Clonostachys rosea

Transcriptome of C. rosea

comparision

{'age': 'youth', 'strain': 'C-24-1', 'tissue': 'mycelium', 'dev_stage': 'mycelium', 'sample_type': 'culture', 'geo_loc_name': 'China', 'biosamplemodel': 'Microbe, viral or environmental', 'collection_date': '2017-05-20', 'isolation_source': 'soil'}

Transcriptome of C. rosea

comparision

{'age': 'youth', 'strain': 'S-24-3', 'tissue': 'mycelium', 'dev_stage': 'mycelium', 'sample_type': 'culture', 'geo_loc_name': 'China', 'biosamplemodel': 'Microbe, viral or environmental', 'collection_date': '2017-05-20', 'isolation_source': 'soil'}

Transcriptome of C. rosea

comparision

{'age': 'youth', 'strain': 'S-8-1', 'tissue': 'mycelium', 'dev_stage': 'mycelium', 'sample_type': 'culture', 'geo_loc_name': 'China', 'biosamplemodel': 'Microbe, viral or environmental', 'collection_date': '2017-05-20', 'isolation_source': 'soil'}

RNA-Seq of Clonostachys rosea: Glucose PCL medium

The preserved C. rosea RNA was extracted using an RNeasy Mini Kit (Qiagen, Hilden, Germany) according to the manufacturers instructions, with some modifications. Before starting, -mercaptoethanol (-ME) was added to Buffer RLT at a ratio of 10 l -ME per 1 ml Buffer RLT. Buffer RPE was prepared by adding four volumes of ethanol (96-100%) to obtain a working solution.To extract RNA, 60 mg of flash-frozen fungal biomass was weighed in 2 mL microfuge tubes and then subjected to cell lysis. The cell lysis process involved using a pre-chilled stainless steel adapter block, 2.8 mm stainless steel grinding balls, and a Geno/Grinder tissue homogenizer (SPEX SamplePrep, Metuchen, NJ, USA). Cell lysis was performed at 1050 strokes/min for 1 min, followed by the addition of 700 l Buffer RLT. The samples were ground twice more at the same rate for 1 min each time and then ground once more for 2 min. After grinding, the samples were allowed to thaw at room temperature for 5 min. The RNA extraction process continued using a Qiagen RNeasy Mini Kit, following the manufacturers instructions, and eluting in RNAse-free water. Transcriptome sequencing was performed at Auckland Genomics, the University of Auckland, NZ. Before sequencing, the concentration and purity of the RNA were determined using a NanoDrop spectrophotometer (Thermo Fisher Scientific, Waltham, MA, USA), and the integrity of the RNA was assessed with an Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA). Library preparation for sequencing was conducted using the Illumina Stranded mRNA Prep Kit according to the manufacturers instructions (Illumina, Inc., San Diego, CA, USA). Quality control checks were performed on the prepared library using a Bioanalyzer 2100 to confirm appropriate fragment size distribution, and the library was then quantified using a Qubit 2.0 Fluorometer (Invitrogen, Carlsbad, CA, USA). Normalization and pooling of the libraries were done as required by the sequencing facility, and the final pool underwent another round of quality control. The RNA library was then sequenced on an Illumina HiSeq platform utilizing a 2x150 bp paired-end sequencing strategy.

{'elev': '0', 'depth': '10 cm', 'strain': 'PCL', 'lat_lon': '38.1446 S 176.2378 E', 'env_medium': 'soil', 'geo_loc_name': 'New Zealand', 'neg_cont_type': 'distilled water', 'pos_cont_type': 'polycaprolactone-emulsified M9 medium', 'biosamplemodel': 'MIGS/MIMS/MIMARKS.soil', 'collection_date': '2019-03-01', 'env_broad_scale': 'soil', 'env_local_scale': 'soil', 'isolation_source': 'soil', 'isol_growth_condt': 'Potato dextrose agar (PDA)'}

Control 1

Total RNA was extracted using Trizol reagent (Invitrogen, CA, USA) following the manufacturer's procedure. The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 1000 Nano LabChip Kit (Agilent, CA, USA) with RIN number >7.0. Poly(A) RNA is purified from total RNA(5ug) using poly-T oligo-attached magnetic beads using two rounds of purification. Following purification, the mRNA is fragmented into smallpieces using divalent cations under elevated temperature. Then the cleaved RNA fragments werereverse-transcribed to create the final cDNA library in accordance with the protocol for the mRNASeq sample preparation kit (Illumina, San Diego, USA), the average insert size for the paired-endlibraries was 300 bp (50 bp). And then we performed the paired-end sequencing on an Illumina Novaseq 6000 at the (LC Sceiences,USA) following the vendors recommended protocol.

{'isolate': 'Shiqing Sun', 'replicate': 'replicate = biological replicate 1', 'sample_type': 'single cell', 'geo_loc_name': 'China: Jiaxing', 'biosamplemodel': 'Microbe, viral or environmental', 'collection_date': '2022-03-01'}

Control 3

Total RNA was extracted using Trizol reagent (Invitrogen, CA, USA) following the manufacturer's procedure. The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 1000 Nano LabChip Kit (Agilent, CA, USA) with RIN number >7.0. Poly(A) RNA is purified from total RNA(5ug) using poly-T oligo-attached magnetic beads using two rounds of purification. Following purification, the mRNA is fragmented into smallpieces using divalent cations under elevated temperature. Then the cleaved RNA fragments werereverse-transcribed to create the final cDNA library in accordance with the protocol for the mRNASeq sample preparation kit (Illumina, San Diego, USA), the average insert size for the paired-endlibraries was 300 bp (50 bp). And then we performed the paired-end sequencing on an Illumina Novaseq 6000 at the (LC Sceiences,USA) following the vendors recommended protocol.

{'isolate': 'Shiqing Sun', 'replicate': 'replicate = biological replicate 2', 'sample_type': 'single cell', 'geo_loc_name': 'China: Jiaxing', 'biosamplemodel': 'Microbe, viral or environmental', 'collection_date': '2022-03-01'}