Whole genome assembly and gap closure of the toxic bloom-forming cyanobacterium Anabaena sp. strain 90

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dc.contributor.author Wang, Hao en
dc.contributor.other Helsingin yliopisto, Maatalous-metsätieteellinen tiedekunta MMETT, MMKEL, MMEKO, MMSBL, MMKEM en
dc.date.accessioned 2008-11-21T10:35:22Z en
dc.date.accessioned 2009-09-01T08:05:03Z
dc.date.available 2008-11-21T10:35:22Z en
dc.date.available 2009-09-01T08:05:03Z
dc.date.issued 2008-11-21T10:35:22Z en
dc.identifier.uri http://hdl.handle.net/1975/8356
dc.description Biotechnology en
dc.description.abstract Anabaena is a common member of the phytoplankton in lakes, reservoirs and ponds throughout the world. This is a filamentous, nitrogen-fixing cyanobacterial genus and is frequently present in the lakes of Finland. Anabaena sp. strain 90 was isolated from Lake Vesijärvi and produces microcystins, anabaenopeptilides and anabaenopeptins. A whole genome shotgun sequencing project was undertaken to obtain the complete genome of this organism in order to better understand the physiology and environmental impact of toxic cyanobacteria. This work describes the genome assembly and finishing, the genome structure, and the results of intensive computational analysis of the Anabaena sp. strain 90 genome. Altogether 119,316 sequence reads were generated from 3 genomic libraries with 2, 6 and 40 kb inserts from high throughput Sanger sequencing. The software package Phred/Phrap/Consed was used for whole genome assembly and finishing. A combinatorial PCR method was used to establish relationships between remaining contigs after thorough scaffolding and gap-filling. The final assembly results show that there is a single 4.3 Mb circular chromosome and 4 circular plasmids with sizes of 820, 80, 56 and 20 kb respectively. Together, these 4 plasmids comprise nearly one-fifth of the total genome. Genomic variations in the form of 79 single nucleotide polymorphisms and 3 sequence indels were identified from the assembly results. Sequence analysis revealed that 7.5 percent of the Anabaena sp. strain 90 genome consists of repetitive DNA elements. The genome sequence of Anabaena sp. strain 90 provides a more solid basis for further studies of bioactive compound production, photosynthesis, nitrogen fixation and akinete formation in cyanobacteria. en
dc.language.iso en en
dc.subject Cyanobacteria, Anabaena, genome, assembly, scaffold, gap closure, finishing, repeat en
dc.title Whole genome assembly and gap closure of the toxic bloom-forming cyanobacterium Anabaena sp. strain 90 en
dc.type Master's thesis en
dc.identifier.laitoskoodi 800 fi
dc.creator.corporateName Maatalous-metsätieteellinen tiedekunta fi
dc.creator.corporateName Faculty of Agriculture and Forestry en
dc.creator.corporateName Agrikultur-forstvetenskapliga fakulteten sv
dc.identifier.urn URN:NBN:fi:hulib-201507211599
dct.identifier.urn URN:NBN:fi:hulib-201507211599

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