Complete Genome Sequence of the Attenuated Novobiocin-Resistant Streptococcus iniae Vaccine Strain ISNO

Pridgeon, Julia W.; Zhang, Dunhua; Zhang, Lee

doi:10.1128/genomea.00510-14

Cited by 6 publications

(11 citation statements)

References 16 publications

(20 reference statements)

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“…The genomes of ISET0901 and ISNO were both assembled from Illumina data using BioNumerics (Applied Math) with the genome of S. iniae SF1 as a reference [12, 13]. S.…”

Section: Resultsmentioning

confidence: 99%

A high-quality reference genome for the fish pathogen Streptococcus iniae

et al. 2022

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Fish mortality caused by Streptococcus iniae is a major economic problem in aquaculture in warm and temperate regions globally. There is also risk of zoonotic infection by S. iniae through handling of contaminated fish. In this study, we present the complete genome sequence of S. iniae strain QMA0248, isolated from farmed barramundi in South Australia. The 2.12 Mb genome of S. iniae QMA0248 carries a 32 kb prophage, a 12 kb genomic island and 92 discrete insertion sequence (IS) elements. These include nine novel IS types that belong mostly to the IS3 family. Comparative and phylogenetic analysis between S. iniae QMA0248 and publicly available complete S. iniae genomes revealed discrepancies that are probably due to misassembly in the genomes of isolates ISET0901 and ISNO. Long-range PCR confirmed five rRNA loci in the PacBio assembly of QMA0248, and, unlike S. iniae 89353, no tandemly repeated rRNA loci in the consensus genome. However, we found sequence read evidence that the tandem rRNA repeat existed within a subpopulation of the original QMA0248 culture. Subsequent nanopore sequencing revealed that the tandem rRNA repeat was the most prevalent genotype, suggesting that there is selective pressure to maintain fewer rRNA copies under uncertain laboratory conditions. Our study not only highlights assembly problems in existing genomes, but provides a high-quality reference genome for S. iniae QMA0248, including manually curated mobile genetic elements, that will assist future S. iniae comparative genomic and evolutionary studies.

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“…The genomes of ISET0901 and ISNO were both assembled from Illumina data using BioNumerics (Applied Math) with the genome of S. iniae SF1 as a reference [12, 13]. S.…”

Section: Resultsmentioning

confidence: 99%

A high-quality reference genome for the fish pathogen Streptococcus iniae

et al. 2022

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“…The 1,978 predicted protein-encoding genes belong to 315 subsystems and include 287 genes involved in carbohydrates, 187 genes in protein metabolism, 153 genes in amino acids and derivatives, 116 genes in cell wall and capsule, 102 genes in RNA metabolism, 96 genes in DNA metabolism, 81 genes in cofactors, vitamins, prosthetic groups, and pigments, 70 genes in fatty acid, lipids, and isoprenoids, 64 genes in nucleosides and nucleotides, 54 genes in virulence, disease, and defense, 47 genes in membrane transport, 39 genes in stress response, 36 genes in phosphorus metabolism, 31 genes in cell division and the cell cycle, 25 genes in regulation and cell signaling, 23 genes in iron acquisition and metabolism, 22 genes in miscellaneous, 15 genes in respiration, 10 genes in sulfur metabolism, eight genes in secondary metabolism, five genes in potassium metabolism, two genes in motility and chemotaxis, two genes in the metabolism of aromatic compounds, and one gene in dormancy and sporulation. The complete genome sequence of S. iniae 89353 was determined to identify potential virulence genes and candidate immunogens for vaccine development against streptococcosis by comparative genomics analysis with S. iniae strains isolated from tilapia ( 5 , 6 ) and flounder ( 7 , 8 ).…”

Section: Genome Announcementmentioning

confidence: 99%

Complete Genome Sequence of Streptococcus iniae 89353, a Virulent Strain Isolated from Diseased Tilapia in Taiwan

Gong

Chen

et al. 2017

Genome Announc

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“…ISET0901 (accession: CP007586) is reported to be a highly virulent strain, which was isolated from diseased Nile tilapia during an outbreak in Israel (2005) (12). The strain ISNO (accession: CP007587) was obtained through selection for resistance of S. iniae ISET0901 to novobiocin (13).…”

