Genome Assembly and Annotation Pipeline

Total DNA was extracted by the phenol-chloroform method [41 (link)]. Library preparation was performed using the Nextera DNA Flex Library Prep (Illumina) kit. DNA concentration and quantification were assessed using QuBit 4 with the DNA High Sensitivity test. Fragment size was visualized using Tapestation (Agilent Technologies) with the D1000 ScreenTape System. Genomic DNA was sequenced with the Illumina NextSeq 550. The quality of the read libraries was assessed using the FastQC v0.11.9 tool [42 ]. Pre-processing was performed with the Trim Galore v0.6.7 [43 ]. Genome assembly was conducted with SPAdes v. 3.15.4 [44 (link)]. Gene prediction was performed with Prokka v1.14.15 [45 (link)] and the genome completeness was calculated with the CheckM v1.1.11 tool [46 (link)]. The complete genome of strain 34SFC-3 is deposited at NCBI under the BioProject PRJNA894989.