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Fig. 5. | BMC Biology

Fig. 5.

From: Comparative gene retention analysis in barley, wild emmer, and bread wheat pangenome lines reveals factors affecting gene retention following gene duplication

Fig. 5.

Natural selection, evolutionary pattern, and transcriptional divergence of HPT2-pattern-like genes. Comparing the distribution patterns of Ks (A), Ka (B), and Ka/Ks (C) for the target 326 HPT2-pattern-like genes (brown color) of decreasing retention rates in barley, wild emmer, and bread wheat pangenome lines to their homologous background genes (blue color). D Comparing the relative Ka/Ks value of target genes (brown) and background genes (blue) to the mean Ka/Ks for each orthologous group. A relative Ka/Ks value higher than 1 indicates elevated Ka/Ks. E–L Display 8 example gene trees from the 326 target genes exhibiting a gene dosage effect. Corresponding barley gene ID, annotated gene function, Ka/Ks values (labelled above branch line) for target (brown) and background (blue) HOG groups, and the calculated gene retention rates (below gene tree) for target genes were presented. Barley gene ID were truncated by removing “MOREX.r2”. M Bar chart displaying the identified amino acid sites under positive selection for genes in E–L. The number, percentage, and Ka/Ks value of the positively selected sites for each gene were displayed. N Displays the transcriptional divergence of background (left) and target (right) barley genes based on transcriptome data in six barley tissues in Morex cultivar. Caryopsis: developing grain 5DPA; inflorescence: 1–1.5 cm; lemma: 42 DPA; palea: 42 DPA; shoot: 10 cm stage; root: 28 DPA

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