Why there are 40 chromosomes of Gallus gallus in NCBI and in the in karyotype studies there is only evidence of 39 chromosome

Question

[BenAawf]

Hi,

I'm working on assembling the genome of a bird species closely related to Gallus gallus. This species, like G. gallus, has a diploid chromosome number of 2n=78. However, I'm seeing some conflicting information regarding the chromosome count in G. gallus and how it relates to my assembly.

Literature: Most literature reports 2n=78 (39 pairs) for G. gallus.
NCBI RefSeq: The latest G. gallus RefSeq assembly (GCF_016699485.2) shows 40 chromosomes.
My Assembly: My assembly, based on Hi-C data and synteny with G. gallus, also suggests 40 chromosomes. However, the Hi-C contact map only clearly resolves 34 chromosomes.

I'm trying to understand this discrepancy and convince my lab team that 40 chromosomes is the correct count for our species. Could someone explain:

• Why does the literature often report 78 chromosomes for G. gallus when the actual number seems to be 80 (40 pairs)?
• Why might my Hi-C data only resolve 34 chromosomes (matrix_plot ) when the assembly and synteny suggest 40?
• How can I strengthen my argument for 40 chromosomes, even with the limitations of the Hi-C data?

Any insights from a genomics perspective would be greatly appreciated!

Thank you

[GenoMax]

genome of a bird species closely related to Gallus gallus.

How closely related? Your species need not have the same chromosome number.

Gallus gallus has 38 pairs of autosomes and two sex chromosomes. ZZ in Males and ZW in females.

[BenAawf]

GenoMax , Thanks for your reply, can you kindly redirect me a reference or a publication that mention those 80 chromosome that you pointed out because i could not find any reference. my species is the red legged partridge share a common ancestor with g. gallus.

[GenoMax]

Original chicken genome paper https://www.nature.com/articles/nature03154 mentions

Most avian karyotypes contain chromosomes of markedly different lengths, termed the macro- and microchromosomes, and thus bird karyotypes are quite distinctive as compared with those of mammals. The chicken karyotype (2n = 78) is made up of 38 autosomes and one pair of sex chromosomes, with the female as the heterogametic sex (ZW female, ZZ male).

[Dave Carlson]

But note that the Refseq Gallus gallus genome that the OP mentioned (GCF_016699485) appears to have 39 pairs of autosomes and two sex chromosomes. Hence, I suspect, the original question.

[GenoMax]

We are now on release 6 of the genome build so things have changed since release of original paper . It is noted in the comment highlighted above that the chromosomes can be very different.

Interestingly the number seems to have gone up over time

The Gallus_gallus-4.0 assembly of the chicken genome was produced in November 2011 by the International Chicken Genome Consortium. It consists of 31 chromosomes, 2 linkage groups and 14,093 unplaced scaffolds.

[BenAawf]

The 39 pairs of autosome chromosomes in both sex what make me confused and contradicted with the Original chicken genome paper. So I can say that third-generation sequencing helped to fully assemble/capture the whole Chicken genome in terms of chromosome number which was not possible by the previous technology (case of Gallus_gallus-4.0 and Gallus_gallus-5.0 ). Just to sum up G.gallus, has 40 pairs of chromosomes 39 autosomes, plus one pair of sex chromosomes (ZW female, ZZ male) is that what you saying thank GenoMax and @davecarlson