Phylogenic diversityand tissue specificity of fungal endophytesassociated with the pharmaceutical plant, Stellera chamaejasme L. revealed by a cultivation-independent approach
Hui Jin• Xiaoyan Yang• Dengxue Lu • Chunjie Li •Zhiqiang Yan• Xiuzhuang Li• Liming Zeng•Bo Qin
H. Jin • X.-Y. Yang •Z.-Q Yan• X.-Z Li • L.-M Zeng •B. Qin ()
Key Laboratory of Chemistry of Northwestern Plant Resources and Key Laboratory for Natural Medicine ofGansu Province, Lanzhou Institute of Chemical Physics, Chinese Academy of Sciences, Lanzhou 730000, China
D.-X Lu
Institute of Biology, Gansu Academy of Sciences, Lanzhou 730000, China
C.-J Li
State Key Laboratory of Grassland Agro-Ecosystems, College of Pastoral Agricultural Science and Technology, Lanzhou University, Lanzhou 730000, China
H.Jin
Key Laboratory of Tobacco Diseases and Insect Pests Monitoring Controlling and Integrated Management, Institute of Tobacco Research, Chinese Academy of Agricultural Sciences, Qingdao 266101, China
B. Qin ()
Key Laboratory of Chemistry of Northwestern Plant Resources and Key Laboratory for Natural Medicine ofGansu Province, Lanzhou Institute of Chemical Physics, Chinese Academy of Sciences, Lanzhou 730000, China
Tel.: +86 931 4968371; fax: +86 931 8277088
e-mail: (B.Qin)
Table S1Summary of the fungal endophytes derived from rhizosphere and various tissues of S. chamaejasme with their respective clone codes, GenBank accession numbers, and closest affiliations of the representative OTUs in the GenBank according to rRNA ITSanalysis
(Accession no.) / Maximum identity (%) / Taxonomic group / Source of the closest relatives
Rs01 / Uncultured Mortierellales 2B12
(FN689675) / 98 / Mortierellales / Rhizosphere of
tomato plants
Rs02 / Mortierella sp. T12 (JF439487) / 99 / Mortierellales / Terrestrial fungi from
Zijin mountain
Rs03 / Mortierella sp. T10 (JF439491) / 99 / Mortierellales / Terrestrial fungi from
Zijin mountain
Rs04 / Mortierella sp. QLF15
(FJ025162) / 97 / Mortierellales / Alpine grassland in
Qilian mountains
Rs05 / Mortierella alpina QLF27
(FJ025187) / 99 / Mortierellales / Alpine grassland in
Qilian mountains
Rs06 / Mortierellales sp. QLF86
(FJ025158) / 98 / Mortierellales / Alpine grassland in
Qilian mountains
Rs07 / Mortierellales sp. QLF91
(FJ025154) / 97 / Mortierellales / Alpine grassland in
Qilian mountains
Rs08 / Uncultured ascomycete clone
23d (EU003079) / 99 / Ascomycete / The root of apple
seedling
Rs09 / Uncultured Mortierella clone
G17p2c5 (GU327521) / 98 / Mortierellales / Mycorrhizal seedling
Rs10 / Mortierella sp. TR065
(HQ608097) / 99 / Mortierellales / Trachymyrmex
septentrionalis nest
Rs11 / Uncultured Cryptococcus clone
7_d10 (HQ211959) / 99 / Filobasidiales / Arctic soil
Rs12 / Uncultured Filobasidialesclone
2B16 (FN689678) / 99 / Filobasidiales / Rhizosphere of tomato
plants
Rs13 / Uncultured Thelephoraceae
isolate M2 (AY916075) / 99 / Thelephorales / The roots of Salix
caprea
Rs14 / Uncultured Tomentella clone
4S4.04.F04 (EF619820) / 98 / Thelephorales / Forest soil
Rs15 / Uncultured Thelephoraceae
clone LP110011 (JQ318599) / 100 / Thelephorales / Quercus liaotungensis
forest
Rs16 / Resinicium bicolor Z-3-4
(FJ872065) / 99 / Hymenochaetales / Roots ofPinus mugo
Rs17 / Urocystis eranthidis voucher
hmk292(JN367299) / 97 / Urocystales / Sweet grasses
Rs18 / Amanita sp. 2isolate 3037
(HE814194) / 100 / Agaricales / Root tips
Rs19 / Truncatella angustata strain
G26(GU566260) / 100 / Xylariales / Rhizosphere of
Phalaris arundinacea
Rs20 / Xylariales sp. EMF50
(JF273550) / 96 / Xylariales / An evergreen
broad-leavedforest
Rs21 / Uncultured ascomycete isolate 4(AY833031) / 95 / Ascomycete / Orchid mycorrhiza
Rs22 / Gibberella avenaceaVL146
(JF440596) / 99 / Hypocreales / Xylem of Pinus mugo
Turra
Rs23 / Fusarium sp. isolate 5/97-45
(AJ279478) / 99 / Hypocreales / Common reed
Rs24 / Gibberella sp. FPGLXJ02
(FJ196601) / 99 / Hypocreales / The bulbs of genera
Fritillaria
Rs25 / Fusarium acuminatumstrain
strain P24_D3_2(JF311926) / 100 / Hypocreales / The rooting soil of
chickpea
Rs26 / Fusarium sp. Dzf2(DQ446211) / 99 / Hypocreales / Dioscorea zingiberensis
rhizomes
Rs27 / Fusarium redolens strain Ppf2
(EF495234) / 99 / Hypocreales / The Rhizomes of Paris
polyphylla var.
