We have whole genome sequence data of Paenibacillus sp. and Arthrobacter sp. On submission of the sequence data with NCBI we got queries (a) If this is a circular genome, are the ends of the sequence contiguous around the circle with no overlap and no gap? (b) Should there be a gap at the end of the sequence? If there should be a gap, do you know the gap size or should this be an unknown length gap?
Dear Dr. Tobias Goris ,
Thanks for your reply. We have complete genome sequence without any gaps (one contiq) but we haven't checked its Ori.
This a myth of cheap sequencing. Not all bacterial genomes are circular. Some contain both rhodobacter comes to mind. So wet lab is needed for high resolution such as optical mapping and pfge. Plasmids are very common. Usually if you have reads spanning throughout it's a complete circle. Without reads spanning it could be linear
Yes Richard, I completely agree about the myth! Bacteria have all sorts of combinations of linear and circular chromosomes and plsamids and things that are sometimes called megaplasmids sometimes chromosomes. In addition linear chromosome ends are not always the same..; some as in Borrelia have hairpin ends, which isn't the case in Streptomyces (terminal proteins covalently bound to the free 5'-ends) etc. So indeed sequencing alone isn't going to give an answer here!
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