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Complete genome sequencing and comparative genomic analysis of functionally diverse Lysinibacillus sphaericus III(3)7.

ABSTRACT: Lysinibacillus sphaericus III(3)7 is a native Colombian strain, the first one isolated from soil samples. This strain has shown high levels of pathogenic activity against Culex quinquefaciatus larvae in laboratory assays compared to other members of the same species. Using Pacific Biosciences sequencing technology we sequenced, annotated (de novo) and described the genome of strain III(3)7, achieving a complete genome sequence status. We then performed a comparative analysis between the newly sequenced genome and the ones previously reported for Colombian isolates L. sphaericus OT4b.31, CBAM5 and OT4b.25, with the inclusion of L. sphaericus C3-41 that has been used as a reference genome for most of previous genome sequencing projects. We concluded that L. sphaericus III(3)7 is highly similar with strain OT4b.25 and shares high levels of synteny with isolates CBAM5 and C3-41.

SUBMITTER: Rey A

PROVIDER: S-EPMC4932437 | biostudies-literature | 2016 Sep

REPOSITORIES: biostudies-literature

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Complete genome sequencing and comparative genomic analysis of functionally diverse Lysinibacillus sphaericus III(3)7.

Rey Andrés A Silva-Quintero Laura L Dussán Jenny J

Genomics data 20160626

Lysinibacillus sphaericus III(3)7 is a native Colombian strain, the first one isolated from soil samples. This strain has shown high levels of pathogenic activity against Culex quinquefaciatus larvae in laboratory assays compared to other members of the same species. Using Pacific Biosciences sequencing technology we sequenced, annotated (de novo) and described the genome of strain III(3)7, achieving a complete genome sequence status. We then performed a comparative analysis between the newly se ...[more]

PMID: 27419068

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Project description:BackgroundEarly in the 1990s, it was recognized that Lysinibacillus sphaericus, one of the most popular and effective entomopathogenic bacteria, was a highly heterogeneous group. Many authors have even proposed it comprises more than one species, but the lack of phenotypic traits that guarantee an accurate differentiation has not allowed this issue to be clarified. Now that genomic technologies are rapidly advancing, it is possible to address the problem from a whole genome perspective, getting insights into the phylogeny, evolutive history and biology itself.ResultsThe genome of the Colombian strain L. sphaericus OT4b.49 was sequenced, assembled and annotated, obtaining 3 chromosomal contigs and no evidence of plasmids. Using these sequences and the 13 other L. sphaericus genomes available on the NCBI database, we carried out comparative genomic analyses that included whole genome alignments, searching for mobile elements, phylogenomic metrics (TETRA, ANI and in-silico DDH) and pan-genome assessments. The results support the hypothesis about this species as a very heterogeneous group. The entomopathogenic lineage is actually a single and independent species with 3728 core genes and 2153 accessory genes, whereas each non-toxic strain seems to be a separate species, though without a clear circumscription. Toxin-encoding genes, binA, B and mtx1, 2, 3 could be acquired via horizontal gene transfer in a single evolutionary event. The non-toxic strain OT4b.31 is the most related with the type strain KCTC 3346.ConclusionsThe current L. sphaericus is actually a sensu lato due to a sub-estimation of diversity accrued using traditional non-genomics based classification strategies. The toxic lineage is the most studied with regards to its larvicidal activity, which is a greatly conserved trait among these strains and thus, their differentiating feature. Further studies are needed in order to establish a univocal classification of the non-toxic strains that, according to our results, seem to be a paraphyletic group.

Project description:BackgroundAntimonite [Sb(III)]-oxidizing bacterium has great potential in the environmental bioremediation of Sb-polluted sites. Bacillus sp. S3 that was previously isolated from antimony-contaminated soil displayed high Sb(III) resistance and Sb(III) oxidation efficiency. However, the genomic information and evolutionary feature of Bacillus sp. S3 are very scarce.ResultsHere, we identified a 5,436,472 bp chromosome with 40.30% GC content and a 241,339 bp plasmid with 36.74% GC content in the complete genome of Bacillus sp. S3. Genomic annotation showed that Bacillus sp. S3 contained a key aioB gene potentially encoding As (III)/Sb(III) oxidase, which was not shared with other Bacillus strains. Furthermore, a wide variety of genes associated with Sb(III) and other heavy metal (loid) s were also ascertained in Bacillus sp. S3, reflecting its adaptive advantage for growth in the harsh eco-environment. Based on the analysis of phylogenetic relationship and the average nucleotide identities (ANI), Bacillus sp. S3 was proved to a novel species within the Bacillus genus. The majority of mobile genetic elements (MGEs) mainly distributed on chromosomes within the Bacillus genus. Pan-genome analysis showed that the 45 genomes contained 554 core genes and many unique genes were dissected in analyzed genomes. Whole genomic alignment showed that Bacillus genus underwent frequently large-scale evolutionary events. In addition, the origin and evolution analysis of Sb(III)-resistance genes revealed the evolutionary relationships and horizontal gene transfer (HGT) events among the Bacillus genus. The assessment of functionality of heavy metal (loid) s resistance genes emphasized its indispensable role in the harsh eco-environment of Bacillus genus. Real-time quantitative PCR (RT-qPCR) analysis indicated that Sb(III)-related genes were all induced under the Sb(III) stress, while arsC gene was down-regulated.ConclusionsThe results in this study shed light on the molecular mechanisms of Bacillus sp. S3 coping with Sb(III), extended our understanding on the evolutionary relationships between Bacillus sp. S3 and other closely related species, and further enriched the Sb(III) resistance genetic data sources.

Dataset Information

Complete genome sequencing and comparative genomic analysis of functionally diverse Lysinibacillus sphaericus III(3)7.

Publications

Complete genome sequencing and comparative genomic analysis of functionally diverse Lysinibacillus sphaericus III(3)7.

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