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Mitogenome polymorphism in a single branch sample revealed by SOLiD deep sequencing of the Lophelia pertusa coral genome
Authors:Emblem Ase  Karlsen Bård Ove  Evertsen Jussi  Miller David J  Moum Truls  Johansen Steinar D
Abstract:We present an initial genomic analysis of the non-symbiotic scleractinian coral Lophelia pertusa, the dominant cold-water reef-building coral species in the North Atlantic Ocean. A significant fraction of the deep sequencing reads was of mitochondrial and microbial origins. SOLiD deep sequencing reads from fragment library experiments of total DNA and PCR amplified mitogenome generated about 21,000 times and 136,000 times coverage, respectively, of the 16,150bp mitogenome. Five polymorphic sites that include two non-synonymous sites in the NADH dehydrogenase subunit 5 genes were detected in both experiments. This observation is surprising since anthozoans in general exhibit very low mtDNA sequence variation at intraspecific level compared to nuclear sequences. More than fifty bacterial species associated with the coral isolate were also sequence detected, representing at least ten complete genomes. Most reads, however, were predicted to originate from the Lophelia nuclear genome.
Keywords:SOLiD, sequencing by oligo ligation and detection   Mb, Megabase   mtDNA, mitochondrial DNA   OG, gene ontology   rRNA, ribosomal RNA   ITS, internal transcribed spacer   rDNA, ribosomal DNA   NUMT, nuclear mitochondrial pseudogene   Mt-SNP, mitochondrial single nucleotide polymorphism   SSU, small ribosomal subunit   LSU, large ribosomal subunit
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