matK. Amaranthaceae. Gomphrena Globosa. Globe amaranth .... Taxus baccata. Common Yew. HQ619788 ..... Taxaceae. Taxus globosa. EF660647. Taxaceae.
Additional Files Click here to download Additional Files: Tab. S1.doc
Table S1. List of universal primers and PCR conditions for each candidate barcode tested in the study
Marker
Primer Name
rbcL
a_f
Direction
Sequence 5'-3'
1
Forward
ATGTCACCACAAACAGAGACTAAAGC
26
Reverse
GTAAAATCAAGTCCACCRCG
20
Forward
CGTACAGTACTTTTGTGTTTACGAG
25
Reverse
ACCCAGTCCATCTGGAAATCTTGGTTC
27
Forward
CGATCTATTCATTCAATATTTC
22
Reverse
TCTAGCACACGAAAGTCGAAGT
22
Forward
CTGGATYCAAGATGCTCCTT
20
Reverse
GGTCTTTGAGAAGAACGGAGA
21
a_rev
matK_a
3F_KIM
2
1R_KIM matk_b
390f
3
1326r matK_c
NY552 NY1150
1.
Length (bp)
Source
4
PCR conditions 95°C 10 min (94°C 30s, 55°C 30s,72°C 1min) x 35 cycles 72°C 10min Protocol 1 95°C 10 min (94°C 30s, 55°C 30s,72°C 1min) x 35 cycles 72°C 10min Protocol 2 95°C 10 min (94°C 30sec, 55°C 1min,72°C 1min30s) x 35 cycles 72°C 10min Protocol 3 95°C 10 min (94°C 30s, 54°C 30s,72°C 45s) x 35 cycles 72°C 10min Protocol 4 95°C 10 min (94°C 30s, 52°C 45s,72°C 45s) x 35 cycles 72°C 10min
1. Kress WJ, Erickson DL (2007) A Two-Locus Global DNA Barcode for Land Plants: The Coding rbcL Gene Complements the Non-Coding trnH psbA Spacer Region. PLoS ONE 2(6): e508. doi:10.1371/journal.pone.0000508 *David Erickson’s modified reverse primer (different from the PLOS One paper) 2. CBOL Plant Working Group (2009) A DNA barcode for land plants. PNAS 106, 12794-12797. 3.Cuénoud, P., Savolainen, V., Chatrou, L. W., Powell, M., Grayer, R. J. and Chase, M. W. 2002. Molecular phylogenetics of Caryophyllales based on nuclear 18S rDNA 3. and plastid rbcL, atpB, and matK DNA sequences. Am. J. Bot. 89, 132-144. 4. 4. In gymnosperms D.Little (unpublished)
Additional Files Click here to download Additional Files: Tab. S2.doc
Table S2 List of plant species and GenBank accession numbers Family
Species Scientific name
Amaranthaceae Apiaceae Apocynaceae Apocynaceae Araliaceae Arecaceae Asteraceae Asteraceae Asteraceae Berberidaceae Boraginaceae Brassicaceae Brassicaceae Brassicaceae Brassicaceae Brassicaceae Buxaceae Cannabaceae Caprifoliaceae Caprifoliaceae Caprifoliaceae Caryophyllaceae Cupressaceae Cupressaceae Fabaceae Fabaceae Fagaceae Fagaceae Fagaceae Ginkgoaceae Lamiaceae Lamiaceae Lauraceae Magnoliaceae Magnoliaceae Oleaceae Oleaceae Oxalidaceae Pinaceae Pinaceae Pinaceae Pinaceae Pinaceae Pinaceae Pittosporaceae Plantaginaceae Poaceae Poaceae Poaceae
Gomphrena Globosa Daucus Carota Nerium oleander Vinca minor Hedera helix Trachycarpus fortunei Cichorium intybus Senecio vulgaris Taraxacum officinale Mahonia aquifolium Pulmonaria officinalis Brassica oleracea Brassica napus Capsella bursa-pastoris Cardamine hirsuta Erophila verna Buxus sempervirens Cannabis sativa Lonicera xylosteum Viburnum lantana Viburnum tinus Cerastium glomeratum Chamaecyparis lawsoniana Calocedrus decurrens Albizia julibrissin Trifolium pratense Quercus robur Quercus rubra Quercus petraea Ginkgo biloba Rosmarinus officinalis Lamium purpureum Laurus nobilis Liriodendron tulipifera Magnolia grandiflora Ligustrum vulgare Olea europaea Oxalis incarnata Abies alba Cedrus atlantica Cedrus deodara Picea abies Pinus nigra Pinus sylvestris Pittosporum tobira Plantago major Chimonobambusa quadrangularis Bromus sterilis Poa annua
GenBank Accession no. Common name
rbcL
matK
Globe amaranth Carrot Oleander Lesser Periwinkle Common Ivy Windmill Palm Common Chicory Common Groundsel Dandelion Oregon Grapeholly Common Lungwort Wild Mustard Rapeseed Shepherd's-purse Hairy Bittercress Common Whitlow Grass Common Box Marjiuana Fly Honeysuckle Wayfaring Tree Laurustinus Sticky Chickweed Lawson Cypress Incense Cedar Silk Tree Red Clover English Oak Northern Red Oak Sessile Oak Common Ginkgo Rosemary Red Deadnettle Bay Laurel Tulip Tree Southern Magnolia Wild Privet Olive Pale Pink-Sorrel Silver Fir Atlas Cedar Deodar Cedar Norway Spruce Black Pine Norway Pine Japanese Cheesewood Common Plantain Bamboo Barren Brome Annual Blue Grass
HQ619725 HQ619726 HQ619727 HQ619728 HQ619729 HQ619730 HQ619731 HQ619732 HQ619733 HQ619734 HQ619735 HQ619736 HQ619737 HQ619738 HQ619739 HQ619740 HQ619741 HQ619742 HQ619743 HQ619744 HQ619745 HQ619747 HQ619746 HQ619748 HQ619749 HQ619750 HQ619751 HQ619752 HQ619753 HQ619754 HQ619755 HQ619756 HQ619757 HQ619758 HQ619759 HQ619760 HQ619761 HQ619762 HQ619763 HQ619764 HQ619765 HQ619766 HQ619767 HQ619768 HQ619769 HQ619770 HQ619771 HQ619772
HQ619789 HQ619790 HQ619791 HQ619792 HQ619793 HQ619794 HQ619795 HQ619796 HQ619797 HQ619798 HQ619799 HQ619800 HQ619801 HQ619802 HQ619803 HQ619804 HQ619805 HQ619806 HQ619807 HQ619808 HQ619809 HQ619810 HQ619811 HQ619812 HQ619813 HQ619814 HQ619815 HQ619816 HQ619817 HQ619818 HQ619819 HQ619820 HQ619821 HQ619822 HQ619823 HQ619824 HQ619825 HQ619826 HQ619827 HQ619828
Table S2 (continued) Family
Species Scientific name
Primulaceae Ranunculaceae Ranunculaceae Rosaceae Rosaceae Rosaceae Rosaceae Rubiaceae Salicaceae Scrophulariaceae Scrophulariaceae Scrophulariaceae Solanaceae Solanaceae Solanaceae Taxaceae
Primula vulgaris Helleborus viridis Ranunculus bulbosus Crataegus monogyna Fragaria vesca Prunus cerasifera Prunus laurocerasus Galium mollugo Populus nigra Veronica arvensis Veronica sublobata Veronica persica Nicotiana tabacum Solanum lycopersicum Solanum tuberosum Taxus baccata
GenBank Accession no. Common name
rbcL
matK
Wild Primrose Green Hellebore Common Buttercup Common Hawthorn Woodland Strawberry Cherry Plum Cherry Laurel White Bedstraw Black Poplar Corn Speedwell Ivy Speedwell Bird-eye Speedwell Tobacco Tomato Potato Common Yew
HQ619773 HQ619774 HQ619775 HQ619776 HQ619777 HQ619778 HQ619779 HQ619780 HQ619781 HQ619782 HQ619783 HQ619784 HQ619785 HQ619786 HQ619787 HQ619788
HQ619829 HQ619830 HQ619831 HQ619832 HQ619833 HQ619834 HQ619835 HQ619836 HQ619837 HQ619838 HQ619839 HQ619840 HQ619841 HQ619842
Additional Files Click here to download Additional Files: Tab. S3.doc
Table S3 List of plant species and corresponding GenBank accession numbers retrieved from the database for sequence diversity analysis at the genus level for rbcL gene. Overall, 28 genera (265 sequences) for rbcL were available from GenBank database for alignment and subsequent statistical computation. Family
Species
Asteraceae
Senecio polypodioides
Asteraceae Asteraceae Asteraceae Asteraceae Asteraceae
Senecio mikanioides Senecio medley-woodii Senecio scandens Senecio aquaticus Senecio deltoideus Brassica juncea Brassica rapa Viburnum sp. SH-2010 Viburnum acerifolium Viburnum opulus Viburnum lentago Viburnum cotinifolium Cerastium fontanum Cerastium capense Albizia lebbeck Albizia saman Trifolium repens Trifolium burchellianum Trifolium subterraneum Quercus virginiana Quercus macrocarpa Quercus cf. velutina Quercus alba Quercus frainetto Quercus pubescens Quercus crenata Quercus ithaburensis Quercus suber Quercus trojana Quercus cerris Quercus ilex Quercus coccifera Quercus nigra Quercus hemisphaerica Quercus gemelliflora Quercus palustris Quercus oidocarpa Quercus lyrata Quercus argentata Quercus mongolica Quercus hondae Quercus miyagii
