We found that the nucleotide divergence of intermediate-chromosomes was slightly lower than that of the macro-chromosomes, and the nucleotide divergence of micro-chromosomes was slightly higher than that of macro-chromosomes and intermediate-chromosomes.
In most avian species, the karyotype contains both macro-chromosomes and micro-chromosomes unlike that of mammals.
To compare the mutation rates between different chromosomes, we collect orthologous sequence alignments of intronic regions from macro-chromosomes and Z chromosomes.
These 27 chromosomes cover over 90% of the chicken genome, and include all macro-chromosomes and many of the micro-chromosomes.
Since the gene density (number of genes per Mb) of macro-chromosomes was significantly lower than that of micro-chromosomes [ 25], we assume that this explains the slight difference observed between macro-chromosomes and micro-chromosomes.
The emu Z and W chromosomes are similar in size and as large as some chicken macro chromosomes; chromosome painting revealed that the emu Z and W and chicken Z chromosomes are broadly homologous across their entire length [ 60].
The majority of the zebra finch (female) iPSC-like lines (90%) also displayed normal karyotype of macro chromosomes.
The chicken iPSC-like lines displayed a normal karyotype of macro chromosomes in the majority of the spreads analyzed (90%; 18 out of 20) compared to a standard (Nanda et al., 1999), control fibroblasts.
The chicken karyotype comprises 39 pairs of chromosomes, which are divided into 8 pairs of cytologically distinct macro-chromosomes, Z and W sex chromosomes, and 30 pairs of micro-chromosomes.
Chromosome-level assembly and analysis of conserved synteny had been previously reported for the largest (macro-) chromosomes of chicken, turkey and zebra finch [ 14, 20, 21].
GC content varies strongly between micro- and macro-chromosomes in birds and, unless controlled for, the observed GC bias in expression ratios leads to an underestimation of m:f ratios on large chromosomes (including Z) and overestimation of m:f ratios on small micro-chromosomes.
