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I've been stumbling on multiple genome of birds where there is a "1A" chromosome and a "1" chromosome. For example, the zebra finch has 1A and 4A. What does that mean?

Do you have any resource about naming conventions for chromosomes and if this naming convention is specific to birds?

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I would suggest looking at some of the reference genome papers. My guess is that the chromosomes are named as such based on their synteny to the chicken genome; e.g. look at Accessory Figure 3 here for your zebra finch, and note that chromsomes 1 and 4 are split in the zebra finch relative to Gallus.

The direct comparison from that paper is to an Accessory Table 1 that I can't actually find.

I would guess that in most cases it's because of a synteny comparison to some reference, in this case chicken that splits a chromosome in the new genome. For example sequences homologous to the chicken chr1 are on two finch chromosomes 1 and 1A.

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  • $\begingroup$ This is my suspicion as well, similar to the ape chromosomes 2A and 2B. $\endgroup$ – canadianer Sep 15 '19 at 23:46

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