![]() ![]() The DNA was then purified using the Qiagen Genomic Tip 100/G according to the manufacturer protocol. Around 10 8 cells were harvested for DNA extraction using a phenol-chloroform extraction. DNA extraction was performed in 2015, new batch of cells were taken up from the cryopreserved stock, cultured until confluent and DNA extracted directly to ensure minimal accumulation of mutations. salmonicida ATCC isolate were cryopreserved in liquid nitrogen. Cells were obtained from American Type Culture Collection (ATCC) in 2008 and grown axenically in slanted polypropylene tubes using a modified liver digest yeast extract (LYI) medium 11 at 16 ☌. salmonicida (ATCC 50377), previously known as Spironucleus barkhanus 2, was isolated from a muscle abscess in Atlantic salmon grown in Vesterålen Sea in northern Norway. Diplomonad genomes in near-complete chromosomes make it possible to study gene organization at the chromosomal level, and provide ground for studying chromosomal evolution. salmonicida in near-complete chromosomes. With similar sequencing and assembly strategy, we obtain a high-quality reference genome of S. We recently published two Giardia genome assemblies, Giardia intestinalis WB 9 and Giardia muris 10, in near-complete chromosomes using Pacbio reads alone or in combination with optical maps. PC1, and comparative genomics have shown that the free-living life style most likely is a secondary adaptation and evolved from its parasitic ancestor 7, 8. There are also free-living diplomonads like Trepomonas sp. salmonicida possesses an extended metabolic repertoire and more extensive gene regulation, probably making it more adapted to cope with environmental fluctuations 6. It was shown in our previous study that S. salmonicida is a well-adapting pathogen that can colonize different sites in the host 5. All members of the Giardia genus are strictly intestinal parasites, while S. salmonicida, for example Giardia species which cause diarrhoea in various animals including humans 4. salmonicida belongs to diplomonads, a group of unicellular protists with two diploid nuclei bearing different life styles. This makes studies of the parasite important in order to develop alternative strategies to manage the parasite 3. salmonicida develops internal haemorrhaging, splenomegaly and granulomatous lesions in the liver and spleen, and drug treatment is not possible. Outbreaks of spironucleosis in farmed Atlantic salmon, Salmo salar, is a recurring problem and causes mass mortality and economical loss in for example Northern Norway. Spironucleus salmonicida (“the salmonid killer”) causes systemic infections in farmed Atlantic salmon, Chinook salmon and Arctic char 1, 2, thus poses a threat to sustainable aquaculture. This near-complete reference genome will aid comparative genomics at chromosomal level, and serve as a valuable resource for the diplomonad community and protist research. This new genome assembly is not only more complete sequence-wise but also more complete at annotation level, providing more details into gene families, gene organizations and chromosomal structure. salmonicida genome assembly in nine near-complete chromosomes with only three internal gaps at long repeats. Combining Pacbio long-read sequencing technology and optical maps, we are presenting here this new S. In our previous Giardia genome study, we have shown how a fragmented genome assembly can be improved with long-read sequencing technology complemented with optical maps. However, the genome assembly is fragmented without assignment of the sequences to chromosomes. salmonicida genome assembly was published 2014 and has been a valuable reference genome in protist research. Spironucleus salmonicida is a diplomonad causing systemic infection in salmon. ![]()
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