yunnanensis
Rs28 / Uncultured Chaetothyriales
clone plB2F(HM136629) / 90 / Chaetothyriales / Plant roots
Rs29 / Exophiala sp. LX M8-6
(HE605222) / 88 / Chaetothyriales / Black stain on cave
sediment
Rs30 / Rhinocladiella sp. YH-2009a
isolate XJ07086-2(JX839531) / 95 / Chaetothyriales / Rock
Rs31 / Uncultured Ascomycota clone
796(HM162206) / 89 / Ascomycota / Grass roots
Rs32 / Uncultured ascomycete isolate
dfmo1059_109 (AY970123) / 90 / Ascomycota / Mixed hardwood
A-horizon soil
Rs33 / Trichoglossum hirsutum strain OSC61726(AY789314) / 96 / Geoglossales / Not mentioned
Rs34 / Geomyces sp. F29 (JF439476) / 99 / Leotiomycetes incertae sedis / Terrestrial fungi from
Zijin mountain
Rs35 / Cadophora sp. REF024
(JN859244) / 100 / Helotiales / Plant root
Rs36 / Helotiales sp. REF055
(JN859275) / 99 / Helotiales / Plant root
Rs37 / Cladosporium sp. CPC 15516
(GU214631) / 99 / Capnodiales / Pyrus communis
Rs38 / Uncultured Basidiomycota
clone 7_i08(HQ212044) / 92 / Basidiomycota / Arctic soil
Rs39 / Uncultured Ascomycota clone
NHPY04(FJ440863) / 98 / Ascomycota / Roots of Pyrola plants
Rs40 / Ascobolus crenulatus isolate
AFTOL-ID 181(DQ491504) / 94 / Pezizales / Not mentioned
Rs41 / Aspergillus sp. MS-2011-F36
(HE608802) / 99 / Eurotiales / Marine sponge
Rs42 / Phoma herbarumstrain BLE15
(FN868459) / 94 / Pleosporales / Pinus halepensis
Rs43 / Scytalidium lignicola isolate
Ppf45(GU586849) / 100 / Leotiomycetes / The Rhizomes of Paris
polyphylla var.
