Genome Skimming Provides Well Resolved Plastid and Nuclear

Australian Systematic Botany, 2019, 32, 243–254 ©CSIRO 2019 <a href="/goto?url=https://doi.org/10.1071/SB18057" target="_blank">https://doi.org/10.1071/SB18057 </a>Supplementary material Genome skimming provides well resolved plastid and nuclear phylogenies, showing patterns of deep reticulate evolution in the tropical carnivorous plant genus Nepenthes (Caryophyllales) Lars NauheimerA,B,C,G, Lujing CuiD,E, Charles ClarkeA, Darren M. CraynA,B,C,D Greg BourkeF and Katharina NargarA,B,C,D ,AAustralian Tropical Herbarium, James Cook University, PO Box 6811, Cairns, Qld 4878, Australia. BCentre for Tropical Environmental Sustainability Science, James Cook University, McGregor Road, Smithfield, Qld 4878, Australia. CCentre for Tropical Bioinformatics and Molecular Biology, James Cook University, McGregor Road, Smithfield, Qld 4878, Australia. DNational Research Collections Australia, Commonwealth Industrial and Scientific Research Organisation (CSIRO), GPO Box 1700, Canberra, ACT 2601, Australia. ESchool of Computer Science and Engineering, University of New South Wales, NSW 2052, Australia. FBlue Mountains Botanic Garden, Bells Line of Road, Mount Tomah, NSW 2758, Australia. GCorresponding author. Email: [email protected] Page 1 of 6 Australian Systematic Botany ©CSIRO 2019 <a href="/goto?url=https://doi.org/10.1071/SB18057" target="_blank">https://doi.org/10.1071/SB18057 </a>Table S1. List of accessions used for phylogenetic analyses with sectional association, voucher number, geographic origin and DNA number All herbarium vouchers are located in the Australian Tropical Herbarium in Cairns (CNS) Species Nepenthes ampullaria Jack Nepenthes benstonei C.Clarke Section Urceolatae Pyrophytae Voucher Clarke, C. & Bourke, G. 2 Clarke, C. & Bourke, G. 38 Malay Peninsula, Malaysia G07897 Origin Borneo, Malaysia DNA number G07903 Nepenthes bokorensis Mey × Nepenthes ventricosa Blanco Nepenthes bongso Korth. Nepenthes borneensis J.H.Adam & Wilcock Nepenthes boschiana Korth. Nepenthes burkei Hort.Veitch × ventricosa Blanco Nepenthes burkei Veitch Nepenthes copelandii Merr. ex Macfarl. Nepenthes ephippiata Danser <ul style="display: flex;"><li style="flex:1">Pyrophytae × Insignes Clarke, C. & Bourke, G. 54 Horticulatural </li><li style="flex:1">G07899 </li></ul>G07898 G07870 G07855 G07877 G07875 G07883 G07900 G07887 G07893 G07901 G07884 G07891 G07866 Montanae Regiae Clarke, C. & Bourke, G. 19 Sumatra, Indonesia Clarke, C. & Bourke, G. 23 Regiae Regiae Clarke, C. & Bourke, G. 32 Borneo, Malaysia Clarke, C. & Bourke, G. 32 Borneo, Malaysia Insignes <ul style="display: flex;"><li style="flex:1">Clarke, C. & Bourke, G. 5 </li><li style="flex:1">Mindoro, Phiippines </li></ul>Villosae Regiae Regiae Montanae Montanae Tentaculatae Montanae Montanae × Insignes Clarke, C. & Bourke, G. 24 Mindanao, Philippines Clarke, C. & Bourke, G. 36 Borneo, Malaysia Clarke, C. & Bourke, G. 20 Sulawesi, Indonesia Clarke, C. & Bourke, G. 12 Sumatra, Indonesia Nepenthes eymae Sh.Kurata Nepenthes gymnamphora Reinw. ex Nees Nepenthes gymnamphora Reinw. ex Nees Nepenthes hamata J.R.Turnbull & A.T.Middleton Nepenthes izumiae Troy Davis, C.Clarke & Tamin Nepenthes izumiae Troy Davis, C.Clarke & Tamin × Nepenthes ventricosa Blanco <ul style="display: flex;"><li style="flex:1">Clarke, C. & Bourke, G. 8 </li><li