title: 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.
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.
authors.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.
authors.forename: Rui
authors.initials: R
authors.lastname: Wang
authors.affiliation: Guangxi Key Laboratory for Aquatic Genetic Breeding and Healthy Aquaculture, Guangxi Academy of Fishery Sciences, Nanning, 530021, People's Republic of China. pinglili2000@163.com.
authors.forename: Liping
authors.initials: L
authors.lastname: Li
authors.affiliation: Guangxi Center for Disease Control and Prevention, Nanning, 530028, People's Republic of China. huangyangxdx@163.com.
authors.forename: Yan
authors.initials: Y
authors.lastname: Huang
authors.affiliation: Liuzhou's Aquaculture Technology Extending Station, Liuzhou, 545006, People's Republic of China. luofuguang3563@163.com.
authors.forename: Fuguang
authors.initials: F
authors.lastname: Luo
authors.affiliation: Guangxi Key Laboratory for Aquatic Genetic Breeding and Healthy Aquaculture, Guangxi Academy of Fishery Sciences, Nanning, 530021, People's Republic of China. nnlww@126.com.
authors.forename: Wanwen
authors.initials: W
authors.lastname: Liang
authors.affiliation: Guangxi Key Laboratory for Aquatic Genetic Breeding and Healthy Aquaculture, Guangxi Academy of Fishery Sciences, Nanning, 530021, People's Republic of China. ganxipaper@163.com.
authors.forename: Xi
authors.initials: X
authors.lastname: Gan
authors.affiliation: Guangxi Key Laboratory for Aquatic Genetic Breeding and Healthy Aquaculture, Guangxi Academy of Fishery Sciences, Nanning, 530021, People's Republic of China. htwish@163.com.
authors.forename: Ting
authors.initials: T
authors.lastname: Huang
authors.affiliation: Guangxi Key Laboratory for Aquatic Genetic Breeding and Healthy Aquaculture, Guangxi Academy of Fishery Sciences, Nanning, 530021, People's Republic of China. nnleiaiying@sina.com.
authors.forename: Aiying
authors.initials: A
authors.lastname: Lei
authors.affiliation: Guangxi Key Laboratory for Aquatic Genetic Breeding and Healthy Aquaculture, Guangxi Academy of Fishery Sciences, Nanning, 530021, People's Republic of China. cm990919@163.com.
authors.forename: Ming
authors.initials: M
authors.lastname: Chen
authors.affiliation: Institute of Applied Mycology, Huazhong Agricultural University, Wuhan, 430070, People's Republic of China. chenllianfu@foxmail.com.
authors.forename: Lianfu
authors.initials: L
authors.lastname: Chen
mesh_terms: D000818:Animals; D002417:Cattle; D055028:Comparative Genomic Hybridization; D005260:Female; D005516:Food Microbiology; D016680:Genome, Bacterial; D006801:Humans; D008414:Mastitis, Bovine / Q000235:genetics / Q000382:microbiology; D010802:Phylogeny; D017384:Sequence Deletion / Q000235:genetics*; D013290:Streptococcal Infections / Q000235:genetics* / Q000382:microbiology; D013292:Streptococcus agalactiae / Q000235:genetics* / Q000472:pathogenicity; D017210:Tilapia / Q000382:microbiology*