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

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dc.contributor Helsingin yliopisto, Maatalous-metsätieteellinen tiedekunta, Soveltavan kemian ja mikrobiologian laitos fi
dc.contributor University of Helsinki, Faculty of Agriculture and Forestry, Department of Applied Chemistry and Microbiology en
dc.contributor Helsingfors universitet, Agrikultur- och forstvetenskapliga fakulteten, Institutionen för tillämpad kemi och mikrobiologi sv
dc.contributor.author Wang, Hao
dc.date.issued 2008
dc.identifier.uri URN:NBN:fi:hulib-201507211599
dc.identifier.uri http://hdl.handle.net/1975/8356
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
dc.publisher Helsingfors universitet sv
dc.publisher University of Helsinki en
dc.publisher Helsingin yliopisto fi
dc.subject Cyanobacteria en
dc.subject Anabaena en
dc.subject genome en
dc.subject assembly en
dc.subject scaffold en
dc.subject gap closure en
dc.subject finishing en
dc.subject repeat en
dc.title Whole genome assembly and gap closure of the toxic bloom-forming cyanobacterium Anabaena sp. strain 90 en
dc.type.ontasot pro gradu-avhandlingar sv
dc.type.ontasot pro gradu -tutkielmat fi
dc.type.ontasot master's thesis en
dc.subject.discipline Bioteknik sv
dc.subject.discipline Mikrobiologi sv
dc.subject.discipline Biotechnology en
dc.subject.discipline Microbiology en
dc.subject.discipline Biotekniikka fi
dc.subject.discipline Mikrobiologia fi
dct.identifier.urn URN:NBN:fi:hulib-201507211599

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