Comprehensive genome sequencing and annotation

DNA was extracted from the pure culture using a Bacterial Genome DNA Rapid Extraction Kit (Huiling Biotechnology Co., Ltd., Shanghai, China), following the manufacturer’s instructions. The exact concentration of the DNA was measured using a Qubit 4 Fluorometer (Thermo Fisher Scientific, Waltham, MA, USA), and DNA purity and integrity were detected via agarose gel electrophoresis. Genome sequencing was completed using PacBio sequencing technology and Illumina PE150 sequencing for high-accuracy assembly. The genome was assembled using SMRT Link software (version 5.0.1) [31 (link)], and the protein-coding genes were predicted using GeneMarkS software (Version 4.17) [32 (link)]. The tRNA was predicted by the software tRNAscan-SE (version 1.3.1) [33 (link)], the rRNA genes were predicted using RNAmmer software (version 1.2) [34 (link)], and small RNA was identified against the Rfam database [35 (link)] using CMsearch (version 1.1rc4) [36 (link)]. The genomic island was predicted using IslandPath-DIOMB (version 0.2) [37 (link)], and the CRISPR (clustered regularly interspaced short palindromic repeat) sequences were predicted using CRISPRdigger software (version 1.0) [38 (link)]. A display of the entire genomic map was generated using Circos (version 0.69) [39 (link)], along with the prediction results of the protein-coding genes.

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Lv Z., Ding J., Wang H., Wan J., Chen Y., Liang L., Yu T., Wang Y, & Wang F. (2022). Isolation of a Novel Thermophilic Methanogen and the Evolutionary History of the Class Methanobacteria. Biology, 11(10), 1514.

Publication 2022

Qubit 4 Fluorometer PE150 sequencing

Agarose gel electrophoresis Bacterial dna Bacterial genome Clustered regularly interspaced short palindromic repeat Genome Genomic island Protein genes Rrna genes Smrt Trna

Corresponding Organization : Shanghai Jiao Tong University

Other organizations : Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou)

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Variable analysis

independent variables

DNA extraction method (Bacterial Genome DNA Rapid Extraction Kit)
Sequencing technology (PacBio and Illumina PE150)
Genome assembly method (SMRT Link software version 5.0.1)
Gene prediction methods (GeneMarkS, tRNAscan-SE, RNAmmer, CMsearch)
Genomic island prediction (IslandPath-DIOMB)
CRISPR sequence prediction (CRISPRdigger)

dependent variables

DNA concentration (measured using Qubit 4 Fluorometer)
DNA purity and integrity (detected via agarose gel electrophoresis)
Genome assembly quality
Protein-coding gene prediction
TRNA, rRNA, and small RNA prediction
Genomic island identification
CRISPR sequence identification

control variables

Bacterial pure culture used for DNA extraction
Manufacturer's instructions followed for DNA extraction kit

Annotations

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