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. 2018 Aug 10;46(21):e126. doi: 10.1093/nar/gky730

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© The Author(s) 2018. Published by Oxford University Press on behalf of Nucleic Acids Research.

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 reuse, distribution, and reproduction in any medium, provided the original work is properly cited.

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Figure 2. — Relationships between LAI and other genome metrics among genomes with variable assembly quality. LAI is significantly correlated with (A) intact LTR-RT content (r² = 0.51) and marginally correlated with (G) contig N50 (r² = 0.09) and (H) scaffold N50 (r² = 0.07). LAI is independent of (B) total LTR-RT content, (C) the mean LTR identity of the genome, (D) percentage of solo LTR among all LTR-RT sequences, (E) CEGMA completeness of 248 genes, (F) BUSCO completeness of 1,440 genes and (I) haploid genome size (P ≥ 0.10). Each dot represents a plant genome (n = 44) that contain > 5% of LTR sequence. The coefficient of determination (r²) and F-test P value between x- and y-axis are indicated on each plot with outliers also indicated. Significant and non-significant linear regressions are indicated in red- and gray-dotted lines, respectively.