Brassicaceae Brassicaceae Caprifoliaceae Caprifoliaceae Caprifoliaceae Caprifoliaceae Caprifoliaceae Caryophyllaceae Caryophyllaceae Fabaceae Fabaceae Fabaceae Fabaceae Fabaceae Fagaceae Fagaceae Fagaceae Fagaceae Fagaceae Fagaceae Fagaceae Fagaceae Fagaceae Fagaceae Fagaceae Fagaceae Fagaceae Fagaceae Fagaceae Fagaceae Fagaceae Fagaceae Fagaceae Fagaceae Fagaceae Fagaceae Fagaceae
Genbank Accession No. rbcL EU385017 L13933 GU817783 GQ436472 AY395561 GU817782 GQ436652 GQ184371 AB586172 L01959 EU677071 EU677069 GQ248707 FJ395574 AM234949 GU135158 Z70149 GQ436346 AM235018 EU849487 AF119175 EU676971 EU676969 EU676968 FN675742 FN675737 FN675732 FN675729 FN675728 FN675725 FN675724 FN675719 FN675715 EU002284 AF119176 AB125019 AB125023 AB125022 AB125021 AB125016 AB060584 AB060583 AB060582
Fagaceae Fagaceae Fagaceae Fagaceae Fagaceae Fagaceae Fagaceae Fagaceae Fagaceae Fagaceae Fagaceae Lamiaceae Lamiaceae Lamiaceae Lamiaceae Lamiaceae Magnoliaceae Magnoliaceae Magnoliaceae Magnoliaceae Magnoliaceae Magnoliaceae Magnoliaceae Magnoliaceae Oleaceae Oleaceae Oleaceae Oleaceae Oxalidaceae Oxalidaceae Oxalidaceae Pinaceae Pinaceae Pinaceae Pinaceae Pinaceae Pinaceae Pinaceae Pinaceae Pinaceae Pinaceae Pinaceae Pinaceae Pinaceae Pinaceae Pinaceae Pinaceae Pinaceae Pinaceae Pinaceae
Quercus aliena Quercus acuta Quercus dentata Quercus acutissima Quercus sessilifolia Quercus gilva Quercus variabilis Quercus phillyraeoides Quercus myrsinifolia Quercus glauca Quercus salicina Lamium album Lamium amplexicaule Lamium maculatum Lamium garganicum Lamium galeobdolon Magnolia tripetala Magnolia soulangeana Magnolia salicifolia Magnolia hypoleuca Magnolia kobus Magnolia virginiana Magnolia guatemalensis Magnolia macrophylla Ligustrum sp. SH-2010 Ligustrum lucidum Ligustrum sinense Ligustrum quihoui Oxalis dillenii Oxalis latifolia Oxalis corniculata Abies hidalgensis Abies lasiocarpa Abies bracteata Abies magnifica Abies numidica Abies pinsapo Abies nordmanniana Abies nebrodensis Abies procera Abies amabilis Abies concolor Abies grandis Abies fraseri Abies nephrolepis Abies koreana Abies sibirica Abies holophylla Abies fargesii Abies fabri
AB060581 AB060580 AB060579 AB060578 AB060577 AB060575 AB060574 AB060573 AB060572 AB060571 AB060570 FJ395588 AB266225 Z37402 Z37401 Z37400 AF206791 M58393 L12656 L12655 AY743438 GQ248639 GQ248638 X54345 AB586459 GU135151 GU135150 GQ436544 L01938 EU002282 AB233943 EU269028 AY664855 AF456380 EU331458 AB019827 AB029656 AB029654 AB029653 AB029651 AB029650 AB029648 AB029646 AB029644 AB029643 AB029642 AB029641 AB029640 AB029639 AB029638
Pinaceae Pinaceae Pinaceae Pinaceae Pinaceae Pinaceae Pinaceae Pinaceae Pinaceae Pinaceae Pinaceae Pinaceae Pinaceae Pinaceae Pinaceae Pinaceae Pinaceae Pinaceae Pinaceae Pinaceae Pinaceae Pinaceae Pinaceae Pinaceae Pinaceae Pinaceae Pinaceae Pinaceae Pinaceae Pinaceae Pinaceae Pinaceae Pinaceae Pinaceae Pinaceae Pinaceae Pinaceae Pinaceae Pinaceae Pinaceae Pinaceae Pinaceae Pinaceae Plantaginaceae Plantaginaceae Plantaginaceae Plantaginaceae Plantaginaceae Plantaginaceae Poaceae
Abies sachalinensis Abies mariesii Abies veitchii Picea mariana Picea crassifolia Picea glehnii Picea Koyamae Picea Meyeri Picea Likiangensis Picea Obovata Picea Omorika Picea Retroflexa Picea Rubens Picea Torano Picea koraiensis Picea jezoensis Picea asperata Picea wilsonii Picea spinulosa Picea schrenkiana Picea pungens Picea morrisonicola Picea farreri Picea brachytyla Picea sitchensis Picea martinezii Picea alcoquiana Picea chihuahuana Picea breweriana Picea orientalis Picea mexicana Pinus tabuliformis Pinus thunbergii Pinus densiflora Pinus kesiya Pinus yunnanensis Pinus hwangshanensis Pinus halepensis Pinus echinata Pinus praetermissa Pinus taeda Pinus leiophylla Pinus contorta Plantago lanceolata Plantago depressa Plantago asiatica Plantago rugelii Plantago ovata Plantago crassifolia Bromus hordeaceus
AB015651 AB015650 AB015649 EF440585 EF440576 EF440580 EF440583 EF440589 EF440590 EF440592 EF440593 EF440599 EF440600 EF440605 EF440582 EF440581 EF440572 EF440606 EF440604 EF440601 EF440597 EF440591 EF440578 EF440573 EF440602 EF440586 EF440571 EF440575 EF440574 EF440594 EF440588.1| AY555717 FJ899562 DQ353731 AY497253 AY555695 FJ906722 FN689375 AY947435 DQ353727 AF119177.1 AB063380 AY497230 L36454 GQ436318 GQ436317 EU676937 GQ248675 AM235049 AY395531
Poaceae Poaceae Poaceae Poaceae Poaceae Poaceae Poaceae Primulaceae Primulaceae Primulaceae Primulaceae Primulaceae Primulaceae Primulaceae Primulaceae Primulaceae Primulaceae Primulaceae Primulaceae Primulaceae Primulaceae Primulaceae Primulaceae Primulaceae Primulaceae Primulaceae Primulaceae Primulaceae Primulaceae Ranunculaceae Ranunculaceae Ranunculaceae Ranunculaceae Ranunculaceae Ranunculaceae Ranunculaceae Ranunculaceae Ranunculaceae Rosaceae Rosaceae Rosaceae Rosaceae Rosaceae Rosaceae Rosaceae Rosaceae Rosaceae Rosaceae Rosaceae Rubiaceae
Bromus arvensis Bromus arenarius Bromus interruptus Bromus commutatus Bromus erectus Poa compressa Poa trivialis Primula veitchiana Primula cortusoides Primula sikkimensis Primula gaubaeana Primula edelbergii Primula palinuri Primula miyabeana Primula hidakana Primula floribunda Primula cusickiana Primula dryadifolia Primula malacoides Primula alpicola Primula bulleyana Primula chungensis Primula veris Primula modesta Primula ioessa Primula capitata Primula muscarioides Primula verticillata Primula cuneifolia Helleborus orientalis Helleborus thibetanus Helleborus atrorubens Helleborus croaticus Ranunculus lyallii Ranunculus ficaria Ranunculus acris Ranunculus trichophyllus Ranunculus macranthus Crataegus pinnatifida Crataegus columbiana Prunus armeniaca Prunus sibirica Prunus tomentosa Prunus domestica Prunus persica Prunus davidiana Prunus mume Prunus pseudocerasus Prunus padus Galium aparine
AY836154 AY691632 GQ248558 AJ746287 AJ746286 EU676942 AJ746301 AF213802 AF213800 AF213799 AF213798 AF213797 AF213801 AF395003 AF394998 AF394996 AF394995 AF394994 AF394990 AF394987 AF394985 AF394984 AF394982 AF394978 AF394972 AF394971 AF394970 AF394968 AF394962 EU053915 AY954485 GQ248616 GQ248617 EU053921 EU053919 AY395557 L08766 DQ069502 GU363811 U06799 AF411489 GQ436604 AF411495 AF227901 GQ436598 GQ436591 AF411491 GQ436608 GU363800 X81091
