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. 2020 Jul 27;52(9):950–957. doi: 10.1038/s41588-020-0671-9

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© The Author(s) 2020

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Fig. 2 — a, Proportion of the pan and core sets for fl-LTRs and genes with increasing line numbers. b, Percentage of pairwise shared and still-intact fl-LTRs at syntenic positions for seven maize lines. Reading direction is column to row; for example, EP1 shares 27% of its fl-LTRs with F7 and F7 shares 28% with EP1. On the basis of the similarity matrix, the seven lines cluster into a relationship context that separates flint and dent. Within flint and dent, around 30% of the locations are shared; between flint and dent, most of the values are reduced to about 20%, except for PE0075 (25%). The most pronounced overlap of intact and shared fl-LTR locations is found between W22 and B73 (32%); the least pronounced is found between EP1 and Mo17 (18%). A corresponding evalution for genes gives pairwise shared numbers between 82 and 91%. c, Insertion age (y axis) and chromosomal distribution of all fl-LTRs (top row), line unique (label 1) and cluster constellations of increased sharing ranging from two to all eight lines. The chromosomal location is collapsed for all ten chromosomes and given in percentage of the respective chromosome length. The line-specific or shared among fewer lines fl-LTRs contain a higher proportion of younger elements and are less frequently found in the central, low recombining regions. There is a continuous shift towards a more pericentromeric location and towards older elements with the increase of lines sharing corresponding elements.