A B C Guillenia lasiophylla Caulanthus amplexicaulis Streptanthus heterophyllus Brassicaceae sp Streptanthus arizonicus Sisymbrium leucocladum Isatis lusitanica Isatis tinctoria Myagrum perfoliatum Sinapis alba Hirschfeldia incana Eruca vesicaria Sisymbrium brassiciforme Cakile maritima Crambe hispanica Psychine stylosa Thlaspi arvense Calepina irregularis Goldbachia laevigata Cochlearia officinalis Teesdalia nudicaulis Farsetia aegyptia Lobularia maritima Iberis amara Schizopetalum walkeri Lunaria annua Capsella bursa-pastoris Olimoarabidopsis pumila Physaria acutifolia Turritis glabra Erysimum cheiranthoides Malcomia maritima Descurainia pinnata Descurainia sophioides Lepidium ruderale Lepidium sativuum Barbarea bracteosa Rorippa islandica Nasturtium officinale Cardamine hirsuta Meniocus linifolius Euclidium syriacum Matthiola longipetala Hesperis matronalis Diptychocarpus strictus Chorispora tenella Aethionema arabicum Tarenaya hassleriana Cleomaceae sp Melidiscus giganteus Gynandropsis gynandra Arivela viscosa Coalisina paradoxa Coalisina angustifolia Polanisia trachysperma Polanisia dodecandra Polanisia graveolens Polanisia sp Cleome arabica Cleome africana \Cleome violacea Cleomella serrulata Capparaceae sp Capparis fascicularis Boscia sp Cadaba natalensis Reseda odorata Ochradenus baccatus Batis maritima Moringa oleifera Carica papaya 0% 25% 50% 75% 100% 0% 25% 50% 75% 100% Proportion of repetitive elements by Superfamily Proportion of repetitive elements by Order other non−ltr other ltr RandI RTE L1 Novosib Harbinger Helitron non−ltr_retrotransposon retrotransposon retrotransposon other dna RTEX Copia MuDR SINE2/tRNA Penelope Gypsy hAT transposon ltr_retrotransposon dna_transposon Supplemental Figure 1. Proportion plots of transposable element abundance scaled to 100%. (A) phylogeny of taxa, (B) by superfamily, (C) by order. Family Bataceae Brassicaceae Capparaceae Cariaceae Cleomaceae Moringaceae Resadaceae Supplemental Figure 2. Comparison of phylogenetic relationships across Brassicales in the ASTRAL tree obtained from transcriptome data (left) and based on hierarchical clustering of TE abundances (right). A Meniocus linifolius Olimoarabidopsis pumila Descurainia sophioides Capsella bursa-pastoris Descurainia pinnata Farsetia aegyptia Olimoarabidopsis pumila Caulanthus amplexicaulis Capsella bursa-pastoris Descurainia sophioides Physaria acutifolia Crambe hispanica Turritis glabra Turritis glabra Erysimum cheiranthoides Euclidium syriacum Malcomia maritima Psychine stylosa Lepidium ruderale Cardamine hirsuta Lepidium sativuum Meniocus linifolius Cardamine hirsuta Lepidium ruderale Nasturtium officinale Guillenia lasiophylla Rorippa islandica Streptanthus heterophyllus Barbarea bracteosa Malcomia maritima Farsetia aegyptia Lepidium sativuum Lobularia maritima Hirschfeldia incana Iberis amara Descurainia pinnata Goldbachia laevigata Sinapis alba Calepina irregularis Rorippa islandica Psychine stylosa Goldbachia laevigata Crambe hispanica Calepina irregularis Hirschfeldia incana Sisymbrium brassiciforme Sinapis alba Isatis tinctoria Sisymbrium brassiciforme Barbarea bracteosa Eruca vesicaria Nasturtium officinale Cakile maritima