style="flex:1">Sumatra, Indonesia </li></ul>Clarke, C. & Bourke, G. 14 Sulawesi, Indonesia Clarke, C. & Bourke, G. 10 Sumatra, Indonesia Clarke, C. & Bourke, G. 51 Horticulatural Nepenthes jacquelineae C.Clarke, Troy Davis & Tamin Nepenthes kampotiana Lecomte Nepenthes khasiana Hook.f. Nepenthes kongkandana M. Catal. & Kruetr. Nepenthes maxima Reinw. Nepenthes minima Jebb & Cheek Nepenthes mira Jebb & Cheek Nepenthes petiolata Danser Nepenthes philippinensis Macfarl. Nepenthes rowanae F.M.Bailey Nepenthes rowanae F.M.Bailey Nepenthes sanguinea Lindl. Nepenthes singalana Becc. Nepenthes sp. Montanae Pyrophytae Nepenthes Pyrophytae Regiae Regiae Regiae Villosae Regiae Incertae sedis Incertae sedis Pyrophytae Montanae Regiae Montanae Montanae Montanae Incertae sedis Tentaculatae Montanae Clarke, C. & Bourke, G. 9 Clarke, C. & Bourke, G. 49 Indochina Clarke, C. & Bourke, G. 15 India Clarke, C. & Bourke, G. 48 Malay Peninsula, Malaysia G07869 Clarke, C. & Bourke, G. 40 Unclear Clarke, C. & Bourke, G. 50 Sulawesi, Indonesia Clarke, C. & Bourke, G. 4 Clarke, C. & Bourke, G. 22 Mindanao, Philippines Clarke, C. & Bourke, G. 1 Schulte, K. 258B <ul style="display: flex;"><li style="flex:1">Sumatra, Indonesia </li><li style="flex:1">G07873 </li></ul>G07895 G07874 G07894 G07872 G07902 G07881 G07878 G05999 G06028 Palawan, Philippines Palawan, Philippines Australia <ul style="display: flex;"><li style="flex:1">Australia </li><li style="flex:1">Gray, B. 9126 </li></ul>Clarke, C. & Bourke, G. 26 Malay Peninsula, Malaysia G07858 Clarke, C. & Bourke, G. 7 Clarke, C. & Bourke, G. 33 Luzon, Philippines Clarke, C. & Bourke, G. 28 Sumatra, Indonesia Clarke, C. & Bourke, G. 16 Sumatra, Indonesia Clarke, C. & Bourke, G. 11 Sumatra, Indonesia Schulte, K. 260 Clarke, C. & Bourke, G. 17 Borneo, Malaysia Clarke, C. & Bourke, G. 34 Sumatra, Indonesia <ul style="display: flex;"><li style="flex:1">Sumatra, Indonesia </li><li style="flex:1">G07880 </li></ul>G07886 G07896 G07890 G07888 G06000 G07885 G07871 Nepenthes spathulata Danser Nepenthes spectabilis Danser Nepenthes talangensis Nerz & Wistuba Nepenthes tenax C.Clark & R.Kruger Nepenthes tentaculata Hook.f. Australia Nepenthes tobaica Danser Page 2 of 6 Australian Systematic Botany ©CSIRO 2019 <a href="/goto?url=https://doi.org/10.1071/SB18057" target="_blank">https://doi.org/10.1071/SB18057 </a>Nepenthes truncata Macfarl. Nepenthes ventricosa Blanco Nepenthes xiphioides B.R.Salmon & R.G.Maulder Drosera regia Stephens Villosae Clarke, C. & Bourke, G. 41 Mindanao, Philippines Clarke, C. & Bourke, G. 47 Luzon, Philippines Clarke, C. & Bourke, G. 13 Sumatra, Indonesia G07889 G07865 G07876 Insignes Montanae Outgroup Outgroup Oxyria sinensis Hemsl. Page 3 of 6 Australian Systematic Botany ©CSIRO 2019 <a href="/goto?url=https://doi.org/10.1071/SB18057" target="_blank">https://doi.org/10.1071/SB18057 </a>Table S2. Alignment length of all parts of the ribosomal array (external transcribed spacer– non-transcribed-spacer, ETS-NTS) with the amount of phylogenetic informative sites (PIS) and the percentage of PIS among all 39 included Nepenthes accessions <ul style="display: flex;"><li style="flex:1">Locus </li><li style="flex:1">Length PIS PIS (%) </li></ul><ul style="display: flex;"><li style="flex:1">ITS1 </li><li style="flex:1">268 </li></ul>233 49 53 18.28 22.75 33.04 14.31 1.11 ITS2 <ul style="display: flex;"><li style="flex:1">ETS </li><li style="flex:1">920 </li><li style="flex:1">304 </li></ul><ul style="display: flex;"><li style="flex:1">78 </li><li style="flex:1">NTS </li><li style="flex:1">545 </li></ul><ul style="display: flex;"><li style="flex:1">18S </li><li style="flex:1">1809 </li></ul>152 20 <ul style="display: flex;"><li style="flex:1">5.8S </li><li style="flex:1">7</li><li style="flex:1">4.61 </li></ul><ul style="display: flex;"><li style="flex:1">26S </li><li style="flex:1">2998 </li></ul>4959 1966 653 <ul style="display: flex;"><li style="flex:1">78 </li><li style="flex:1">2.60 </li></ul>Ribosomal RNAs (18S,5.8S,26S) Spacer (ETS, ITS1, ITS2, NTS) ITS1, 5.8S, ITS2 105 484 109 589 2.12 24.62 16.69 <ul style="display: flex;"><li style="flex:1">8.51 </li><li style="flex:1">Total </li><li style="flex:1">6925 </li></ul>Page 4 of 6 Australian Systematic Botany ©CSIRO 2019 <a href="/goto?url=https://doi.org/10.1071/SB18057" target="_blank">https://doi.org/10.1071/SB18057 </a>Table S3. Alignment length of all 95 used plastid loci representing 81 plastid genes with the amount of phylogenetic informative sites (PIS) and the percentage of PIS among all 39 included Nepenthes accessions Locus accD atpA atpB atpE atpF-p1 atpF-p2 atpH atpI ccsA cemA clpP-p1 clpP-p2 clpP-p3 infA Length 1548 1524 1497 402 144 411 249 744 993 690 71 292 270 286 189 1563 559 539 777 756 363 1508 306 2303 531 1183 508 477 866 966 642 496 114 96 PIS 14 14 15 40826 25 11 02131 33 15 10 0 PIS (%) 0.90 0.92 1.00 1.00 0 1.95 0.80 0.81 2.52 1.59 0 0.68 0.37 1.05 0.53 2.11 2.68 1.86 0 0.13 1.10 1.06 0.98 2.39 2.64 1.35 0.59 1.68 1.27 1.76 0lhbA matK ndhA-p1 ndhA-p2 ndhB-p1 ndhB-p2 ndhC ndhD ndhE ndhF ndhG ndhH ndhI ndhJ ndhK petA petB-p2 petD-p2 petG 14 16 3 55 14 16 38 11 17 071 1.41 0.88 0petL 0petN psaA psaB psaC psaI psaJ psbA psbB psbC psbD psbE psbF psbH psbI psbJ psbK psbL psbM psbN psbT <ul style="display: flex;"><li style="flex:1">90 </li><li style="flex:1">1</li></ul>9 11 32 1.11 0.40 0.50 1.22 1.80 0.74 1.04 0.79 0.56 0.38 0.79 0.83 0.90 1.80 0.81 0.53 0 2253 2205 246 111 135 1062 1527 1422 1062 252 120 222 111 123 189 117 105 132 108 189 1 11 12 8421221101103 0.95 0.76 0psbZ 1.59 Page 5 of 6 Australian Systematic Botany ©CSIRO 2019 <a href="/goto?url=https://doi.org/10.1071/SB18057" target="_blank">https://doi.org/10.1071/SB18057 </a>Locus rbcL rpl14 rpl16-p2 rpl2-p1 rpl2-p2 rpl20 rpl22 rpl23 rpl32 rpl33 Length 1428 369 399 393 435 393 615 282 181 201 114 1008 3213 432 1617 4172 417 114 232 26 PIS 11 22205 14 13 PIS (%) 0.77 0.54 0.50 0.51 0 1.27 2.28 0.35 1.66 1.49 0 2.18 0.96 0.69 0.93 1.51 2.88 0 30rpl36 rpoA rpoB 22 31 3 15 63 12 0004 13 0964 12 17 10 0rpoC1-p1 rpoC1-p2 rpoC2 rps11 rps12-p1 rps12-p2 rps12-p3 rps14 00 303 291 40 1.32 4.47 0 3.07 1.43 1.43 1.68 2.59 1.65 0 0.99 4.23 0.26 2.42 0 0.65 0.18 0rps15 rps16-p1 rps16-p2 rps18 rps19 rps2 rps3 rps4 rps7 rps8 293 421 279 714 657 606 468 405 5727 6879 124 116 153 555 42 4ycf1 ycf2 242 18 301102ycf3-p1 ycf3-p2 ycf3-p3 ycf4 ycf68-p1 ycf68-p2 <ul style="display: flex;"><li style="flex:1">505 </li><li style="flex:1">0.40 </li></ul>70ꢀ263 <ul style="display: flex;"><li style="flex:1">Total </li><li style="flex:1">931 </li><li style="flex:1">1.33 </li></ul>Page 6 of 6

Genome Skimming Provides Well Resolved Plastid and Nuclear

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