Rubiaceae Rubiaceae Rubiaceae Rubiaceae Rubiaceae Rubiaceae Rubiaceae Salicaceae Salicaceae Salicaceae Salicaceae Salicaceae Salicaceae Salicaceae Salicaceae Salicaceae Salicaceae Salicaceae Scrophulariaceae Scrophulariaceae Scrophulariaceae Scrophulariaceae Scrophulariaceae Scrophulariaceae Scrophulariaceae Scrophulariaceae Scrophulariaceae Scrophulariaceae Scrophulariaceae Scrophulariaceae Scrophulariaceae Scrophulariaceae Scrophulariaceae Scrophulariaceae Scrophulariaceae Solanaceae Solanaceae Solanaceae Solanaceae Solanaceae Solanaceae Solanaceae Solanaceae Solanaceae Solanaceae Solanaceae Solanaceae Solanaceae Solanaceae Solanaceae
Galium parisiense Galium corsicum Galium album Galium scabrum Galium palustre Galium lucidum Galium elongatum Populus tremuloides Populus deltoides Populus cathayana Populus alba Populus grandidentata Populus balsamifera Populus tremula Populus tomentosa Populus szechuanica Populus maximowiczii Populus wilsonii Veronica salicifolia Veronica arguta Veronica officinalis Veronica vandewateri Veronica anagallis-aquatica Veronica melanocaulon Veronica salicornioides Veronica odora Veronica macrantha Veronica formosa Veronica cupressoides Veronica benthamii Veronica elliptica Veronica nivea Veronica raoulii Veronica quadrifaria Veronica densifolia Nicotiana petunioides Nicotiana noctiflora Nicotiana sylvestris Nicotiana debneyi Nicotiana tomentosiformis Solanum nigrum Solanum laciniatum Solanum lepidotum Solanum torvum Solanum tampicense Solanum viarum Solanum jamaicense Solanum diphyllum Solanum dulcamara Solanum panduriforme
X81102 X81096 X81090 X81105 X81101 X81100 X81098 AF206812 AF133677 FJ788565 FN689368 EU676961 EU676955 GQ248681 AF527489 AJ418837 AJ418836 AJ418830 AF307921 AY034025 AY034024 AY034023 AY034021 AY034020 AY034019 AY034017 AY034016 AY034015 AY034014 AY034013 AY034011 AY034010 AY034009 AY034008 AY034007 GQ248656 GQ248655 AB237912 D70815 NC_007602 GQ436617 GQ436613 GQ981879 GU135251 GU135238 GU135237 GU135229 GU135208 EU677012 EU213515
Taxaceae Taxaceae Taxaceae Taxaceae Taxaceae
Taxus wallichiana Taxus fuana Taxus canadensis Taxus cuspidata Taxus brevifolia
GQ436390 GQ436389 GQ436388 GQ436387 AF249666
Additional Files Click here to download Additional Files: Tab. S4.doc
Table S4 List of plant species and corresponding GenBank accession numbers retrieved from the database for sequence diversity analysis at the genus level for matK gene. Overall, 21 genera (276 sequences) for matK were available from GenBank database for alignment and subsequent statistical computation. Family
Species
Amaranthaceae
Gomphrena ferruginea Gomphrena fuscipellita
Amaranthaceae Amaranthaceae Amaranthaceae Amaranthaceae Brassicaceae Brassicaceae Brassicaceae Brassicaceae Brassicaceae Brassicaceae Brassicaceae Brassicaceae Brassicaceae Brassicaceae Brassicaceae Brassicaceae Brassicaceae Brassicaceae Brassicaceae Caprifoliaceae Caprifoliaceae Caprifoliaceae Caprifoliaceae Fabaceae Fabaceae Fabaceae Fabaceae Fabaceae Fabaceae Fabaceae Fabaceae Fabaceae Fabaceae Fabaceae Fabaceae Fabaceae Fabaceae Fabaceae Fabaceae Fabaceae Fabaceae Fabaceae Fabaceae
Gomphrena pulchella Gomphrena mandonii Gomphrena haageana Brassica insularis Brassica rapa Brassica incana Brassica montana Brassica hilarionis Brassica cretica Brassica villosa Brassica rupestris Brassica macrocarpa Brassica barrelieri Brassica carinata Brassica nigra Cardamine rivularis Cardamine penzesii Cardamine amara Lonicera maackii Lonicera japonica Lonicera nervosa Lonicera orientalis Albizia lebbeck Albizia harveyi Albizia bermudiana Albizia versicolor Albizia sinaloensis Albizia kalkora Albizia plurijuga Albizia myriophylla Trifolium wormskioldii Trifolium willdenovii Trifolium thalii Trifolium subterraneum Trifolium striatum Trifolium spumosum Trifolium semipilosum Trifolium repens Trifolium patulum Trifolium nanum Trifolium microcephalum Trifolium lupinaster
Genbank Accession No. matK AM887524 AM887525 AY514802 AY514801 AY514800 AY541614 AB354276 AY541613 AY541617 AY541612 AY541611 AY541622 AY541620 AY541615 AB354270 AB354275 AB354272 AF144365 AF144364 AF144337 GU168651 GQ997392 AF446903 AJ430196 EU812047 EU812003 EU812001 AF274210 AF274121 AF523083 AF523080 AB504374 AF522138 AF522137 AF522136 AF522135 AF522134 AF522133 AF522132 AF522131 AF522130 AF522129 AF522128 AF522127
Fabaceae Fabaceae Fabaceae Fabaceae Fabaceae Fabaceae Fabaceae Fabaceae Fabaceae Fabaceae Fabaceae Fagaceae Fagaceae Fagaceae Fagaceae Fagaceae Fagaceae Fagaceae Fagaceae Fagaceae Fagaceae Fagaceae Fagaceae Fagaceae Fagaceae Fagaceae Fagaceae Fagaceae Fagaceae Fagaceae Fagaceae Fagaceae Fagaceae Fagaceae Fagaceae Fagaceae Lamiaceae Lamiaceae Magnoliaceae Magnoliaceae Magnoliaceae Magnoliaceae Magnoliaceae Magnoliaceae Magnoliaceae Magnoliaceae Magnoliaceae Magnoliaceae Magnoliaceae Magnoliaceae Magnoliaceae
Trifolium incarnatum Trifolium hybridum Trifolium hirtum Trifolium gracilentum Trifolium fragiferum Trifolium cheranganiense Trifolium caucasicum Trifolium burchellianum Trifolium resupinatum Trifolium albopurpureum Trifolium beckwithii Quercus tomentella Quercus suber Quercus myrsinifolia Quercus nigra Quercus mongolica Quercus gemelliflora Quercus hondae Quercus palustris Quercus oidocarpa Quercus lyrata Quercus ilex Quercus coccifera Quercus cerris Quercus argentata Quercus miyagii Quercus aliena Quercus acuta Quercus dentata Quercus acutissima Quercus sessilifolia Quercus gilva Quercus variabilis Quercus phillyraeoides Quercus glauca Quercus salicina Lamium maculatum Lamium album Magnolia dealbata Magnolia dodecapetala Magnolia mexicana Magnolia splendens Magnolia wilsonii Magnolia officinalis Magnolia gigantifolia Magnolia pterocarpa Magnolia liliifera Magnolia henryi Magnolia panamensis Magnolia sinica Magnolia pacifica
AF522126 AF522125 AF522124 AF522123 AF522122 AF522120 AF522119 AF522118 AF522117 AF522116 AY386946 FJ185058 FJ185049 FJ185048 EU002188 AB107616 AB125036 AB060074 AB125040 AB125039 AB125038 AB125037 AB125035 AB125034 AB125033 AB060077 AB060073 AB060071 AB060070 AB060069 AB060068 AB060066 AB060065 AB060064 AB060062 AB060061 AF531780 AJ429332 AY009008 AY009005 AY009004 AY009003 AY009002 AY009001 AY009000 AY008999 AY008998 AY008997 AY008996 AY008990 AB055521
Magnoliaceae Magnoliaceae Magnoliaceae Magnoliaceae Magnoliaceae Magnoliaceae Oxalidaceae Oxalidaceae Oxalidaceae Oxalidaceae Oxalidaceae Oxalidaceae Oxalidaceae Oxalidaceae Oxalidaceae Oxalidaceae Oxalidaceae Oxalidaceae Oxalidaceae Pinaceae Pinaceae Pinaceae Pinaceae Plantaginaceae Plantaginaceae Plantaginaceae Poaceae Poaceae Poaceae Poaceae Poaceae Poaceae Poaceae Poaceae Poaceae Poaceae Poaceae Primulaceae Primulaceae Primulaceae Primulaceae Primulaceae Primulaceae Primulaceae Primulaceae Primulaceae Primulaceae Primulaceae Primulaceae Primulaceae Primulaceae
