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Table 2 Reconstruction obtained by reduction to ILP for plastid chromosome structures with paralogs in brown algae

From: Chromosome structures: reduction of certain problems with unequal gene content and gene paralogs to integer linear programming

Ectocarpus siliculosus (l)

rpl32_1 rpl21_1 *rps4 *rps16 *rps1 rpl9 rpl11 rpl1 rpl12 *rps10 *tufa *rps7 *rps12 *rpl31 *rps9 *rpl13 *rpoa *rps11 *rps13 *rpl36 *rps5 *rpl18 *rpl6 *rps8 *rpl5 *rpl24 *rpl14 *rps17 *rpl29 *rpl16 *rps3 *rpl22 *rps19 *rpl2 *rpl23 *rpl4 *rpl3 *rpl21_2 *rpl32_2 *rpl35 rpl20 *rpl19 rpl27 rpl34 rps20 rpob rpoc1 rpoc2 rps2 rps14 *rps18 *rpl33 clpc rbcl (C)

Fucus vesiculosus (l)

*rpl19 rpl27 rpl34 rps20 rpob rpoc1 rpoc2 rps2 rpl35 rpl20 rbcl rps14 *clpc rpl33 rps18 *rpl32_2 rps16 rps4 rps1 rpl9 rpl11 rpl1 rpl12 *rps10 *tufa *rps7 *rps12 *rpl31 *rps9 *rpl13 *rpoa *rps11 *rps13 *rpl36 *rps5 *rpl18 *rpl6 *rps8 *rpl5 *rpl24 *rpl14 *rps17 *rpl29 *rpl16 *rps3 *rpl22 *rps19 *rpl2 *rpl23 *rpl4 *rpl3 *rpl21_2 (C)

Saccharina japonica (l)

*rps2 *rpoc2 *rpoc1 *rpob *rps20 *rpl34 *rpl27 rpl19 rpl35 rpl20 rbcl rps14 *rps18 *rpl33 clpc rpl32_1 rpl21_1 rpl3 rpl4 rpl23 rpl2 rps19 rpl22 rps3 rpl16 rpl29 rps17 rpl14 rpl24 rpl5 rps8 rpl6 rpl18 rps5 rpl36 rps13 rps11 rpoa rpl13 rps9 rpl31 rps12 rps7 tufa rps10 *rpl12 *rpl1 *rpl11 *rpl9 rps1 *rps4 *rps16 (C)

Inner non-root node

*rpl19 rpl27 rpl34 rps20 rpob rpoc1 rpoc2 rps2 rpl35 rpl20 rbcl rps14 rpl32_2 *rps18 *rpl33 clpc rpl32_1 rpl21_1 *rps4 *rps16 *rps1 rpl9 rpl11 rpl1 rpl12 *rps10 *tufa *rps7 *rps12 *rpl31 *rps9 *rpl13 *rpoa *rps11 *rps13 *rpl36 *rps5 *rpl18 *rpl6 *rps8 *rpl5 *rpl24 *rpl14 *rps17 *rpl29 *rpl16 *rps3 *rpl22 *rps19 *rpl2 *rpl23 *rpl4 *rpl3 *rpl21_2 (C)

Tree root

rpl32_1 rpl21_1 *rps4 *rps16 *rps1 rpl9 rpl11 rpl1 rpl12 *rps10 *tufa *rps7 *rps12 *rpl31 *rps9 *rpl13 *rpoa *rps11 *rps13 *rpl36 *rps5 *rpl18 *rpl6 *rps8 *rpl5 *rpl24 *rpl14 *rps17 *rpl29 *rpl16 *rps3 *rpl22 *rps19 *rpl2 *rpl23 *rpl4 *rpl3 *rpl21_2 *rpl19 rpl27 rpl34 rps20 rpob rpoc1 rpoc2 rps2 rps14 rpl32_2 *rps18 *rpl33 clpc rpl35 rpl20 rbcl (C)

  1. Paralog numbers are given after the underscore. For other designations, see Table 1
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