Extended Data Fig. 5: Full-length LTR-retrotransposon detection in different maize lines.
From: European maize genomes highlight intraspecies variation in repeat and gene content
a, De novo detection and stringent quality filtering of fl-LTR elements. b, Retrieved fl-LTR numbers as proxy for assembly quality. Upper data points give candidate fl-LTRs, lower data points give filtered, high-quality fl-LTR numbers. Five of the six assemblies contain the expected number of fl-LTRs. The by 50% reduced numbers of high-quality elements in PH207 reflect an older not optimized assembly approach. c, Insertion age distribution of fl-LTRs. The four NRGene assemblies have very similar age distribution patterns. The B73 assembly has a higher proportion of very young Copia and Gypsy elements, which can probably be attributed to technical assembly differences. In PH207, the young elements are completely missing in the assembly and thus explain the reduced numbers. Due to their (almost) identical long terminal repeats the correct structure of young elements is more difficult to resolve.