Magnolia yoroconte Magnolia portoricensis Magnolia sieboldii Magnolia carsonii Magnolia caricifragrans Magnolia minor Oxalis eckloniana Oxalis tomentosa Oxalis bifida Oxalis capillacea Oxalis polyphylla Oxalis tenella Oxalis flava Oxalis melanosticta Oxalis caprina Oxalis dentata Oxalis purpurascens Oxalis corniculata Oxalis hedysaroides Abies firma Abies holophylla Abies bracteata Abies hidalgensis Plantago rugelii Plantago media Plantago argentea Bromus suksdorfii Bromus inermis Bromus secalinus Bromus erectus Poa billardierei Poa andina Poa alpina Poa compressa Poa pratensis Poa violacea Poa bulbosa Primula veris Primula edelbergii Primula borealis Primula nutans Primula eximia Primula faberi Primula amethystina Primula dryadifolia Primula forbesii Primula capillaris Primula cusickiana Primula angustifolia Primula rusbyi Primula parryi
AB055522 AB055523 AB055526 AB055529 AB055533 AB055535 EU437359 EU437358 EU437357 EU437356 EU437355 EU437354 EU437348 EU437346 EU437342 EU437341 EU437340 EU437337 FM179935
AF143436 AF143441 AF456365 EU269026 DQ317070 AY667474 AJ429344 DQ786894 AF164398 AM23457 AM234570 DQ786935 DQ786934 DQ786933 EU749333 AF164402 AM234605 AM234594 AY647530 AY647528 AY647527 AY647526 AY647525 AY647524 AY647523 AY647521 AY647520 AY647519 AY647518 AY647514 AY647513 AY647512
Primulaceae Primulaceae Primulaceae Primulaceae Primulaceae Primulaceae Primulaceae Primulaceae Primulaceae Primulaceae Primulaceae Primulaceae Primulaceae Primulaceae Primulaceae Primulaceae Primulaceae Primulaceae Primulaceae Primulaceae Primulaceae Primulaceae Primulaceae Primulaceae Primulaceae Primulaceae Primulaceae Primulaceae Primulaceae Primulaceae Primulaceae Primulaceae Primulaceae Primulaceae Primulaceae Primulaceae Primulaceae Primulaceae Primulaceae Primulaceae Primulaceae Primulaceae Primulaceae Primulaceae Primulaceae Primulaceae Primulaceae Primulaceae Primulaceae Primulaceae Primulaceae
Primula suffrutescens Primula nipponica Primula cuneifolia Primula integrifolia Primula hirsuta Primula deorum Primula glutinosa Primula minima Primula marginata Primula clusiana Primula palinuri Primula septemloba Primula aromatica Primula blattariformis Primula partschiana Primula pycnoloba Primula malvacea Primula saturata Primula wangii Primula barbicalyx Primula calyptrata Primula chapaensis Primula rugosa Primula amethystina Primula sikkimensis Primula capitata Primula caveana Primula smithiana Primula geraniifolia Primula obconica Primula sinolisteri Primula sinomollis Primula helodoxa Primula malacoides Primula celsiiformis Primula blinii Primula polyneura Primula deflexa Primula bellidifolia Primula boreiocalliantha Primula poissonii Primula calliantha Primula serratifolia Primula efarinosa Primula watsonii Primula moupinensis Primula secundiflora Primula interjacens Primula latisecta Primula celsiiformis Primula alpicola
AY647510 AY647508 AY647506 AY647501 AY647499 AY647498 AY647496 AY647494 AY647492 AY647491 AY647489 FJ828656 FJ828655 FJ828654 FJ828653 FJ828652 FJ828651 FJ828650 FJ828649 FJ828647 FJ828646 FJ828645 FJ828644 FJ828643 FJ828642 FJ828641 FJ828640 FJ828639 FJ828638 FJ828636 FJ828635 FJ828634 FJ828633 FJ828631 FJ828629 FJ828628 FJ828627 FJ828626 FJ828621 FJ828620 FJ828619 FJ828618 FJ828617 FJ828616 FJ828615 FJ828614 FJ828613 FJ828610 FJ828608 FJ828607 FJ828606
Primulaceae Primulaceae Primulaceae Primulaceae Primulaceae Primulaceae Primulaceae Primulaceae Primulaceae Primulaceae Primulaceae Ranunculaceae Ranunculaceae Ranunculaceae Ranunculaceae Ranunculaceae Ranunculaceae Ranunculaceae Ranunculaceae Ranunculaceae Ranunculaceae Ranunculaceae Ranunculaceae Ranunculaceae Ranunculaceae Ranunculaceae Ranunculaceae Ranunculaceae Rosaceae Rosaceae Rosaceae Rosaceae Rosaceae Rosaceae Rosaceae Solanaceae Solanaceae Solanaceae Solanaceae Solanaceae Solanaceae Solanaceae Solanaceae Solanaceae Solanaceae Solanaceae Solanaceae Solanaceae Solanaceae Solanaceae Solanaceae
Primula ovalifolia Primula sertulum Primula pinnatifida Primula yunnanensis Primula chionantha Primula bella Primula rupestris Primula cicutariifolia Primula algida Primula partschiana Primula caldaria Helleborus orientalis Helleborus multifidus Helleborus thibetanus Ranunculus sardous Ranunculus polyanthemoides Ranunculus brutius Ranunculus submarginatus Ranunculus pensylvanicus Ranunculus weyleri Ranunculus polyanthemos Ranunculus fascicularis Ranunculus macounii Ranunculus repens Ranunculus septentrionalis Ranunculus multifidus Ranunculus muricatus Ranunculus peduncularis Prunus lusitanica Prunus cerasus Prunus domestica Prunus avium Prunus virginiana Prunus persica Prunus dulcis Nicotiana goodspeedii Nicotiana x sanderae Nicotiana attenuata Nicotiana alata Nicotiana langsdorfii Nicotiana bonariensis Nicotiana occidentalis Nicotiana simulans Nicotiana umbratica Nicotiana benthamiana Nicotiana exigua Nicotiana nesophila Nicotiana plumbaginifolia Nicotiana longiflora Nicotiana forgetiana Nicotiana megalosiphon
FJ828605 FJ828604 FJ828603 FJ828602 FJ828601 FJ828600 FJ828599 FJ828598 FJ828595 FJ828593 FJ828592 AY515247 AY515246 FJ626500 AY954186 FM242801 FM242795 FM242777 AY954190 AY954189 AY954185 FM242786 FM242764 AY954182 FM242768 EU288384 AY954191 AY954180 FJ899120 FJ899111 FJ899110 FJ899109 AF288118 AF288117 AF288115 AJ585890 AJ585841 AB040009 AB040000 AB039999 AB039986 AJ585889 AB040020 AB040015 AB040014 AJ585856 AJ585854 AB040003 AB040002 AB040001 AJ585855
Solanaceae Solanaceae Solanaceae Solanaceae Solanaceae Solanaceae Solanaceae Solanaceae Solanaceae Solanaceae Solanaceae Solanaceae Solanaceae Solanaceae Solanaceae Solanaceae Solanaceae Solanaceae Solanaceae Solanaceae Solanaceae Taxaceae Taxaceae Taxaceae Taxaceae Taxaceae Taxaceae Taxaceae Taxaceae
Nicotiana amplexicaulis Nicotiana velutina Solanum elaeagnifolium Solanum cinereum Solanum linnaeanum Solanum aculeastrum Solanum stupefactum Solanum hoplopetalum Solanum asymmetriphyllum Solanum sejunctum Solanum heteropodium Solanum oedipus Solanum melanospermum Solanum clarkiae Solanum diversiflorum Solanum chippendalei Solanum leopoldense Solanum petraeum Solanum carduiforme Solanum dioicum Solanum tudununggae Taxus brevifolia Taxus wallichiana Taxus canadensis Taxus fuana Taxus floridana Taxus globosa Taxus sumatrana Taxus mairei
AB040019 AJ585887 EU983576 EU983575 EU983574 EU983573 EU983572 EU983571 EU983570 EU983568 EU983567 EU983566 EU983565 EU983564 EU983563 EU983562 EU983560 EU983559 EU983558 EU983554 EU983552 EU078561 EF660663 EF660661 EF660660 EF660652 EF660647 EF660646 AB024001
Additional Files Click here to download Additional Files: Tab. S5.doc
Table S5 Size distribution of PCR products and number of successfully sequenced individuals in different families Family
All samples Amaranthaceae Apiaceae Apocynaceae Araliaceae Arecaceae Asteraceae Berberidaceae Boraginaceae Brassicaceae Buxaceae Cannabaceae Caprifoliaceae Caryophyllaceae*** Cupressaceae*** Fabaceae Fagaceae Ginkgoaceae Lamiaceae Lauraceae Magnoliaceae Oleaceae Oxalidaceae Pinaceae Pittosporaceae Plantaginaceae Poaceae
Length (bp)
Nb successfully sequenced individuals
rbcL
matK
rbcL
matK
553-554 553 553 553 553 553 553 553 553 553 553 553 553 553 553 553 553 553 553 553 553 553 553 553-554 553 553 553
