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Do whole genome sequencing techniques detect B chromosomes if such chromosomes are present?

My understanding is as follows:

How the DNA material in a B Chromosome is mapped depends on the reference map and not on how the material is packaged into chromosomes for the sample being sequenced.

Is this correct?

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You can use differences in coverage (number of reads mapping to certain regions in reference) to infer if there is a B chromosome.

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The analysis of NGS reads coverage rate can give information on B chromosome genomic content. Have a look at the article mentioned below:


Valente GT et al. (2014). Origin and evolution of B chromosomes in the cichlid fish Astatotilapia latifasciata based on integrated genomic analyses. Mol Biol Evol. 2014 Aug;31(8):2061-72

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  • $\begingroup$ Can you add a little explanation on how coverage can be used to infer B chromosome genomic content. An illustrative figure from the mention reference would also do. We would greatly appreciate some explanation in addition to providing a link to the reference. $\endgroup$ – WYSIWYG Oct 14 '15 at 16:48
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enter image description here

The attached figure shows the Illumina reads coverage for two 0B, two 1B and one 2B samples. Note that the figure shows a specific genomic regions with a higher reads coverage for the 1B and 2B samples compared to the 0B ones.

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  • $\begingroup$ Welcome to Bio. Could you provide sources to your data and answer? References are encouraged here. $\endgroup$ – AliceD Jan 29 '16 at 17:58

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