示出多条条带。