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Comparative genome analysis identifies two large deletions in the genome of highly-passaged attenuated Streptococcus agalactiae strain YM001 compared to the parental pathogenic strain HN016.

Wang R, Li L, Huang Y, Luo F, Liang W, Gan X, Huang T, Lei A, Chen M, Chen L - BMC Genomics (2015)

Bottom Line: The global outbreaks of Streptococcus disease in tilapia cause huge economic losses and threaten human food hygiene safety as well.Comparative genome analysis indicated that compared with HN016, YM001 genome had two significant large deletions, at the sizes of 5832 and 11,116 bp respectively, resulting in the deletion of three rRNA and ten tRNA genes, as well as the deletion and functional damage of ten genes related to metabolism, transport, growth, anti-stress, etc.The deleted and mutated functional genes all encode metabolism- and growth-related proteins, not the known virulence proteins, indicating that the metabolism- and growth-related genes are important for the pathogenesis of S. agalactiae.

View Article: PubMed Central - PubMed

Affiliation: Guangxi Key Laboratory for Aquatic Genetic Breeding and Healthy Aquaculture, Guangxi Academy of Fishery Sciences, Nanning, 530021, People's Republic of China. raywongxx@163.com.

ABSTRACT

Background: Streptococcus agalactiae (S. agalactiae), also known as group B Streptococcus (GBS), is an important pathogen for neonatal pneumonia, meningitis, bovine mastitis, and fish meningoencephalitis. The global outbreaks of Streptococcus disease in tilapia cause huge economic losses and threaten human food hygiene safety as well. To investigate the mechanism of S. agalactiae pathogenesis in tilapia and develop attenuated S. agalactiae vaccine, this study sequenced and comparatively analyzed the whole genomes of virulent wild-type S. agalactiae strain HN016 and its highly-passaged attenuated strain YM001 derived from tilapia.

Methods: We performed Illumina sequencing of DNA prepared from strain HN016 and YM001. Sequencedreads were assembled and nucleotide comparisons, single nucleotide polymorphism (SNP) , indels were analyzed between the draft genomes of HN016 and YM001. Clustered regularly interspaced short palindromic repeats (CRISPRs) and prophage were detected and analyzed in different S. agalactiae strains.

Results: The genome of S. agalactiae YM001 was 2,047,957 bp with a GC content of 35.61 %; it contained 2044 genes and 88 RNAs. Meanwhile, the genome of S. agalactiae HN016 was 2,064,722 bp with a GC content of 35.66 %; it had 2063 genes and 101 RNAs. Comparative genome analysis indicated that compared with HN016, YM001 genome had two significant large deletions, at the sizes of 5832 and 11,116 bp respectively, resulting in the deletion of three rRNA and ten tRNA genes, as well as the deletion and functional damage of ten genes related to metabolism, transport, growth, anti-stress, etc. Besides these two large deletions, other ten deletions and 28 single nucleotide variations (SNVs) were also identified, mainly affecting the metabolism- and growth-related genes.

Conclusions: The genome of attenuated S. agalactiae YM001 showed significant variations, resulting in the deletion of 10 functional genes, compared to the parental pathogenic strain HN016. The deleted and mutated functional genes all encode metabolism- and growth-related proteins, not the known virulence proteins, indicating that the metabolism- and growth-related genes are important for the pathogenesis of S. agalactiae.

No MeSH data available.


Related in: MedlinePlus

Whole genome alignment between S. agalactiae HN016 and YM001. The genomes of HN016 and YM001 were compared with each other using progressive MAUVE with default parameters. The colinearity of the genomes and the two deletions between HN016 and YM001 are shown
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Fig1: Whole genome alignment between S. agalactiae HN016 and YM001. The genomes of HN016 and YM001 were compared with each other using progressive MAUVE with default parameters. The colinearity of the genomes and the two deletions between HN016 and YM001 are shown

Mentions: As shown in Fig. 1, YM001 genome had two large deletions compared to HN016. The deletion one was a 5832-bp sequence, which contained a repetitive sequence of 5621 bp separated by a 211-bp fragment in the genome of HN016. There were two repetitive sequences in the genome of HN016, whereas only one repetitive fragment left in the genome of YM001. This repetitive sequence contained 5S rRNA, 16S rRNA, and 23S rRNA genes, as well as other ten different tRNA genes (see Additional file 1: Table S1). The deletion two was a 11,116-bp sequence, which resulted in a truncation of two genes and deletion of 8 genes (see Additional file 2: Table S2); they were four genes of the ABC transporter family, MarR family transcriptional regulator, Ser/Thr protein phosphatase (STP), peptide deformylase, glutamate dehydrogenase, membrane protein of unknown function, and acetyltransferase.Fig. 1


Comparative genome analysis identifies two large deletions in the genome of highly-passaged attenuated Streptococcus agalactiae strain YM001 compared to the parental pathogenic strain HN016.

