Question: Number Of Chromosomes
0
gravatar for James
6.1 years ago by
James60
James60 wrote:

Hi guys,

How is the number of chromosomes determined from a newly sequenced bacteria genome. Can this be verified from the sequence data?

Thanks

James

ADD COMMENTlink modified 5.6 years ago by Biostar ♦♦ 20 • written 6.1 years ago by James60
8
gravatar for JC
6.1 years ago by
JC7.7k
Mexico
JC7.7k wrote:

Bacteria (generally) has only one circular chromosome (but can contain multiple plasmids), therefore your sequencing must show only one large contig.

ADD COMMENTlink modified 6.1 years ago • written 6.1 years ago by JC7.7k
5

I guess this may be true for many bacteria, but as with many things in biology there are always exceptions. There are bacteria with linear chromosomes and multiple chromosomes (as well as collections of plasmids). See e.g. http://microbewiki.kenyon.edu/index.php/Chromosomes_in_Bacteria:_Are_they_all_single_and_circular%3F#Multiple_Chromosomes and http://micro.cornell.edu/cals/micro/research/labs/angert-lab/genomes.cfm.

To the original question: I think it would be unusual to assess chromosome count from sequence alone. The typical way would be genetic experiments (see papers in the references above) or maybe FISH or PFGE. This isn't my area so I might be very wrong.

In principle, with very high coverage sequencing and long reads, you could assemble the sequencing reads and the number of contigs would equal the number of chromosomes. In practice, of course, repetitive sequence and other problems would break up the chromosomes and you'd have many more contigs than chromosomes.

ADD REPLYlink modified 6.1 years ago • written 6.1 years ago by matted7.0k

I agree, biology always comes with exceptions.

ADD REPLYlink written 6.1 years ago by JC7.7k
1
gravatar for swbarnes2
6.1 years ago by
swbarnes25.2k
United States
swbarnes25.2k wrote:

The short answer is no. Even a very very good de novo assembly will have more contigs than chromosomes.

ADD COMMENTlink written 6.1 years ago by swbarnes25.2k
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