Section: Introductionmentioning

confidence: 99%

“…Discrepancies between the S. iniae genomes are likely due to misassemblyTaken together, our comparative analyses suggest that one or more of the S. iniae genomes under comparison have been misassembled. The genomes ISET0901 and ISNO were both assembled from Illumina data using BioNumerics (Applied Math) and the genome S. iniae SF1 as a reference(12,13). S. iniae SF1 was assembled de novo from a combination of 454 GS FLX+, Illumina MiSeq and Sanger sequencing(12).…”

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confidence: 99%

A high quality reference genome for the fish pathogenStreptococcus iniae

Zakour

Forde

Silayeva

et al. 2019

Preprint

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25Fish mortality caused by Streptococcus iniae is a major economic problem in fish 26 aquaculture in warm and temperate regions globally. There is also risk of zoonotic 27 infection by S. iniae through handling of contaminated fish. In this study, we 28 present the complete genome sequence of S. iniae strain QMA0248, isolated from 29 farmed barramundi in South Australia. The 2.12 Mb genome of S. iniae QMA0248 30 carries a 32 Kb prophage, a 12 Kb genomic island, and 92 discrete insertion 31 sequence (IS) elements. These include 9 novel IS types that belong mostly to the 32 IS3 family. Comparative and phylogenetic analysis between S. iniae QMA0248 and 33 publicly available complete S. iniae genomes revealed discrepancies that are likely 34 due to misassembly in the genomes of isolates ISET0901 and ISNO. We also 35 determined by long-range PCR that a tandem duplication of an rRNA region in the 36 PacBio assembly of QMA0248 was an assembly error. We suggest that a similar 37 rRNA duplication in the PacBio genome of S. iniae 89353 may also be a 38 misassembly. Our study not only highlights assembly problems in existing 39 genomes, but provides a high quality reference genome for S. iniae QMA0248, 40 including manually curated mobile genetic elements, that will assist future S. iniae 41 comparative genomic and evolutionary studies. 42 43 chronic rheumatic heart disease (3, 4). S. iniae pathogenesis is imparted through 50 a repertoire of virulence factors (VF) including surface proteins, secreted toxins, 51 and capsular polysaccharide (CPS) (4). VFs can be acquired through lateral gene 52 transfer (LGT) of mobile genetic elements (MGE) such as composite transposons, 53 genomic islands (GI) or prophages. 54 55 MGEs are a means by which bacterial pathogens acquire traits that help adapt to 56 changing conditions including vaccination, antibiotics, a new host or environment 57 (5, 6). Indeed, they are considered the main drivers of gene flux in bacteria, 58contributing to diversity within species (7). Insertion sequence (IS) elements, for 59 instance, are small MGEs (0.7-3.5 Kb) that have an important role in evolution and 60 genome plasticity. IS insertion within bacterial chromosomes or plasmids can 61 result in genetic modifications through insertional inactivation of genes or up-62 regulation of adjacent intact genes through outward-facing promoter sequences 63 carried by some IS (8, 9). In some cases pairs of IS can mobilize intervening 64 sequence as a composite transposon (8). The mobility of IS elements leads to their 65 expansion or loss within bacterial lineages. Expansion is associated with 66 accumulation of pseudogenes, which is considered an early stage in genome 67 reduction as a mechanism for adaptation (9). Accordingly, to obtain the complete 68 evolutionary picture within bacterial species it is important to study the 69 distribution and abundance of IS elements. 70 71As yet there is no study that focuses on the diversity and distribution of MGEs in 72 S. iniae genomes. In fact, only four complete S. inia...

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Complete Genome Sequence of the Attenuated Novobiocin-Resistant Streptococcus iniae Vaccine Strain ISNO

Cited by 6 publications

References 16 publications

A high-quality reference genome for the fish pathogen Streptococcus iniae

A high-quality reference genome for the fish pathogen Streptococcus iniae

Complete Genome Sequence of Streptococcus iniae 89353, a Virulent Strain Isolated from Diseased Tilapia in Taiwan

A high quality reference genome for the fish pathogenStreptococcus iniae

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