Lobularia maritima Caulanthus amplexicaulis Iberis amara Guillenia lasiophylla Erysimum cheiranthoides Streptanthus heterophyllus Eruca vesicaria Brassicaceae sp Brassicaceae sp Streptanthus arizonicus Myagrum perfoliatum Sisymbrium leucocladum Isatis lusitanica Isatis tinctoria Teesdalia nudicaulis Isatis lusitanica Diptychocarpus strictus Myagrum perfoliatum Chorispora tenella Thlaspi arvense Aethionema arabicum Cochlearia officinalis Cochlearia officinalis Teesdalia nudicaulis Streptanthus arizonicus Schizopetalum walkeri Sisymbrium leucocladum Lunaria annua Hesperis matronalis Euclidium syriacum Physaria acutifolia Matthiola longipetala Matthiola longipetala Hesperis matronalis Cakile maritima Diptychocarpus strictus Thlaspi arvense Chorispora tenella Schizopetalum walkeri Aethionema arabicum Lunaria annua B Gynandropsis gynandra Gynandropsis gynandra Tarenaya hassleriana Tarenaya hassleriana Cleomaceae sp Cleomaceae sp Melidiscus giganteus Polanisia sp Arivela viscosa Polanisia graveolens Coalisina angustifolia Polanisia dodecandra Coalisina paradoxa Polanisia trachysperma Polanisia sp Arivela viscosa Polanisia graveolens Coalisina angustifolia Polanisia dodecandra Melidiscus giganteus Polanisia trachysperma Coalisina paradoxa Cleome violacea Cleome violacea Cleome arabica Cleome arabica Cleome africana Cleome africana C Capparaceae sp Capparaceae sp Capparis fascicularis Capparis fascicularis Boscia sp Cadaba natalensis Cadaba natalensis Boscia sp Supplemental Figure 3. Comparison of phylogenetic relationships in the ASTRAL tree obtained from transcriptome data (black) and based on hierarchical clustering of TE abundances (red) in (A) Brassicaceae, (B) Cleomaceae, and (C) Capparaceae. Supplemental Table 1. Taxon sampling with genome size, chromosome counts, and repetitive element abundance. Chromosome counts as in http://legacy.tropicos.org/Project/IPCN. Asterisks (*) indicate samples with known ploidy level. ltr - on on L1 hAT RTE Copia (Mbp) Gypsy RandI RTEX MuDR Family Species Novosib other ltr ltr other Helitron Penelope count (n) Total_RE Harbinger other DNA other transposon Genome Size Size Genome other non other SINE2/tRNA Chromosome Chromosome retrotranspos retrotranspos Bataceae 356.97 11 0.0734 0.1192 0.0058 0.0138 0.0571 0.0075 0.0625 1.38E-02 4.17E-04 0.00E+00 8.34E-04 0.00E+00 4.17E-04 8.34E-04 0.00E+00 0.00E+00 0.3556 Batis maritima Brassicaceae 933.99 11 0.1557 0.1632 0.0129 0.0235 0.0811 0.0163 0.115 1.23E-02 1.36E-02 4.04E-04 2.16E-03 2.70E-04 0.00E+00 0.00E+00 0.00E+00 0.00E+00 0.5964 Aethionema arabicum* Brassicaceae 899.76 0.0997 0.1382 0.0098 0.0132 0.0581 0.0049 0.0768 7.48E-03 1.23E-03 3.79E-04 5.68E-04 0.00E+00 9.47E-05 2.84E-04 9.47E-05 0.00E+00 0.4107 Meniocus linifolius Brassicaceae 268.95 8 0.1068 0.2629 0.0124 0.0218 0.0637 0.0073 0.0491 1.13E-02 3.59E-03 7.98E-05 5.59E-04 1.92E-03 0.00E+00 3.19E-04 0.00E+00 0.00E+00 0.5417 Barbarea bracteosa Brassicaceae 1383.87 9 0.1463 0.3109 0.0133 0.0082 0.0225 0.0101 0.0444 1.03E-02 1.33E-03 0.00E+00 6.66E-04 1.38E-02 0.00E+00 0.00E+00 0.00E+00 0.00E+00 0.5817 Cakile maritima* Brassicaceae 254.28 14 0.0957 0.2056 0.0104 0.0213 0.0483 0.0095 0.0471 1.57E-02 2.97E-03 6.20E-04 