825-898 831 834 831-840 828 837 843 840 837 822 837 840 837 − − 837 837 888* 843 837 837 837 837 831 828 825 837
64 1 1 2 1 1 3 1 1 5 1 1 2 1 2 2 3 1 2 1 2 2 1 6 1 1 3
54 1 1 2 1 1 3 1 1 5 1 1 3 0 0 2 3 1 1 1 2 2 1 1 1 1 3
matK primer pair used°
matK_a, matk_b, matK_c matK_a matK_a matK_a matK_a matK_a matK_a matK_a matK_a matK_a matK_a matK_a matK_a matK_a, matk_b matK_a, matk_b, matK_c matK_a matK_a matK_c matK_a, matk_b matK_a matK_a matK_a matK_a matK_a, matk_b, matK_c matK_a matK_a matK_a
Taxon composition
34 families,55 genera, 65 species 1 genera, 1 species 1 genera, 1 species 2 genera, 2 species 1 genera, 1 species 1 genera, 1 species 3 genera, 3 species 1 genera, 1 species 1 genera, 1 species 4 genera, 5 species 1 genera, 1 species 1 genera, 1 species 2 genera, 3 species 1 genera, 1 species 2 genera, 2 species 2 genera, 2 species 1 genera, 3 species 1 genera, 1 species 2 genera, 2 species 1 genera, 1 species 2 genera, 2 species 2 genera, 2 species 1 genera, 1 species 4 genera, 6 species 1 genera, 1 species 1 genera, 1 species 3 genera, 3 species
Family
Primulaceae Ranunculaceae Rosaceae Rubiaceae Salicaceae*** Scrophulariaceae Solanaceae
Length (bp)
Nb successfully sequenced individuals
rbcL
matK
rbcL
matK
553 553 553-554 553 553 553 553 553
892** 840,895** 825-843 895** − 843,898** 837 834
1 2 4 1 1 3 3 1
1 2 4 1 0 2 3 1
Taxaceae * amplicon size with matK_c primers ** amplicon size with matK_b primers
*** Nucleotide sequence for matK not determined (see text) ° Primer name as mentioned in TableS1
matK primer pair used°
Taxon composition
matK_a, matk_b matK_a, matk_b matK_a matK_a, matk_b matK_a, matk_b matK_a, matk_b matK_a matK_a
1 genera, 1 species 2 genera, 2 species 3 genera, 4 species 1 genera, 1 species 1 genera, 1 species 1 genera, 3 species 2 genera, 3 species 1 genera, 1 species
Additional Files Click here to download Additional Files: Tab. S6.doc
Table S6 Results of the statistical analysis for the three molecular diversity indices calculated at family level rbcL Family (number of species)
Np/Na
Mean number of pairwise differences
matK Nucleotide diversity (average over loci)
12.190 +/- 8.966 Apocynaceae ( 2 spp.) 12 /553 (2.2%) 12.210 +/- 7.647 18/553 (3.2%) Asteraceae (3 spp.) 12.400 +/- 6.767 25/553 (4.5%) Brassicaceae (5 spp.) 2.000 +/- 1.732 2/553 (0.4%) Caprifoliaceae (3 spp.)c 6.000 +/- 4.582 6/553 (1.1%) Cupressaceae (2 spp.)b 43.000 +/- 30.757 43/553 (7.8%) Fabaceae (2 spp.) 0.667 +/- 0.667 1/553 (0.2%) Fagaceae (3 spp.) b 18.000 +/- 13.077 18/553 (3.2%) Lamiaceae (2 spp.) 17.000 +/- 12.369 17/553 (3.1%) Magnoliaceae (2 spp.) 1.000 +/- 1.000 Oleaceae (2 spp.) 1/553 (0.2%) b 24.933 +/- 12.812 62/554 (11.2%) Pinaceae (6 spp.) 28.333 +/- 17.287 42/553 (7.6%) Poaceae (3 spp.) 30.000 +/- 21.564 30/553 (5.4%) Ranunculaceae (2 spp.) 17.000 +/- 9.641 32/554 (5.8%) Rosaceae (4 spp) 14.000 +/- 8.718 21/553 (3.8%) Scrophulariaceae (3 spp.)d 6.667 +/- 4.328 10/553 (1.8%) Solanaceae (3 spp.) a Np= number of polymorphic sites; N= total number of sites compared b Molecular diversity indices for matK not calculated c Stastical values for the marker rbcL included only two of the three species sampled d Stastical values for the marker matK included only two of the three species sampled
Np/Na
Mean number of pairwise differences
Nucleotide diversity (average over loci)
0.022 +/- 0.223 0.022 +/- 0.017 0.022 +/- 0.014 0.003 +/- 0.004 0.011 +/- 0.012 0.078 +/- 0.079 0.001 +/- 0.001 0.032 +/- 0.033 0.031 +/- 0.032
58/840 (6.9%) 40/843 (4.7%) 93/822 (11.3%) 65/837 (7.8%) 109/837 (13%) 5/837 (0.6%) 17/837 (2%)
51.024 +/- 36.432 27.312 +/- 16.677 43.900 +/- 23.089 43.333 +/- 26.253 109.000 +/- 77.427 3.333 +/- 2.323 17.000 +/- 12.369
0.060 +/- 0.061 0.032 +/- 0.025 0.053 +/- 0.032 0.052 +/- 0.039 0.130 +/- 0.131 0.004 +/- 0.003 0.020 +/- 0.021
0.002 +/- 0.003 0.044 +/- 0.026 0.051 +/- 0.039 0.054 +/- 0.055 0.031 +/- 0.021 0.025 +/- 0.020 0.012 +/- 0.010
12/837 (1.4%) 79/837 (9.4%) 98/811 (12.1%) 136/843 (16%) 65/814 (8%) 19/837 (2.3%)
12.000 +/- 8.832 55.000 +/- 33.225 98.000 +/- 69.649 73.167 +/- 40.343 65.000 +/- 46.314 12.667 +/- 7.920
0.014 +/- 0.015 0.066 +/- 0.049 0.121 +/- 0.121 0.086 +/- 0.057 0.080 +/- 0.080 0.015 +/- 0.012
1
2
Additional Files Click here to download Additional Files: Tab. S7.doc
Table S7 Results of the statistical analysis for the three molecular diversity indices calculated between congeneric species rbcL Np/Na
Mean number of pairwise differences
Nucleotide diversity (average over loci)
Senecio (7 spp.)
17/553 (3.1%)
6.952 +/- 3.722
0.012 +/- 0.008
Brassica (4 spp.)
1/553 (0.2%)
0.500 +/- 0.519
0.001 +/- 0.001
Viburnum (7 spp.)
7/553 (1.3%)
2.381 +/- 1.468
0.004 +/- 0.003
Cerastium (3 spp.)
6/553 (1.1%)
4.000 +/- 2.725
0.007 +/- 0.006
Albizia (3 spp.)
7/553 (1.3%)
4.667 +/- 3.127
0.008 +/- 0.007
Trifolium (4 spp.)
17/553 (3.1%)
10.000 +/- 5.811
0.018 +/- 0.012
Quercus (37 spp.)
7/553 (1.3%)
1.252 +/- 0.809
0.002 +/- 0.002
Lamium (6 spp.)
17/553 (3.1%)
7.133 +/- 3.901
0.014 +/- 0.008
Magnolia (9 spp.)
2/553 (0.4%)
0.722 +/- 0.592
0.001 +/ -0.001
Ligustrum (5 spp.)
4/553 (0.7%)
1.600 +/- 1.128
0.003 +/- 0.002
Oxalis (4 spp.)
25/554 (4.5%)
15.833 +/- 9.003
0.028 +/- 0.019
Abies (23 spp.)
3/553 (0.5%)
0.917 +/- 0.658
0.002 +/- 0.001
Picea (29 spp.)
4/553 (0.7%)
1.258 +/- 0.828
0.002 +/- 0.002
Pinus (23 spp.)
7/553 (1.3%)
1.939 +/- 1.144
0.003 +/- 0.002
Plantago (7 spp.)
27/553 (4.9%)
10.571 +/- 5.492
0.019 +/- 0.011
Bromus (7 spp.)
5/553 (0.9%)
1.905 +/- 1.228
0.003 +/- 0.002
Poa (3 spp.)
6/553 (1.1%)
4.000 +/- 2.725
0.007 +/- 0.006
75/553 (13.6%)
15.925 +/- 7.377
0.029 +/- 0.019
Genus (number of spp.)
Primula (23 spp.)
a
matK
Helleborus (5 spp.)
5/553 (0.9%)
2.000 +/- 1.343
0.004 +/- 0.003
Ranunculus (6 spp.)
30/553 (5.4%)
12.667 +/- 6.674
0.023 +/- 0.014
Crataegus (3 spp.)
1/554 (0.2%)
0.667 +/- 0.667
0.001 +/- 0.001
Prunus (11 spp.)
11/553 (2.0%)
3.127 +/- 1.754
0.006 +/- 0.003
Galium (9 spp.)
20/553 (3.6%)
7.111 +/- 3.685
0.013 +/- 0.007
Populus (12 spp.)
26/553 (4.7%)
6.848 +/- 3.469
0.012 +/- 0.007
Veronica (20 spp.)
46/553 (8.3%)
7.158 +/- 3.503
0.013 +/- 0.007
Nicotiana (6 spp.)
3/553 (0.5%)
1.000 +/- 0.774
0.002 +/- 0.001
Solanum (12 spp.)
23/553 (4.1%)
5.470 +/- 2.831
0.010 +/- 0.006
Taxus (6 spp.)
5/553 (0.9%)
1.867 +/- 1.235
0.003 +/- 0.002
Np/Na
Mean number of pairwise differences
Nucleotide diversity (average over loci)
Gomphrena (6 spp.)
56/831 (6.7%)
21.600 +/- 11.144
0.026 +/- 0.015
Brassica (13 spp.) Cardamine (4 spp.) Lonicera (5 spp.) Albizia (9 spp.) Trifolium (24 spp.) Quercus (28 spp.) Lamium (3 spp.) Magnolia (20 spp.) Oxalis (14 spp.) Abies (5 spp.) Plantago (4 spp.) Bromus (5 spp.) Poa (8 spp.) Primula (74 spp.) Helleborus (4 spp.) Ranunculus (15 spp.) Prunus (9 spp.) Nicotiana (21 spp.) Solanum (21 spp.) Taxus (9 spp.)
