Table 6 Database, software, and parameters used in this study.

Trimmomatic

v0.33

QC

LEADING:3 TRAILING:3 SLIDINGWINDOW:50:20 MINLEN:100

https://github.com/usadellab/Trimmomatic

Spades

v3.6.2

Assembled

-m 300 -k 21,33,55,77,99,127 --cov-cutoff auto

https://github.com/ablab/spades

prodigal

v2.6.3

Gene prediction

-m -f gff -p single -q

https://github.com/hyattpd/Prodigal

GO

releases20180910

Annotation

—

http://geneontology.org/docs/download-ontology/

Blast2GO

v2.5

Annotation

—

https://www.blast2go.com/

eggNOG

v4.0

Annotation

—

http://eggnog45.embl.de/

KEGG

kegg_201703

Annotation

—

https://www.genome.jp/kegg/

Nr

nr-2019-03

Annotation

—

https://ftp.ncbi.nlm.nih.gov/blast/db/FASTA/

Pfam

v32.0

Annotation

—

https://pfam.xfam.org/

Swiss-Prot

swissprot-2019-07-31

Annotation

—

https://www.uniprot.org/help/downloads

TrEMBL

trembl-2019-07-13

Annotation

—

https://www.uniprot.org/help/downloads

BUSCO

V5.8.2

QC

-l bacteria_odb12 -m genome

https://busco.ezlab.org/

MAFFT

v7

Aligned sequences

auto

https://mafft.cbrc.jp/alignment/server/index.html

BioEdit

v7.0.9.0

Sequence alignment editor

—

—

raxmlGUI

v2.0.16

Combination sequence

—

https://antonellilab.github.io/raxmlGUI/

MEGA

v7

Phylogenetic Analyses

NJ Tree: Maximum Composite Likelihood (MCL) method,1000 bootstrap;

https://www.megasoftware.net/

ML Tree:GTR+G+I method,1000 bootstrap.