Structural peculiarities of linear megaplasmid, pLMA1, from Micrococcus luteus interfere with pyrosequencing reads assembly.

Biotechnology Letters
Martin WagenknechtFriedhelm Meinhardt

Abstract

Different strains of Micrococcus luteus, isolated from high-altitude Argentinean wetlands, were recently reported to harbour the linear plasmids pLMA1, pLMH5 and pLMV7, all of which with 5'-covalently attached terminal proteins. The link between pLMA1 and the host's erythromycin resistance as well as further presumptive qualities prompted us to perform a detailed characterization. When the 454 technology was applied for direct sequencing of gel-purified pLMA1, assembly of the reads was impossible. However, combined Sanger/454 sequencing of cloned pLMA1 fragments, covering altogether 23 kb of the 110-kb spanning plasmid, allowed numerous sequence repeats of varying in lengths to be identified thus rendering an explanation for the above 454 assembly failure. A large number of putative transposase genes were identified as well. Furthermore, a region with five putative iteron sequences is possibly involved in pLMA1 replication.

References

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Citations

Nov 10, 2012·Applied Microbiology and Biotechnology·Julián Rafael DibFriedhelm Meinhardt
May 31, 2012·Origins of Life and Evolution of the Biosphere : the Journal of the International Society for the Study of the Origin of Life·Virginia Helena AlbarracínMaría Eugenia Farias
Sep 10, 2014·BMC Genomics·Emma J RaftisPaul W O'Toole
Dec 10, 2015·Photochemistry and Photobiology·Virginia Helena AlbarracínMaría Eugenia Farias
Jun 16, 2015·Frontiers in Microbiology·Julián R DibFriedhelm Meinhardt
May 2, 2019·Frontiers in Microbiology·Dirk TischlerMarco W Fraaije

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Methods Mentioned

BETA
454 sequencing
PCR
X-ray

Software Mentioned

BlastN
Spectral Repeat Finder
GS De Novo Assembler (
GS Reference Mapper
GenBank

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