FIG. 1.— Correlation of RPKM between (A) 1,509 TE families estimated from B73–104 and the in silico data with 5 outliers indicated in gray; (B) 1,514 TE.

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FIG. 1.— Correlation of RPKM between (A) 1,509 TE families estimated from B73–104 and the in silico data with 5 outliers indicated in gray; (B) 1,514 TE families estimated from B73 and luxurians. Values are shown on a log scale, with a pseudocount of 1 added to families with 0 counts. From: Genome Size and Transposable Element Content as Determined by High-Throughput Sequencing in Maize and Zea luxurians Genome Biol Evol. 2011;3:219-229. doi:10.1093/gbe/evr008 Genome Biol Evol | © The Author(s) 2011. 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/2.5), which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

FIG. 2.— Log scale coverage along the unique sequence length of four of the five outlier TE families. Shown is RPKM of B73 (black lines) and in silico data (gray lines). (A) RLX_osed_AC191084-2931, (B) RLX_sela_AC195130-4415, (C) RLX_teki_AC202867-7492, and (D) RLX_sari_AC184117-11. From: Genome Size and Transposable Element Content as Determined by High-Throughput Sequencing in Maize and Zea luxurians Genome Biol Evol. 2011;3:219-229. doi:10.1093/gbe/evr008 Genome Biol Evol | © The Author(s) 2011. 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/2.5), which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

FIG. 3.— Sorted log difference in number of TE hits normalized by coverage between (A) B73 and luxurians, where negative values indicate an excess of TE hits in luxurians; (B) the genic and nested TE regions in B73 (black dots) and luxurians (gray dots), where negative values indicate an excess of TE hits in TE-nested regions. Dashed lines indicate zero difference. From: Genome Size and Transposable Element Content as Determined by High-Throughput Sequencing in Maize and Zea luxurians Genome Biol Evol. 2011;3:219-229. doi:10.1093/gbe/evr008 Genome Biol Evol | © The Author(s) 2011. 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/2.5), which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.