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



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.



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 function.
Department of Microbiology, Oregon State University, 226 Nash Hall, Corvallis, 97331, OR, USA.
Nathan M
NM
Brown
Department of Microbiology, Oregon State University, 226 Nash Hall, Corvallis, 97331, OR, USA.
Ryan S
RS
Mueller
Department of Microbiology, Oregon State University, 226 Nash Hall, Corvallis, 97331, OR, USA.
Jonathan W
JW
Shepardson
Department of Microbiology, Oregon State University, 226 Nash Hall, Corvallis, 97331, OR, USA.
Zachary C
ZC
Landry
Department of Chemistry, Oregon State University, 153 Gilbert Hall, Corvallis, 97331, OR, USA.
Jeffrey T
JT
Morré
Department of Chemistry, Oregon State University, 153 Gilbert Hall, Corvallis, 97331, OR, USA.
Claudia S
CS
Maier
Office of Environmental Public Health Sciences, Washington State Department of Health, Olympia, 98504, WA, USA.
F Joan
FJ
Hardy
Department of Microbiology, Oregon State University, 226 Nash Hall, Corvallis, 97331, OR, USA. theo.dreher@oregonstate.edu.|Center for Genome Research and Biocomputing, Oregon State University, Corvallis, OR, USA. theo.dreher@oregonstate.edu.
Theo W
TW
Dreher
D017033:Anabaena / Q000145:classification / Q000235:genetics* / Q000302:isolation & purification / Q000378:metabolism*; D019295:Computational Biology / Q000379:methods; D000087522:Cyanobacteria Toxins; D004734:Energy Metabolism; D016680:Genome, Bacterial; D023281:Genomics / Q000379:methods; D059014:High-Throughput Nucleotide Sequencing; D053858:Metabolic Networks and Pathways; D055442:Metabolome; D055432:Metabolomics / Q000379:methods; D058977:Molecular Sequence Annotation; D010802:Phylogeny; D011401:Promoter Regions, Genetic; D026801:Synteny; D020080:Tandem Repeat Sequences; D014326:Tropanes / Q000378:metabolism*
D000087522:Cyanobacteria Toxins; D014326:Tropanes; C509783:anatoxin a
Anabaena; Anatoxin-a; Cyanobacteria; Illumina; Long-read sequencing; Mobilome; PacBio; Structural variation; Synteny; Tandem repeat