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. 2018 Sep 18;10(10):2596–2613. doi: 10.1093/gbe/evy193

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© The Author(s) 2018. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.com

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Fig. 7. — —Contribution of pseudogenization to domain family size variation. (A) Relationship between domain family size variability (CoV percentile) and logarithmic number of pseudogenes. (B) Relationship between the number of genes and pseudogenes among Solanaceae species. (C) Correlation between genome size and number of pseudogenes. (D) Correlation between the logarithmic number of genes and pseudogenes in a domain family. Each dot indicates a domain family. The ρ and P value for Spearman’s rank correlation are shown. (E) Proportion of different S. lycopersicum (S.ly) syntenic duplicate pairs that have orthologous sequences in collinear regions in other species. The orthologous sequences were defined giving priority to protein-coding genes over pseudogenes. If orthologous protein-coding genes were not identified for a given gene, then orthologous pseudogenes were searched for. S.pe, S. pennellii; S.tu, S. tuberosum; S.me, S. melongena; C.gl, C. annuum_var. glabriusculum; N.to, N. tomentosiformis; P.ax, P. axillaris; Ps, pseudogene; “–”, no orthologous sequence was found. (F) Proportion of duplicate pairs in S. lycopersicum collinear blocks that are predominantly (>50%) GG, GP, or PP pairs. Each column represents a pair of collinear blocks within S. lycopersicum. GG, gene–gene pair; GP, gene–pseudogene pair; PP, pseudogene–pseudogene pair.