Navaseq pe150

The genomic DNA of P. oxalicum M1816 was extracted using a genomic DNA extraction kit (Tiangen, Beijing, China). The integrity of the genomic DNA was confirmed by agarose gel electrophoresis and the DNA quantified by a Qubit^® 2.0 Fluorometer (Thermo Scientific). The whole genome of P. oxalicum M1816 was sequenced using the Nanopore PromethION platform (Oxford Nanopore Technologies Ltd., Oxford, UK) and Illumina Navaseq PE150 (Illumina, SanDiego, CA, USA) at the Novogene company (Tianjin, China). The sequencing reads were assembled de novo using Unicycler software (Version 0.4.8) [41 (link)]. The results of Illumina sequencing were used as a reference for single-base error correction of the Nanopore assembly results. Genes were predicted with Genewise software (version 2.4.1) using the default parameters [42 (link)]. Coding genes were annotated using basic local alignment search tool (BLAST) in the National Centre for Biotechnology Information (NCBI) NR database. Gene function was annotated using the euKaryotic Orthologous Group (KOG, http://www.ncbi.nlm.nih.gov/COG/, 13 May 2021) database, Kyoto Encyclopedia of Genes and Genomes (KEGG, http://www.genome.jp/kegg/, 10 June 2021) database, and Gene Ontology (GO, http://geneontology.org/, 14 June 2021) database.

For microbial isolation on laboratory culture medium, wheat qu samples were suspended in sterile distilled water, and serial dilutions were plated onto Gauzeˊs Medium (Sigma) for incubation at 30 °C for between 7 to 14 days. Since members of Saccharopolyspora are predominant in wheat qu and HJFM, and were likely the core functional microorganisms in HJFM, especially Saccharopolyspora hirsute, Saccharopolyspora-like colonies^{60 (link)} were isolated, purified, and preserved in 30% w/v glycerol in water at −80 °C. 16 S rRNA gene sequencing using the 16S-27F and 16S-1492 primers was used for taxonomic identification^{61 (link)}. The isolated strains were identified as three S. hirsuta (J1 and J3), two S. rectivirgula (J4 and J5), three S. shandongensis (J6 to J8), and one S. erythraea (J9). S. hirsuta J2 was deposited in China Center for Type Culture Collection under the number CCTCC M 2020103. The whole genome of S. hirsute J2, the strain with the highest activity of amylase, glucoamylase and protease, was sequenced using Nanopore PromethION platform (Oxford Nanopore Technologies Ltd, Oxford, UK) and Illumina Navaseq PE150 (Illumina, SanDiego, CA, USA) at the Beijing Novogene Bioinformatics Technology Co., Ltd.

Genomic DNA was extracted from cultures incubated at 37°C for 48–72 h using a bacterial DNA extraction kit (Sangon Biotech, Shanghai, China). DNA integrity was evaluated by agarose gel electrophoresis, and a Qubit® 2.0 Fluorometer (Thermo Fisher Scientific) was employed to measure the DNA quantity and quality. The whole genome library of S. rosea A22 was produced using the Nanopore PromethION platform (Oxford Nanopore Technologies Ltd., Oxford, United Kingdom) and Illumina Navaseq PE150 (Illumina, SanDiego, CA, United States) at the Novogene Company (Tianjin, China). Genome assembly was employed using Unicycler software (Version 0.4.8) (Wick et al., 2017 (link)). The GeneMarkS (Version 4.17) was used to predict the related coding gene. The databases gene ontology (GO), Kyoto encyclopedia of genes and genomes (KEGG), cluster of orthologous groups of proteins (COG), and carbohydrate-active enZYmes (CAZy) were used to predict gene functions.