43/822 (5.2%) 22/822 (2.7%) 24/839 (2.9%) 74/867 (8.5%) 90/837 (10.8%) 43/855 (5%) 28/843 (3.3%) 32/837 (3.8%) 144/837 (17.2%) 8/831 (1%) 38/825 (4.6%) 14/837 (1.7%) 43/837 (5.1%) 320/902 (35.5%) 16/896 (1.8%) 19/840 (2.3%) 245/879 (27.8%) 12/837 (1.4%) 60/839 (7.2%) 26/834 (3.1%)
10.769 +/- 5.244 11.167 +/- 6.449 10.000 +/- 5.521 19.167 +/- 9.388 16.619 +/- 7.668 7.058 +/- 3.416 18.667 +/- 11.508 7.347 +/- 3.588 29.813 +/- 13.876 4.400 +/- 2.608 19.333 +/- 10.917 6.600 +/- 3.755 15.714 +/- 7.863 44.904 +/- 19.684 8.500 +/- 4.989 4.352 +/- 2.279 75.417+/- 35.957 2.257 +/- 1.292 8.576 +/- 4.129 6.500 +/- 3.395
0.013 +/- 0.007 0.014 +/- 0.009 0.012 +/- 0.008 0.022 +/- 0.012 0.019 +/- 0.010 0.008 +/- 0.004 0.022 +/- 0.017 0.009 +/- 0.005 0.036 +/- 0.019 0.005 +/- 0.004 0.023 +/- 0.016 0.008 +/- 0.005 0.019 +/- 0.011 0.050 +/- 0.024 0.009 +/- 0.007 0.005 +/- 0.003 0.086 +/- 0.046 0.003 +/- 0.002 0.010 +/- 0.005 0.008 +/- 0.005
Genus (number of species)
Np= number of polymorphic sites; N= total number of sites compared
1
Additional Files Click here to download Additional Files: Tab. S8.doc
Table S8. BLAST search results of rbcL and matK for the plant species for which corresponding sequences are published in GenBank Investigated species
Best similar sp. of rbcL
Coverage (%)
Similarity (%)
Daucus carota
Daucus carota
100%
100%
1
Daucus carota
100%
100%
1
Nerium oleander
Nerium oleander
100%
100%
1
Nerium oleander
100%
100%
1
Vinca minor
Vinca minor
100%
100%
3
Vinca minor
100%
100%
3
Hedera helix
Hedera helix
100%
100%
18
Hedera helix
100%
100%
15
Trachycarpus fortunei
Trachycarpus fortunei Chamaerops humilis
100%
100%
1
Trachycarpus fortunei
100%
100%
4
Cichorium intybus
Cichorium intybus
100%
100%
1
Cichorium intybus
97%
100%
1
100%
100%
100%
100%
10
Taraxacum platypecidium
100%
99%
100%
100%
100%
100%
7
Brassica oleracea
100%
100%
15
100%
100%
7
Brassica napus
100%
100%
15
Taraxacum officinale Brassica oleracea
Taraxacum officinale Taraxacum platypecidium Brassica oleracea Brassica napus
Coverage of the exact sp. (%)
100%
Similarity with exact sp. (%)
N° of spp. per genus in GenBank
100%
Best similar sp. of matK
Coverage (%)
Similarity (%)
Coverage of the exact sp. (%)
96%
Similarity with exact sp. (%)
99%
N° of spp. per genus in GenBank
12
Brassica napus
Brassica spp.(3)
100%
100%
Capsella bursa-pastoris
Capsella bursa-pastoris
100%
100%
3
Capsella bursa-pastoris
100%
100%
3
Albizia julibrissin
Albizia julibrissin
100%
99%
18
Albizia julibrissin
100%
100%
18
Buxus sempervirens
Buxus microphylla Buxus sempervirens
100%
100%
100%
100%
4
Buxus sempervirens
100%
100%
7
Viburnum tinus
Viburnum opulus
100%
99%
87%
100%
113
Viburnum rhytidophyllum
100%
99%
88%
100%
113
Cerastium glomeratum
Cerastium glomeratum
100%
99%
11
−
−
−
−
−
12
Calocedrus decurrens
Calocedrus decurrens
100%
100%
4
−
−
−
−
−
4
Quercus robur
Quercus spp. (4)
100%
100%
100%
100%
59
Quercus spp. (8)
100%
100%
100%
100%
84
Quercus rubra
Quercus spp. (10)
100%
100%
100%
100%
59
Quercus spp. (2)
100%
100%
100%
100%
84
Quercus petraea
Quercus spp. (4)
100%
100%
100%
100%
59
Quercus spp. (3)
100%
100%
100%
100%
84
Ginkgo biloba
Ginkgo biloba
100%
100%
1
Ginkgo biloba
100%
100%
Rosmarinus officinalis
Rosmarinus officinalis Salvia spp.(12)
100%
99%
1
−
−
−
−
−
1
Lamium purpureum
Lamium purpureum
100%
100%
100%
99%
100%
99%
14
Laurus nobilis
Laurus nobilis Persea americana
99%
100%
100%
100%
100%
100%
2
Liriodendron tulipifera
Liriodendron tulipifera
100%
100%
Magnolia grandiflora
Magnolia spp. (3)
100%
100%
100%
Chamaecyparis lawsoniana
Chamaecyparis obtusa
100%
99%
97%
100%
99%
10 99%
100%
2
Lamium maculatum Lamium purpureum Laurus nobilis Laurus azorica
1
2
Liriodendron tulipifera
100%
99%
100%
96
Magnolia spp. (4)
100%
100%
100%
100%
112
100%
6
−
−
−
−
−
9
1
2
Table S8 (continued) Investigated species
Best similar sp. of rbcL
Coverage (%)
Similarity (%)
Trifolium pratense
Coverage of the exact species (%)
Trifolium pratense
100%
100%
Olea europaea
Olea europaea
100%
100%
Abies alba
Abies spp. (9)
100%
100%
Picea abies
Picea spp. (12)
100%
100%
Pinus nigra
Pinus spp. (10)
100%
100%
100%
Pinus sylvestris
Pinus spp. (10)
99%
100%
99%
Crataegus monogyna
Crataegus monogyna
100%
Fragaria vesca
Fragaria vesca
Prunus cerasifera
100%
Similarity with exact species (%)
N° of species per genus in GenBank
100%
Best similar sp. of matK
Coverage (%)
Similarity (%)
Coverage of the exact species (%)
Similarity with exact species (%)
N° of species per genus in GenBank
30
Trifolium pratense
100%
99%
42
1
Olea europaea
100%
100%
17
49 37
−
−
−
−
−
37
100%
102
−
−
−
−
−
112
100%
102
−
−
−
−
−
112
100%
11
Crataegus monogyna
100%
100%
9
100%
100%
23
Fragaria vesca
100%
100%
18
Prunus spp. (3)
100%
100%
132
Prunus spinosa
99%
99%
Prunus laurocerasus
Prunus laurocerasus
100%
100%
132
Prunus laurocerasus
100%
100%
Nicotiana tabacum
Nicotiana spp. (6)
100%
100%
17
Nicotiana spp. (3)
100%
100%
Solanum lycopersicum
Solanum lycopersicum
100%
100%
77
Solanum lycopersicum
100%
99%
107
Solanum tuberosum
Solanum tuberosum
100%
100%
77
Solanum tuberosum
100%
100%
107
Taxus baccata
Taxus spp. (3)
100%
100%
100%
100%
13
Taxus baccata
100%
100%
13
Ligustrum vulgare
Ligustrum spp. (7) Olea europea
100%
100%
100%
100%
19
Ligustrum obtusifolium
100%
99%
97%
99%
19
Galium mollugo
Galium mollugo
100%
100%
27
Galium verum
96%
99%
93%
99%
12
Populus nigra
Populus spp. (7)
100%
100%
100%
100%
15
−
−
−
−
−
11
100%
99%
100%
99%
9
Pittosporum undulatum
100%
99%
91%
99%
6
100%
100%
100%
100%
21
Plantago rugelii
100%
99%
96%
100%
14
100%
100%
100%
100%
30
Bromus secalinus
100%
99%
96%
100%
19
100%
100%
16
Poa annua
100%
100%
Pittosporum tobira Plantago major Bromus sterilis Poa annua
Pittosporum tobira Pittosporum pentadrum Plantago major Plantago depressa Bromus sterilis Bromus arenarius Poa annua
100%
100%
100%
100%
2
95%
100%
113 113
100%
100%
62
22
Table S8 (continued) Investigated species
Best similar sp. of rbcL
Coverage (%)
Similarity (%)
Coverage of the exact species (%)
Similarity with exact species (%)
N° of species per genus in GenBank
Primula vulgaris
Primula veris
99%
99%
98%
99%
45
Helleborus viridis
Helleborus croaticus
100%
100%
98%
100%
Veronica arvensis
Veronica arvensis
100%
Veronica persica
Veronica persica
Cedrus atlantica
Coverage (%)
Similarity (%)
Coverage of the exact species (%)
Similarity with exact species (%)
N° of species per genus in GenBank
Primula vulgaris Primula veris
100%
100%
100%
100%
220
7
Helleborus multifidus
100%
99%
97%
100%
17
100%
37
Veronica arvensis
100%
100%
100%
99%
37
−
−
−
−
−
18
Cedrus atlantica
100%
100%
2
−
−
−
−
−
2
Cedrus deodara
100%
100%
2
−
−
−
−
−
2
Cannabis sativa
100%
100%
1
Cannabis sativa
100%
100%
Chimonobambusa quadrangularis Phyllostachys spp. (3)
100%
100%
100%
100%
6
Senecio polypodioides
100%
99%
97%
100%
133
Lonicera xylosteum
Lonicera orientalis