2.48E-04 3.72E-03 0.00E+00 2.48E-04 1.24E-04 0.00E+00 0.4617 Calepina irregularis Brassicaceae 420.54 8,16 0.1275 0.1617 0.0116 0.0218 0.0571 0.0122 0.0631 2.27E-02 7.04E-03 8.80E-04 6.40E-04 1.84E-03 3.20E-04 8.00E-04 1.60E-04 0.00E+00 0.4893 Capsella bursa-pastoris Brassicaceae 489 7,8 0.0911 0.1797 0.0145 0.0153 0.0953 0.0036 0.0608 9.44E-03 1.42E-03 3.78E-04 2.83E-04 4.72E-04 0.00E+00 7.55E-04 0.00E+00 0.00E+00 0.4731 Cardamine hirsuta Brassicaceae 484.11 0.1521 0.1708 0.0084 0.0146 0.0362 0.0074 0.0549 7.60E-03 1.36E-03 3.90E-04 0.00E+00 0.00E+00 9.74E-05 5.84E-04 0.00E+00 0.00E+00 0.4544 Caulanthus amplexicaulis* Brassicaceae 366.75 7 0.174 0.1702 0.0126 0.0175 0.0471 0.0167 0.0578 7.26E-03 3.98E-03 6.96E-04 2.59E-03 8.95E-04 9.94E-05 3.98E-04 0.00E+00 0.00E+00 0.5118 Chorispora tenella Brassicaceae 734 12 0.1941 0.231 0.009 0.0271 0.0615 0.0082 0.0707 1.32E-02 1.12E-03 3.75E-04 2.50E-04 0.00E+00 5.00E-04 9.99E-04 0.00E+00 0.00E+00 0.6181 Cochlearia offcinalis Brassicaceae 660.15 15,30 0.1942 0.1496 0.0099 0.0126 0.0362 0.0053 0.0513 9.91E-03 5.08E-04 2.54E-04 2.54E-04 4.49E-03 0.00E+00 1.69E-04 8.47E-05 0.00E+00 0.4749 Crambe hispanica* Brassicaceae 371.64 7 0.1866 0.1963 0.0069 0.0124 0.0356 0.0056 0.0383 5.44E-03 4.57E-03 3.89E-04 1.36E-03 9.72E-05 9.72E-05 2.91E-04 0.00E+00 0.00E+00 0.4939 Descurainia pinnata* Brassicaceae 195.6 7,14 0.175 0.1532 0.0096 0.014 0.0897 0.0045 0.0412 6.16E-03 2.22E-03 1.01E-04 1.01E-03 3.03E-04 0.00E+00 1.01E-04 0.00E+00 0.00E+00 0.4973 Descurainia sophioides* Brassicaceae 557.46 7 0.1625 0.1509 0.0106 0.0168 0.1085 0.0051 0.0385 1.05E-02 4.98E-03 4.24E-04 4.24E-04 3.18E-04 1.06E-04 3.18E-04 0.00E+00 0.00E+00 0.5101 Diptychocarpus strictus* Brassicaceae 709.05 11 0.1464 0.2511 0.012 0.008 0.0465 0.0053 0.0529 5.58E-03 4.04E-04 2.42E-04 0.00E+00 5.33E-03 1.62E-04 3.23E-04 1.62E-04 0.00E+00 0.5345 Eruca vesicaria* Brassicaceae 420.54 8 0.1424 0.2372 0.0056 0.0196 0.041 0.0093 0.0274 1.84E-02 7.27E-03 2.32E-03 1.83E-04 5.01E-03 2.44E-04 3.05E-04 0.00E+00 0.00E+00 0.5164 Erysimum cheiranthoides Brassicaceae 298.29 7 0.1686 0.1255 0.0105 0.014 0.0591 0.0027 0.0554 7.99E-03 2.00E-03 5.26E-04 4.20E-04 1.05E-04 4.20E-04 4.20E-04 0.00E+00 0.00E+00 0.4477 Euclidium syriacum* Brassicaceae 2004.9 24 0.142 0.1715 0.0101 0.0155 0.0753 0.0067 0.0471 6.58E-03 2.55E-03 8.22E-05 2.47E-04 8.22E-04 8.22E-05 3.29E-04 8.22E-05 0.00E+00 0.479 Farsetia aegyptica Brassicaceae 547.68 14 0.0885 0.2542 0.0076 0.0168 0.0314 0.0072 0.0382 1.14E-02 4.31E-03 1.96E-04 1.96E-04 2.06E-03 2.94E-04 4.89E-04 0.00E+00 0.00E+00 0.463 Goldbachia laevigata Brassicaceae 621.03 0.0908 0.0997 0.0116 0.0153 0.0846 0.0066 0.06 8.36E-03 1.38E-03 2.30E-04 1.53E-04 0.00E+00 1.53E-04 0.00E+00 0.00E+00 0.00E+00 0.3788 Guillenia lasiophylla Brassicaceae 3261.63 7 0.395 0.1763 0.0056 0.0097 0.0321 0.0038 0.0354 4.32E-03 4.75E-03 0.00E+00 0.00E+00 7.38E-04 0.00E+00 0.00E+00 0.00E+00 0.00E+00 0.6677 Hesperis matronalis Brassicaceae 552.57 7 0.1222 0.1947 0.0072 0.0107 0.0505 0.0056 0.0616 6.36E-03 1.47E-03 4.71E-04 5.89E-05 4.59E-03 0.00E+00 1.18E-04 5.89E-05 0.00E+00 0.4655 Hirschefeldia incana Brassicaceae 831.3 7 0.1167 0.1951 0.0173 0.014 0.0897 0.0046