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Structural and functional analysis of the finished genome of the recently isolated toxic Anabaena sp WA102

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https://ir.library.oregonstate.edu/concern/articles/ww72bd503

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  • Background: Very few closed genomes of the cyanobacteria that commonly produce toxic blooms in lakes and reservoirs are available, limiting our understanding of the properties of these organisms. A new anatoxin-a-producing member of the Nostocaceae, Anabaena sp. WA102, was isolated from a freshwater lake in Washington State, USA, in 2013 and maintained in non-axenic culture. Results: The Anabaena sp. WA102 5.7 Mbp genome assembly has been closed with long-read, single-molecule sequencing and separately a draft genome assembly has been produced with short-read sequencing technology. The closed and draft genome assemblies are compared, showing a correlation between long repeats in the genome and the many gaps in the short-read assembly. Anabaena sp. WA102 encodes anatoxin-a biosynthetic genes, as does its close relative Anabaena sp. AL93 (also introduced in this study). These strains are distinguished by differences in the genes for light-harvesting phycobilins, with Anabaena sp. AL93 possessing a phycoerythrocyanin operon. Biologically relevant structural variants in the Anabaena sp. WA102 genome were detected only by long-read sequencing: a tandem triplication of the anaBCD promoter region in the anatoxin-a synthase gene cluster (not triplicated in Anabaena sp. AL93) and a 5-kbp deletion variant present in two-thirds of the population. The genome has a large number of mobile elements (160). Strikingly, there was no synteny with the genome of its nearest fully assembled relative, Anabaena sp. 90. Conclusion: Structural and functional genome analyses indicate that Anabaena sp. WA102 has a flexible genome. Genome closure, which can be readily achieved with long-read sequencing, reveals large scale (e.g., gene order) and local structural features that should be considered in understanding genome evolution and functio
  • Keywords: PacBio, Illumina, Mobilome, Cyanobacteria, Anabaena, Long-read sequencing, Structural variation, Anatoxin-a, Synteny, Tandem repeat
  • Keywords: PacBio, Illumina, Mobilome, Cyanobacteria, Anabaena, Long-read sequencing, Structural variation, Anatoxin-a, Synteny, Tandem repeat
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  • Brown, N. M., Mueller, R. S., Shepardson, J. W., Landry, Z. C., Morré, J. T., Maier, C. S., ... & Dreher, T. W. (2016). Structural and functional analysis of the finished genome of the recently isolated toxic Anabaena sp. WA102. BMC Genomics, 17, 457. doi:10.1186/s12864-016-2738-7
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  • Funding for this study was provided by the Washington State Department of Ecology, Oregon State University Agricultural Experiment Station, and Mabel E. Pernot Trust. The acquisition of the qToF LC-MS/MS system used in this study was made possible 35by NIH grant S10RR027878.
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