Whole Genome Sequencing and Bioinformatics Analysis of Mycoplasma ovipneumoniae GH3-3 Strain

doi:10.13560/j.cnki.biotech.bull.1985.2024-0076

Abstract

Abstract:

【Objective】 This study is aimed to decode the genomic sequence of Mycoplasma ovipneumoniae strain GH3-3, to investigate its pathogenic potential and to elucidate the regulatory mechanisms of its replication, transcription, and translation. 【Method】 M. ovipneumoniae GH3-3 strain was cultured in vitro. When it reached the late logarithmic stage of growth, the genomic DNA of M. ovipneumoniae GH3-3 strain was extracted with bacterial genomic DNA extraction kit and sent for whole genome sequencing and commentary. 【Result】 The genome size of GH3-3 strains of M. ovipneumoniae was 1 060 772 bp, and the GC content was 29.66%. The genome component analysis showed that the genome of GH3-3 strain contained 730 coding genes, with a total length of 914 379 bp and an average length of 1 252.57 bp, accounting for 86.2% of the total genome length. There were 149 tandem repeats with a total length of 20 926 bp, accounting for 1.97% of the total length of the genome. There were 102 microsatellite DNA sequences, 30 tRNA sequences, and 3 rRNA sequences. The 719, 459, 473, 394, 449, 33, 5, 180, 113 and 59 genes were annotated in NR, SwissProt, GOG, KEGG, GO, CARD, CAZy, PHI, TCDB, and RMS databases, respectively. A total of 76 virulence factor-related genes were annotated. The genome sequence was submitted to the NCBI website with the login number: PRJNA1051969. 【Conclusion】 The complete genome information of M. ovipneumoniae GH3-3 strain was acquired, and the gene function was predicted and annotated. Furthermore, the genetic and evolutionary relationships between GH3-3 strain and other strains of M. ovipneumoniae were elucidated globally.

Key words: Mycoplasma ovipneumoniae, GH3-3 strain, whole genome sequencing（WGS）, virulence factor, drug-resistant gene

TIAN Tong-tong, GE Jia-zhen, GAO Peng-cheng, LI Xue-rui, SONG Guo-dong, ZHENG Fu-ying, CHU Yue-feng. Whole Genome Sequencing and Bioinformatics Analysis of Mycoplasma ovipneumoniae GH3-3 Strain[J]. Biotechnology Bulletin, 2024, 40(7): 323-334.

Figures/Tables 17

References 40

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菌株 Strain	基因组大小 Genome size/bp	编码基因数量 Gene number/个	GC含量 GC content/％
GH 3-3株	1 060 772	730	29.66
NXNK2203株	1 014 835	686	29.23
NM2010株	1 084 159	888	29.14
HHHT2017株	1 019 689	807	29.068
SC01株	1 020 601	864	28.85
WXB1株	1 084 159	888	29.14
150株	1 053 380	714	29.15
274株	1 081 404	747	28.82
Y98株	1 021 486	819	29.21

菌株 Strain	基因组大小 Genome size/bp	编码基因数量 Gene number/个	GC含量 GC content/％
GH 3-3株	1 060 772	730	29.66
NXNK2203株	1 014 835	686	29.23
NM2010株	1 084 159	888	29.14
HHHT2017株	1 019 689	807	29.068
SC01株	1 020 601	864	28.85
WXB1株	1 084 159	888	29.14
150株	1 053 380	714	29.15
274株	1 081 404	747	28.82
Y98株	1 021 486	819	29.21

抗生素种类 Drug class	ARO登记号ARO accession	ARO名 ARO name
Aminoglycoside antibiotic	ARO:3005091	RanA
Fluoroquinolone antibiotic	ARO:3003949	efrB
Lincosamide antibiotic	ARO:3002882	lmrD
	ARO:3003746	optrA
	ARO:3002825	ErmY
Macrolide antibiotic	ARO:3003949	efrB
	ARO:3003746	optrA
	ARO:3002825	ErmY
	ARO:3000535	macB
Mupirocin	ARO:3000510	Staphylococcus aureus mupB conferring resistance to mupirocin
Mupirocin	ARO:3000521	Staphylococcus aureus mupA conferring resistance to mupirocin
Nitroimidazole antibiotic	ARO:3003950	msbA
Peptide antibiotic	ARO:3002987	bcrA
Peptide antibiotic	ARO:3000501	rpoB2
Tetracycline antibiotic	ARO:3004032	tetA（46）
	ARO:3000193	tetT
	ARO:3002891	otr（A）
	ARO:3003980	tetA（58）
	ARO:3000556	tet（44）
	ARO:3003980	tetA（58）
	ARO:3003746	optrA
Rifamycin antibiotic	ARO:3003949	efrB
	ARO:3002825	ErmY
	ARO:3000501	rpoB2
Oxazolidinone antibiotic	ARO:3003746	optrA
Pleuromutilin antibiotic	ARO:3003746	optrA
Streptogramin antibiotic	ARO:3003746	optrA
phenicol antibiotic	ARO:3003746	optrA

抗生素种类 Drug class	ARO登记号ARO accession	ARO名 ARO name
Aminoglycoside antibiotic	ARO:3005091	RanA
Fluoroquinolone antibiotic	ARO:3003949	efrB
Lincosamide antibiotic	ARO:3002882	lmrD
	ARO:3003746	optrA
	ARO:3002825	ErmY
Macrolide antibiotic	ARO:3003949	efrB
	ARO:3003746	optrA
	ARO:3002825	ErmY
	ARO:3000535	macB
Mupirocin	ARO:3000510	Staphylococcus aureus mupB conferring resistance to mupirocin
Mupirocin	ARO:3000521	Staphylococcus aureus mupA conferring resistance to mupirocin
Nitroimidazole antibiotic	ARO:3003950	msbA
Peptide antibiotic	ARO:3002987	bcrA
Peptide antibiotic	ARO:3000501	rpoB2
Tetracycline antibiotic	ARO:3004032	tetA（46）
	ARO:3000193	tetT
	ARO:3002891	otr（A）
	ARO:3003980	tetA（58）
	ARO:3000556	tet（44）
	ARO:3003980	tetA（58）
	ARO:3003746	optrA
Rifamycin antibiotic	ARO:3003949	efrB
	ARO:3002825	ErmY
	ARO:3000501	rpoB2
Oxazolidinone antibiotic	ARO:3003746	optrA
Pleuromutilin antibiotic	ARO:3003746	optrA
Streptogramin antibiotic	ARO:3003746	optrA
phenicol antibiotic	ARO:3003746	optrA

毒力因子名称 VFDB name	相关基因 Related genes
<alpha>-Hemolysin	hlyB
Acinetobactin	bauE
Alginate regulation	mucD
Capsule	cpsB、FTT 0793、rpe
Cereulide	cesC
ClpC	ClpC
Cya	cyaB
Cytolysin	cylB
Dot/Icm	lpg2936
EF-Tu	tufA
ESX-1	eccA1
FbpABC	fbpC
FeoAB	feoB
Flagella	flhF
FupA	feoB
HitABC	hitC
HP-NAP	napA
IgA1 protease	zmpC
LOS	licA
LplA1	lplA1
MgtBC	mgtB
MsrAB	msrA/B（pilB）
P97/P102 paralog family	mhp107、mhp683、p102、p97、lppT、p216、mhp385
T4SS effectors	CBU 1566
TlyC	tlyC
TTSS	escN、yscN、pscN
Type 1 fimbriae	fimE