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Genome Skimming Provides Well Resolved Plastid and Nuclear

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Australian Systematic Botany, 2019, 32, 243–254

©CSIRO 2019 https://doi.org/10.1071/SB18057

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 https://doi.org/10.1071/SB18057

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

  • Pyrophytae × Insignes  Clarke, C. & Bourke, G. 54 Horticulatural
  • G07899

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

  • Clarke, C. & Bourke, G. 5
  • Mindoro, Phiippines

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

  • Clarke, C. & Bourke, G. 8
  • Sumatra, Indonesia

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

  • Sumatra, Indonesia
  • G07873

G07895 G07874

G07894 G07872 G07902 G07881 G07878 G05999 G06028
Palawan, Philippines Palawan, Philippines Australia

  • Australia
  • Gray, B. 9126

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

  • Sumatra, Indonesia
  • G07880

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

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Australian Systematic Botany

©CSIRO 2019 https://doi.org/10.1071/SB18057

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 https://doi.org/10.1071/SB18057

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

  • Locus
  • Length PIS PIS (%)

  • ITS1
  • 268

233
49 53
18.28 22.75 33.04 14.31
1.11
ITS2

  • ETS
  • 920
  • 304

  • 78
  • NTS
  • 545

  • 18S
  • 1809

152
20

  • 5.8S
  • 7
  • 4.61

  • 26S
  • 2998

4959 1966
653

  • 78
  • 2.60

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

  • 8.51
  • Total
  • 6925

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Australian Systematic Botany

©CSIRO 2019 https://doi.org/10.1071/SB18057

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
0

lhbA 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
0

petL

0

petN psaA psaB psaC psaI psaJ psbA psbB psbC psbD psbE psbF psbH psbI psbJ psbK psbL psbM psbN psbT

  • 90
  • 1

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
0

psbZ

1.59
Page 5 of 6

Australian Systematic Botany

©CSIRO 2019 https://doi.org/10.1071/SB18057

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
30

rpl36 rpoA rpoB

22 31
3
15 63 12
0004
13
0964
12 17 10
0

rpoC1-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
0

rps15 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
4

ycf1 ycf2

242
18
301102

ycf3-p1 ycf3-p2 ycf3-p3 ycf4 ycf68-p1 ycf68-p2

  • 505
  • 0.40

70ꢀ263

  • Total
  • 931
  • 1.33

Page 6 of 6

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  • Flora Malesiana Nepenthaceae

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    Flora Malesiana Series I - Seed Plants Volume 15 - 2001 Nepenthaceae Martin Cheek & Matthew Jebb ISBN 90-71236-49-8 All rights reserved © 2001 FoundationFlora Malesiana No the this be in part of material protected by copyright notice may reproduced or utilized any electronic form or by any means, or mechanical, including photocopying, recording, or by any and retrieval without written the information storage system, permission from copyright owner. Abstract Flora Malesiana. Series I, Volume 15 (2001) iv + 1—157, published by the Nationaal Herbarium Nederland, Universiteit Leiden branch, The Netherlands, under the aus- pices of FoundationFlora Malesiana. ISBN 90-71236-49-8 for i.e. the Contains the taxonomicrevision ofone family, Nepenthaceae, Malesia, area covering the countries Indonesia, Malaysia, Brunei Darussalam, Singapore, the Philip- pines, and Papua New Guinea. Martin Cheek & Matthew Jebb, Nepenthaceae, pp. 1—157*. A palaeotropical family of lianas, shrubs and herbs, with a single genus, Nepenthes. three There are 83 species of the family in the Malesian area, including nothospecies and one little known species. Most of the species are cultivated and traded across the value. in world as ornamental plants with curiosity Locally Malesia, some species are used for cooking specialist rice dishes, for medicinal uses or for making rope. habitat and ecol- The introductory part consists of chapters on distribution, fossils, ogy, reproductive biology, morphology and anatomy, pitcher function, cytotaxonomy, and characters. conservation, taxonomy, uses, collecting notes, spot Regional keys to the species are given. These are based largely on vegetative charac- ters. distribution, notes Foreach species full references, synonymy, descriptions, ecology, on diagnostic characters and relationships withother species are presented.
  • Nepenthes Naga, a New Species of Nepenthaceae from Bukit Barisan of Sumatra Island

    Nepenthes Naga, a New Species of Nepenthaceae from Bukit Barisan of Sumatra Island