100%
99%
75.6%
100%
27
Oxalis incarnata
Oxalis tomentosa
100%
97%
59%
98%
31
Cedrus deodara Cannabis sativa Chimonobambusa quadrangularis Senecio vulgaris
Senecio polypodioides
100%
99%
98%
100%
12
Best similar sp. of matK
18
1
Ranunculus bulbosus
Ranunculus macranthus
100%
99%
98%
100%
33
Ranunculus bulbosus
100%
100%
Cardamine hirsuta
Cardamine diphylla
100%
99%
98%
100%
13
Cardamine rivularis
100%
98%
93%
100%
13
100%
98%
100%
113
98%
100%
113
98%
98%
99%
3
Viburnum lantana Erophila verna
Viburnum cotinifolium Draba nemorosa
100% 100%
Viburnum rhytidophyllum
100%
99%
Erophila verna
96%
99%
255
3
Gomphrena globosa
Gomphrena ferruginea
100%
98%
84%
Mahonia aquifolium
Berberis bealei
100%
99%
96%
3
99%
7
100%
16
Additional Files Click here to download Additional Files: Tab. S9.doc
Table S9. BLAST Search results of rbcL and matK for the plant species for which corresponding sequences are not published in GenBank Investigated species
rbcL sequence in database at the level of:
N° of species per genus in GenBank
Best similar sp. of rbcL (similarity%)
Gomphrena globosa
Genus
4
Gomphrena serrata (100%)
Mahonia aquifolium
Genus
20
Mahonia japonica (99%)
Pulmonaria officinalis
Genus
1
Lobostemon fruticosus (98%)
Lonicera xylosteum
Genus
3
Oxalis incarnata
Genus
45
Oxalis articulata (99%)
Chimonobambusa quadrangularis
Genus
5
Chimonobambusa marmorea (99%)
Veronica sublobata
Genus
37
Veronica hederifolia (100%)
MatK sequence in database at the level of:
N° of species per genus in GenBank
Best similar sp. of MatK (similarity%)
Genus
1
Pulmonaria obscura (98%)
Genus
17
Veronica hederifolia (98%)
Genus
31
Abies hidalgensis (100%)
−
Abies alba
1
Additional Files Click here to download Additional Files: Tab. S10.doc
Table S10 BOLD-IDS search results for rbcL and matK for the plant species for which corresponding sequences are recorded in BOLD Investigated species
Best similar sp. of rbcL
Coverage (%)
Similarity (%)
Daucus carota
Daucus carota
98%
100%
Populus nigra
Populus spp. (5)
100%
100%
Vinca minor
Vinca minor
100%
100%
100%
100%
100%
100%
99.8%
100%
Hedera helix Olea europaea
Hedera helix Hedera rhombea Olea europaea Olea woodiana
Coverage of the exact sp. (%)
100%
Similarity with exact sp. (%)
N° of spp. per genus in BOLD
Best similar sp. of matK
Coverage (%)
Similarity (%)
93.3%
100%
−
−
Coverage of the exact sp. (%)
Similarity with exact sp. (%)
N° of spp. per genus in BOLD
1
Daucus carota
7
−
1
Vinca minor
94.5%
100%
1
100%
2
Hedera helix
99%
100%
1
99.8%
2
Fraxinus excelsior
99%
99.3%
1
Cichorium intybus
100%
100%
1
6
Crataegus monogyna
98.7%
100%
6
2
Fragaria vesca Fragaria virginiana
94.5%
100%
96.5%
100%
2
Solanum tuberosum
100%
99.2%
96.5%
99.8%
134
100%
1 −
89%
−
99.6%
7
2
Cichorium intybus
Cichorium intybus
100%
100%
Crataegus monogyna
Crataegus spp. (5)
100%
99.8%
Fragaria vesca
Fragaria vesca Fragaria virginiana
100%
100%
Solanum lycopersicum
Solanum lycopersicum
100%
100%
134
Capsella bursa-pastoris
Capsella bursa-pastoris
100%
100%
1
Capsella bursa-pastoris
100%
100%
1
Taxus baccata
Taxus spp. (4)
100%
100%
16
Taxus baccata
98.9%
100%
16
100%
100%
100%
100%
29
96.6%
99.6%
85.9%
99.3%
13
100% 100%
100%
99.8% 100%
100%
Ligustrum vulgare
Ligustrum spp. (8)
100%
100%
100%
100%
29
Ligustrum vulgare Ligustrum sinense
Galium mollugo
Galium verum Galium mollugo
100%
100%
100%
100%
13
Galium verum
Cerastium glomeratum
Cerastium glomeratum
100%
100%
17
−
−
−
−
−
17
Calocedrus decurrens
Calocedrus decurrens
100%
100%
1
−
−
−
−
−
1
Plantago major
Plantago major
100%
100%
5
Plantago major
100%
100%
Quercus rubra
Quercus spp. (3)
100%
100%
100%
100%
33
Quercus macrocarpa
93.5%
99.2%
Bromus sterilis
Bromus sterilis Bromus tectorum
100%
100%
100%
100%
16
Bromus sterilis
95.3%
100%
22
Poa annua
Poa annua
100%
100%
13
Poa annua
97%
100%
14
Primula vulgaris
Primula vulgaris
98%
99.8%
59
Primula vulgaris
99.5%
100%
59
Lamium purpureum
Lamium purpureum
100%
100%
21
Lamium purpureum
98.6%
99.3%
21
Helleborus viridis
Helleborus spp. (3)
100%
100%
4
Helleborus viridis
82.7%
99.7%
2
Liriodendron tulipifera
Liriodendron tulipifera
100%
100%
1
Liriodendron tulipifera
93.3%
99.6%
1
Magnolia grandiflora
Magnolia spp. (3)
100%
100%
3
Magnolia grandiflora
94.3%
100%
3
Veronica arvensis
Veronica arvensis
100%
100%
23
Veronica arvensis
96.9%
99.9%
23
100%
100%
100%
100%
1
4 90%
100%
33
Table S10 (continued) Investigated species
Best similar sp. of rbcL
Coverage (%)
Similarity (%)
Cannabis sativa
Cannabis sativa
100%
100%
Ranunculus bulbosus
Ranunculus spp. (6)
100%
100%
Erophila verna
Erophila verna
97%
99%
Viburnum lantana
Viburnum spp. (5)
100%
100%
Nerium oleander
Nerium oleander Nerium indicum
100%
100%
Rosmarinus officinalis
Rosmarinus officinalis
100%
Cedrus atlantica
Cedrus atlantica
Ginkgo biloba
Ginkgo biloba
Coverage of the exact species (%)
Similarity with exact species (%)
N° of species per genus in BOLD
1 100%
100%
266
Best similar sp. of matK
Coverage (%)
Similarity (%)
Coverage of the exact species (%)
Cannabis sativa
100%
100%
1
Ranunculus bulbosus
96.4%
99.8%
266
Erophila majuscula
95%
98.6%
42
Viburnum spp. (3)
100%
100%
2
Nerium oleander Nerium indicum
100%
100%
100%
100%
2
100%
1
−
−
−
−
−
1
100%
100%
2
−
−
−
−
−
2
100%
100%
1
Ginkgo biloba
100%
100%
100%
100%
100%
100%
46 150
100%
100% 100%
99.6%
N° of species per genus in GenBank
3 100%
89.6%
Similarity with exact species (%)
2 42
1
Abies alba
Abies spp. (9)
100%
100%
100%
100%
46
Abies alba Abies hidalgensis
Pinus sylvestris
Pinus spp. (9)
100%
100%
100%
100%
150
−
−
−
−
−
Cedrus deodara
Cedrus deodara
100%
100%
2
−
−
−
−
−
2
Pinus nigra
Pinus spp. (8)
100%
100%
100%
100%
150
−
−
−
−
−
150
Chamaecyparis lawsoniana
Chamaecyparis lawsoniana
100%
100%
9
−
−
−
−
−
9
Cardamine hirsuta
Cardamine hirsuta
100%
100%
20
Cardamine flexuosa
100%
97.8%
91%
100%
20
Buxus sempervirens
Buxus sempervirens
100%
100%
11
Buxus koreana
100%
99.6%
96.8%
100%
11
Trachycarpus fortunei
Trachycarpus fortunei Chamaerops humilis
100%
100%
100%
100%
1
Trachycarpus fortunei Chamaerops humilis
100%
100%
100%
100%
1
Picea abies
Picea spp. (14)
100%
100%
100%
100%
51
−
−
−
−
−
51
Trifolium pratense
Trifolium pratense
100%
100%
46
Trifolium pratense
100%
100%
Viburnum tinus
Viburnum tinus
100%
100%
42
Viburnum sargentii
100%
99.8%
Albizia julibrissin
Albizia julibrissin
100%
99.8%
30
Albizia julibrissin
100%
99.8%
30
100%
100%
100%
100%
2
Laurus nobilis
100%
100%
2
100%
100%
98%
100%
33
Quercus spp. (6)
100%
99.8%
100%
99.8%
33
100%
100%
98%
100%
33
Quercus spp. (5)
100%
100%
100%
100%
33
Laurus nobilis Quercus petraea Quercus robur
Laurus nobilis Lindera spp. (5) Litsea spp. (4) Quercus spp. (3) Castanopsis spp. (2) Quercus spp. (8) Castanopsis spp. (2)
T 2
46 98.4%
100%
42
Table S10 (continued) Investigated species
Best similar sp. of rbcL
Coverage (%)
Similarity (%)
Taraxacum officinale
