TreeBASE Search-Analyses for study 19076

@ARTICLE{TreeBASE2Ref25710, author = {Nathan Brown and Ryan Mueller and Jonathan Shepardson and Zachary Landry and Claudia Maier and Jeffrey Morre and F Joan Hardy and Theo Wolfgang Dreher}, title = {Structural and Functional Analysis of the Finished Genome of the Recently Isolated Toxic Anabaena sp. WA102}, year = {2016}, keywords = {Anabaena; anatoxin-a; synteny; Cyanobacteria; mobilome; long-read sequencing; PacBio; Illumina; tandem repeat; structural variation}, doi = {}, url = {http://}, pmid = {}, journal = {BMC Genomics}, volume = {}, number = {}, pages = {}, abstract = {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 function.} }