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. 2014 Dec 12;14:250. doi: 10.1186/s12862-014-0250-8

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© Wang et al.; licensee BioMed Central Ltd. 2014

This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.

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Evolution patterns of synonymous sites and non-coding regions in bird genomes. (A-E) We show sequence patterns in introns and synonymous sites of coding regions divided in different chromosome sets or different evolutionary strata (from young to old strata: S2, S1, S0) of Z chromosomes. Microchromosome genes (shown in red) exhibit a very different sequence pattern (dS, codon usage bias, G + C content) relative to macro-chromosomes including the Z, due to their different chromosome size and gene densities [50]. Therefore, we mainly compare the patterns of Z-linked genes to those of chr4 and chr5, which have a similar size and gene number. We also performed comparisons between Z chromosome vs. all macro-chromosomes, and the results are similar (Additional file 3: Table S2). We show the Wilcoxon test significance level of differences with asterisks. ^***:P-value < 0.001. dS: lineage specific synonymous substitution rate. Fop: frequency of optimal codons. GC3: G + C content at the third codon position. GCi: G + C content of introns.