Coverage of the exact species (%)
Taraxacum officinale
100%
100%
Pittosporum tobira
Pittosporum spp. (3)
100%
100%
Mahonia aquifolium
Mahonia aquifolium
100%
100%
Brassica oleracea
Brassica spp. (3)
100%
100%
100%
Brassica napus
Brassica spp. (3)
100%
100%
100%
100%
Similarity with exact species (%)
N° of species per genus in BOLD
Best similar sp. of matK
Coverage (%)
Similarity (%)
Coverage of the exact species (%)
Similarity with exact species (%)
N° of species per genus in GenBank
23
Taraxacum officinale
99.7%
99.4%
12
Pittosporum undulatum
100%
99.4%
91%
99.8%
12
79
Berberis thunbergii
100%
99.3%
96.7%
100%
79
100%
28
Brassica juncea
100%
99.6%
96.8%
100%
28
100%
28
Brassica oleracea
100%
99.6%
91.2%
100%
28
100%
100%
100%
100%
86
96.5%
99.8%
134
100%
Prunus cerasifera
Prunus spp. (6)
100%
100%
100%
100%
86
Prunus cerasifera Prunus domestica
Solanum tuberosum
Solanum lycopersicum
100%
98.9%
37%
98%
134
Solanum lycopersicum
100%
99.2%
Senecio vulgaris
Senecio spp. (3)
100%
100%
100%
100%
36
Senecio vulgaris
100%
100%
Prunus laurocerasus
Prunus laurocerasus
100%
100%
86
Prunus laurocerasus
100%
100%
23
36 86
Oxalis incarnata
Oxalis tomentosa
97%
98.4%
23%
Chimonobambusa quadrangularis
Chimonobambusa quadrangularis Phyllostachys bambusoides
100%
100%
100%
100%
2
−
−
−
−
23
73%
100%
Veronica persica
Veronica spp. (3)
100%
100%
100%
100%
23
−
Nicotiana tabacum
Nicotiana spp. (4)
100%
100%
100%
100%
64
Nicotiana tabacum
100%
100%
Lonicera xylosteum
−
−
−
−
−
46
Lonicera orientalis
99%
99.5%
Gomphrena globosa
Gomphrena celosioides
100%
99.64%
100%
99.46%
9
3
100%
38
64 46
Additional Files Click here to download Additional Files: Tab. S11.doc
Table S11. BOLD-IDS search results for rbcL and matK for the plant species for which corresponding sequences are not recorded in BOLD Investigated species
rbcL sequence in database at the level of:
N° of species per genus in BOLD
Best similar sp. of rbcL (similarity%)
Pulmonaria officinalis
Genus
4
Pulmonaria obscura (100%)
Oxalis incarnata
Genus
37
Oxalis rubra (99.5%)
Gomphrena globosa Chimonobambusa quadrangularis
Genus
1
Chimonobambusa marmorea (99.8%)
Veronica sublobata
Genus
23
Veronica hederifolia (100%)
1
matK sequence in database at the level of:
N° of species per genus in BOLD
Best similar sp. of MatK (similarity%)
Genus
4
Pulmonaria obscura (98.1%)
Genus
9
Gomphrena ferruginea (98.4%)
Genus
23
Veronica hederifolia (98%)
Additional Files Click here to download Additional Files: Tab. S12.doc
TableS12.Sequence recovery rate for the barcode regions considered singly or in two-locus combination DNA Barcode regions Taxonomic Category* Species (n=65)
trnH-psbA
trnL-trnF
rbcL
matK
trnH-psbA+trnL-F
trnHpsbA+matK 63 (100%)
trnLF+rbcL 63 (100%)
trnLF+matK 63 (100%)
rbcL+matK
63 (100%)
trnHpsbA+rbcL 63 (100%)
61(96.8%)
63 (100%)
64 (98.5%)
54 (83.1%)
Genus (n=55)
52(98.1%)
53 (100%)
54 (98.1%)
46 (83.6%)
53 (100%)
53 (100%)
53 (100%)
53 (100%)
53 (100%)
55 (100%)
Family (n=34)
32 (97 %)
33 (100%)
34 (100%)
31 (91.2%)
33 (100%)
33 (100%)
33 (100%)
33 (100%)
33 (100%)
34 (100%)
Order (n=24)
23(95.8%)
24 (100%)
23 (95.8%)
23 (95.8%)
24 (100%)
24 (100%)
24 (100%)
24 (100%)
24 (100%)
24 (100%)
*63 species, 53 genera and 33 families for trnH-psbA and trnL-trnF when considered singly or in combinations For each taxonomic category the absolute number of successes is given along with the percentage relative to the total possible number In the combinations of markers, sequence success is defined as the recovery of any marker
65 (100%)
Additional Files Click here to download Additional Files: Tab. S13.doc
TableS13.BLAST results for frequency of correct species identification of single- and multi-locus barcodes on the subset of species having records available in GenBank and BOLD databases GenBank DNA Barcode Region
Correct assignment at species level (%)
Correct assignment at genus level (%)
Correct assignment at family level (%) Incorrect assignment (%)
rbcL
27/58 (46.6%)
20/58 (34.5%)
4/58 (6.9%)
7/58 (12.1%)
matk
26/51 (51%)
7/51 (13.7%)
1/51 (2.0%)
17/51 (33.3%)
trnH-psbA
31/53 (58.5%)
13/53 (24.5%)
0
9/53 (17%)
trnL-trnF
25/58 (43.1%)
18/58 (31%)
0
15/58 (25.9%)
trnL-trnF+rbcL
34/62 (54.8%)
20/62 (32.3%)
3/62 (4.8%)
5/62 (8.1%)
trnL-trnF+matK
34/62 (54.8%)
16/62 (25.9%)
1/62 (1.6%)
11/62 (17.7%)
trnH-psbA+trnL-trnF
39/63 (61.9%)
14/63 (22.2%)
0
10/63 (15.9%)
trnH-psbA+rbcL
40/60 (66.7%)
14/60 (23.3%)
1/60 (1.7%)
5/60 (8.3%)
trnH-psbA+matK
37/59 (62.7%)
12/59 (20.3%)
1/59 (1.7%)
9/59 (15.3%)
rbcL+matK
33/61 (54.1%)
18/61 (29.5%)
3/61 (4.9%)
7/61 (11.5%)
BOLD DNA Barcode Region
Correct assignment at species level (%)
Correct assignment at genus level (%)
rbcL
28/60 (46.7%)
26/60 (43.3%)
4/60 (6.7%)
2/60 (3.3%)
matk
26/51 (51%)
8/51 (15.7%)
2/51 (3.9%)
15/51 (29.4%)
39/63 (61.9%)
19/63(30.1%)
2/63 (3.2%)
3/63 (4.8%)
rbcL+matk
Correct assignment at family level (%) Incorrect assignment (%)
Additional Files Click here to download Additional Files: Text ESM 1.doc
Supplementary Text ESM 1PCR
was performed in a 10 µl reaction mixture containing approximately 1-5 ng/µl of genomic
DNA template, 2X Qiagen Multiplex Master Mix (Qiagen) and 0.4 µM of each primer on a Veriti 96-well Thermal Cycler (Applied Biosystems) and all samples were amplified under the same cycling conditions for rbcL region (Table S1). MatK required the implementation of 4 different modified PCR protocols to allow successful amplification in most samples by varying annealing condition (Table S1). PCR products were cleaned using ExoSAP-IT kit (USB Corp.,Cleveland, OH, USA). For sequencing, 4 µl of the purified PCR product was used in a 20 µl reaction with BigDye Terminator v1.1 Cycle Sequencing kit (Applied Biosystems) according to the manufacturer protocol, in both forward and reverse direction using original primers. Cycle sequencing protocols were the same for all markers (96 °C 1 min, [96 °C 30 sec, 50°C 5 sec, 60 °C 4 min] x 25 cycles). Sequencing reaction products were finally purified from residual dye terminators using DyeEx 2.0 Spin Kit (Qiagen) and sequence reactions were read with POP-4 performance optimized polymer (Applied Biosystems) on automated capillary sequencer ABI 3130 DNA analyser (Applied Biosystems).
2As
explained in details in the previously work [Ferri et al. 24], a correct identification with the
BLAST tool is achieved when the query sequence pasted in the search window corresponds to the first database entry in the output file, defined as maximum scoring segment pair (MSP), which displays the best concordance (Maximum Score) with the query sequence. A further distinction is made when the sequence search returned a “single best match” (where the query sequence was returned as the unique most likely match) or “multiple best matches” (where the query sequence plus one or more identical sequences were returned as equally likely).