    REINWARDTIA Vol 12, Part 5, pp: 339 – 342 NEPENTHES NAGA, A NEW SPECIES OF NEPENTHACEAE FROM BUKIT BARISAN OF SUMATRA Received July 10, 2007; accepted March 27, 2008. PITRA AKHRIADI Herbarium Universitas Andalas (ANDA), Biologi FMIPA UNAND Padang, Indonesia. E-mail: [email protected] HERNAWATI Herbarium Universitas Andalas (ANDA), Biologi FMIPA UNAND Padang, Indonesia. ALFINDRA PRIMALDHI Division Nepenthes Indonesia, Malang, Indonesia. MUHAMMAD HAMBALI Division Nepenthes Indonesia, Malang, Indonesia. ABSTRACT AKHRIADI, P., HERNAWATI, PRIMALDHI, A. & HAMBALI, M. 2009. Nepenthes naga, a new species of Nepenthaceae from Bukit Barisan of Sumatra. Reinwardtia 12(5): 339 – 342. ⎯ A new species of Nepenthes from North Sumatra is described as Nepenthes naga Akhriadi, Hernawati, Primaldhi & Hambali. The key characters for this species are a triangular dichotomous appendage resembling a snake's tongue inserted sub-apically on the undersurface of the lid, and the undulate lid margin. Keywords: Nepenthes, Nepenthaceae, Sumatra, snake-tongue ABSTRAK AKHRIADI, P., HERNAWATI, PRIMALDHI, A. & HAMBALI, M. 2009. Nepenthes naga, sebuah jenis baru Nepenthaceae dari Bukit Barisan Sumatera. Reinwardtia 12(5): 339 – 342. ⎯ Sebuah jenis baru Nepenthes dari Sumatra Utara dipertelakan sebagai Nepenthes naga Akhriadi, Hernawati, Primaldhi & Hambali. Karakter kunci dari jenis ini adalah adanya apendiks bercabang dua yang menyegi-tiga menyerupai lidah ular yang muncul sebelum ujung dari permukaan bawah tutup kantong dan pinggir tutup kantong yang mengombak. Kata kunci: Nepenthes, Nepenthaceae, Sumatera, lidah ular INTRODUCTION (2007), N. jamban Lee, Hernawati & Akhriadi (2006), N. lingulata Lee, Hernawati & Akhriadi The species of Nepenthes L. (Nepenthaceae) (2006), and N. rigidifolia Akhriadi, Hernawati & are popular plants with the unique character of Tamin (2004). pitchers that inserted from leaf apex through the Several Nepenthes experts have claimed that tendril and are of interest to plant researchers, Sumatra is a hotspot of Nepenthes evolution (e.g.
  • Molecular Phylogenetic Relationships Among Members of the Family Phytolaccaceae Sensu Lato Inferred from Internal Transcribed Sp

    Molecular Phylogenetic Relationships Among Members of the Family Phytolaccaceae Sensu Lato Inferred from Internal Transcribed Sp

    Molecular phylogenetic relationships among members of the family Phytolaccaceae sensu lato inferred from internal transcribed spacer sequences of nuclear ribosomal DNA J. Lee1, S.Y. Kim1, S.H. Park1 and M.A. Ali2 1International Biological Material Research Center, Korea Research Institute of Bioscience and Biotechnology, Yuseong-gu, Daejeon, South Korea 2Department of Botany and Microbiology, College of Science, King Saud University, Riyadh, Saudi Arabia Corresponding author: M.A. Ali E-mail: [email protected] Genet. Mol. Res. 12 (4): 4515-4525 (2013) Received August 6, 2012 Accepted November 21, 2012 Published February 28, 2013 DOI http://dx.doi.org/10.4238/2013.February.28.15 ABSTRACT. The phylogeny of a phylogenetically poorly known family, Phytolaccaceae sensu lato (s.l.), was constructed for resolving conflicts concerning taxonomic delimitations. Cladistic analyses were made based on 44 sequences of the internal transcribed spacer of nuclear ribosomal DNA from 11 families (Aizoaceae, Basellaceae, Didiereaceae, Molluginaceae, Nyctaginaceae, Phytolaccaceae s.l., Polygonaceae, Portulacaceae, Sarcobataceae, Tamaricaceae, and Nepenthaceae) of the order Caryophyllales. The maximum parsimony tree from the analysis resolved a monophyletic group of the order Caryophyllales; however, the members, Agdestis, Anisomeria, Gallesia, Gisekia, Hilleria, Ledenbergia, Microtea, Monococcus, Petiveria, Phytolacca, Rivinia, Genetics and Molecular Research 12 (4): 4515-4525 (2013) ©FUNPEC-RP www.funpecrp.com.br J. Lee et al. 4516 Schindleria, Seguieria, Stegnosperma, and Trichostigma, which belong to the family Phytolaccaceae s.l., did not cluster under a single clade, demonstrating that Phytolaccaceae is polyphyletic. Key words: Phytolaccaceae; Phylogenetic relationships; Internal transcribed spacer; Nuclear ribosomal DNA INTRODUCTION The Caryophyllales (part of the core eudicots), sometimes also called Centrospermae, include about 6% of dicotyledonous species and comprise 33 families, 692 genera and approxi- mately 11200 species.