Wang R, Li L, Huang Y, Luo F, Liang W, Gan X, Huang T, Lei A, Chen M, Chen L - BMC Genomics (2015)

Whole genome alignment between S. agalactiae HN016 and YM001. The genomes of HN016 and YM001 were compared with each other using progressive MAUVE with default parameters. The colinearity of the genomes and the two deletions between HN016 and YM001 are shown
© Copyright Policy - OpenAccess
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC4634907&req=5

Fig1: Whole genome alignment between S. agalactiae HN016 and YM001. The genomes of HN016 and YM001 were compared with each other using progressive MAUVE with default parameters. The colinearity of the genomes and the two deletions between HN016 and YM001 are shown
Mentions: As shown in Fig. 1, YM001 genome had two large deletions compared to HN016. The deletion one was a 5832-bp sequence, which contained a repetitive sequence of 5621 bp separated by a 211-bp fragment in the genome of HN016. There were two repetitive sequences in the genome of HN016, whereas only one repetitive fragment left in the genome of YM001. This repetitive sequence contained 5S rRNA, 16S rRNA, and 23S rRNA genes, as well as other ten different tRNA genes (see Additional file 1: Table S1). The deletion two was a 11,116-bp sequence, which resulted in a truncation of two genes and deletion of 8 genes (see Additional file 2: Table S2); they were four genes of the ABC transporter family, MarR family transcriptional regulator, Ser/Thr protein phosphatase (STP), peptide deformylase, glutamate dehydrogenase, membrane protein of unknown function, and acetyltransferase.Fig. 1

Bottom Line: The global outbreaks of Streptococcus disease in tilapia cause huge economic losses and threaten human food hygiene safety as well.Comparative genome analysis indicated that compared with HN016, YM001 genome had two significant large deletions, at the sizes of 5832 and 11,116 bp respectively, resulting in the deletion of three rRNA and ten tRNA genes, as well as the deletion and functional damage of ten genes related to metabolism, transport, growth, anti-stress, etc.The deleted and mutated functional genes all encode metabolism- and growth-related proteins, not the known virulence proteins, indicating that the metabolism- and growth-related genes are important for the pathogenesis of S. agalactiae.

View Article: PubMed Central - PubMed

Affiliation: Guangxi Key Laboratory for Aquatic Genetic Breeding and Healthy Aquaculture, Guangxi Academy of Fishery Sciences, Nanning, 530021, People's Republic of China. raywongxx@163.com.

ABSTRACT

Background: Streptococcus agalactiae (S. agalactiae), also known as group B Streptococcus (GBS), is an important pathogen for neonatal pneumonia, meningitis, bovine mastitis, and fish meningoencephalitis. The global outbreaks of Streptococcus disease in tilapia cause huge economic losses and threaten human food hygiene safety as well. To investigate the mechanism of S. agalactiae pathogenesis in tilapia and develop attenuated S. agalactiae vaccine, this study sequenced and comparatively analyzed the whole genomes of virulent wild-type S. agalactiae strain HN016 and its highly-passaged attenuated strain YM001 derived from tilapia.

Methods: We performed Illumina sequencing of DNA prepared from strain HN016 and YM001. Sequencedreads were assembled and nucleotide comparisons, single nucleotide polymorphism (SNP) , indels were analyzed between the draft genomes of HN016 and YM001. Clustered regularly interspaced short palindromic repeats (CRISPRs) and prophage were detected and analyzed in different S. agalactiae strains.

Results: The genome of S. agalactiae YM001 was 2,047,957 bp with a GC content of 35.61 %; it contained 2044 genes and 88 RNAs. Meanwhile, the genome of S. agalactiae HN016 was 2,064,722 bp with a GC content of 35.66 %; it had 2063 genes and 101 RNAs. Comparative genome analysis indicated that compared with HN016, YM001 genome had two significant large deletions, at the sizes of 5832 and 11,116 bp respectively, resulting in the deletion of three rRNA and ten tRNA genes, as well as the deletion and functional damage of ten genes related to metabolism, transport, growth, anti-stress, etc. Besides these two large deletions, other ten deletions and 28 single nucleotide variations (SNVs) were also identified, mainly affecting the metabolism- and growth-related genes.

Conclusions: The genome of attenuated S. agalactiae YM001 showed significant variations, resulting in the deletion of 10 functional genes, compared to the parental pathogenic strain HN016. The deleted and mutated functional genes all encode metabolism- and growth-related proteins, not the known virulence proteins, indicating that the metabolism- and growth-related genes are important for the pathogenesis of S. agalactiae.

No MeSH data available.


Related in: MedlinePlus