Expected genome size vs. assembly total bases

SK-N-BE · 02-11-2019, 12:35 AM

Hello,
I sequenced a bacterial genome with an expected genome size of 2,9 Mbp.
One of my sequenced isolate got 2,98 whereas the second one 3,12 Mbp. Are those results in the range expected? How much may the expected and the resulted genome size differ?

Bukowski · 02-11-2019, 04:16 AM

Maybe. There is not enough data here to answer the question. How did you determine the expected genome size? What is the variation in known genome sizes?

Have a look at:

https://www.ncbi.nlm.nih.gov/genome/...lus%20subtilis[Organism]&cmd=DetailsSearch

median total length (Mb): 4.13745

Type strain is 4.22Mb

Now go here:

https://www.ncbi.nlm.nih.gov/genome/genomes/665

Smallest genome is 2.68Mb. Largest is 5.4Mb (ignoring the chimeric one) - but the bulk are 3.8Mb to 4.5Mb - 0.7Mb difference in a relatively small genome.

So I'd look at the variation in the published genomes to decide. The example above is just to show methodology not to start a discussion on the completeness of genomes or genome plasticity in B.subtilis

But your assemblies could be very different in terms of content for a number of reasons, and without assessing them it is impossible to say what is 'expected'

SK-N-BE · 02-11-2019, 05:23 AM

Hello,
thank you for your reply.
I was working with L.monocytogenes and I now found that the Genome size I got is in the range of those genomes that are found on NCBI.

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02-11-2019, 12:35 AM	#1
SK-N-BE Member Location: Germany Join Date: Apr 2018 Posts: 13	Expected genome size vs. assembly total bases Hello, I sequenced a bacterial genome with an expected genome size of 2,9 Mbp. One of my sequenced isolate got 2,98 whereas the second one 3,12 Mbp. Are those results in the range expected? How much may the expected and the resulted genome size differ?

02-11-2019, 04:16 AM	#2
Bukowski Senior Member Location: Aberdeen, Scotland Join Date: Jan 2010 Posts: 373	Maybe. There is not enough data here to answer the question. How did you determine the expected genome size? What is the variation in known genome sizes? Have a look at: https://www.ncbi.nlm.nih.gov/genome/...lus%20subtilis[Organism]&cmd=DetailsSearch median total length (Mb): 4.13745 Type strain is 4.22Mb Now go here: https://www.ncbi.nlm.nih.gov/genome/genomes/665 Smallest genome is 2.68Mb. Largest is 5.4Mb (ignoring the chimeric one) - but the bulk are 3.8Mb to 4.5Mb - 0.7Mb difference in a relatively small genome. So I'd look at the variation in the published genomes to decide. The example above is just to show methodology not to start a discussion on the completeness of genomes or genome plasticity in B.subtilis But your assemblies could be very different in terms of content for a number of reasons, and without assessing them it is impossible to say what is 'expected'

02-11-2019, 05:23 AM	#3
SK-N-BE Member Location: Germany Join Date: Apr 2018 Posts: 13	Hello, thank you for your reply. I was working with L.monocytogenes and I now found that the Genome size I got is in the range of those genomes that are found on NCBI.