yunnanensis
Rs44 / Alternaria sp. OUCMBI101217
(HQ914876) / 99 / Pleosporales / Marine macroalgae
Rs45 / Alternaria sp. G29A
(EF432254) / 100 / Pleosporales / Alliaria petiolata
(garlic mustard)
Rs46 / Trichocladium sp. 19VA01
(JX270542) / 100 / Ascomycota / Soil from bat
hibernaculum
Rs47 / Fusarium oxysporum strain
GY-KG(GU445363) / 100 / Hypocreales / Momordica charantia
L01 / Eurotium amstelodami isolate
JH03(HQ728257) / 99 / Eurotiales / Pu-erh tea with jinhua
L02 / Aspergillus ruber IBL 03114
(DQ778909) / 86 / Eurotiales / Green coffee seeds
L03 / Eurotium cristatum isolate
SAB-A2-T(JX869560) / 100 / Eurotiales / Funeral clothes of
Cardinal Peter
L04 / Penicillium camemberti strain
T14-13(GU325660) / 92 / Eurotiales / Plant Habitats
L05 / Stagonospora sp. 4/99-18
(AJ496627) / 96 / Pleosporales / Seed
L06 / Alternaria sp. SFC2
(GU187964) / 99 / Pleosporales / Iron ore mineral
L07 / Uncultured Pleosporales clone
8WF4cd04(GU910945) / 99 / Pleosporales / Dung
L08 / Uncultured Pleosporales clone
9SB4cf01(GU909682) / 94 / Pleosporales / Dung
L09 / Uncultured Alternaria clone 879(KC206496) / 100 / Pleosporales / Glacier ice
L10 / Uncultured Alternaria clone
d73_4_29(JQ346899) / 100 / Pleosporales / Roots of herbs
L11 / Phomopsis sp. G26(EF432256) / 100 / Diaporthales / Alliaria petiolata
(garlic mustard)
L12 / Alternaria alternata strain
JL-19(JX867224) / 98 / Pleosporales / The stem of Tribulus
terrestris L.
L13 / Alternaria sp. 2 TMS-2011
voucher MS3p_50-33
(HQ630970) / 97 / Pleosporales / Miscanthus giganteus
L14 / Uncultured Capnodiales clone
C1(GU993534) / 99 / Capnodiales / Energy transmission
tower (corrosiondust)
L15 / Cladosporium sp. CPC 15516
(GU214631) / 99 / Capnodiales / Pyrus communis
L16 / Uncultured Davidiella clone
CEgs1176(JX159663) / 99 / Capnodiales / Stool
L17 / Davidiella tassiana strain G20
(GU566258) / 99 / Capnodiales / The rhizosphere of
Phalaris arundinacea
L18 / Fusarium oxysporum isolate
GIFUUHFA11(GQ121292) / 90 / Hypocreales / Ginger rhizome
L19 / Fusarium redolens strain Ppf2
(EF495234) / 99 / Hypocreales / The Rhizomes of Paris
polyphylla var.
yunnanensis
L20 / Fusarium sp. Papochf 05
(HQ731633) / 98 / Hypocreales / Paris polyphylla Smith
L21 / Fusarium sp.Dzf2
(DQ446211) / 99 / Hypocreales / Dioscorea zingiberensis
rhizomes
L22 / Fusarium sp. MG48
(JQ775555) / 99 / Hypocreales / The root of
Acleisanthes lanceolata
S01 / Fusarium redolens strain Ppf2
(EF495234) / 97 / Hypocreales / The Rhizomes of Paris
polyphylla var.
yunnanensis
S02 / Fusarium tricinctum strain
134(3)(FJ238111) / 99 / Hypocreales / Hippophae rhamnoides
L.
S03 / Uncultured Alternaria clone
M66(HQ875439) / 100 / Pleosporales / Soil surrounding edible fungi Chroogomphus
rutilus
S04 / Alternaria compactastrain 18
(FR846403) / 96 / Pleosporales / Wheat grains
S05 / Alternaria sp. KJ-2012 strain
GZU-BCEC204(JN867463) / 98 / Pleosporales / Not mentioned
S06 / Alternaria sp. JF-Alt22
(DQ323694) / 87 / Pleosporales / Onion
S07 / Alternaria alternata strain
JL-19(JX867224) / 100 / Pleosporales / The stem of Tribulus
terrestris L.
S08 / Uncultured Alternaria clone
d177_1_43(JQ346913) / 99 / Pleosporales / Roots of herbs
S09 / Sclerostagonospora sp. CBS
123538(FJ372393) / 100 / Dothideomycetes / Dead culm
S10 / Phaeosphaeria sp. N37
(HF674758) / 88 / Pleosporales / Festuca rubra
S11 / Chaetosphaeronema sp.
PHA-24(JX401961) / 100 / Pleosporales / Phlomis
younghusbandii
S12 / Microdochium sp. KS00012
(FJ536210) / 85 / Xylariales / Tallgrass
S13 / Neofabraea alba isolate
UASWS0753(HQ166526) / 96 / Helotiales / Infected fruit
S14 / Davidiella tassiana strain G20
(GU566258) / 100 / Capnodiales / Rhizosphere
S15 / Rhizopus sp. F36(JQ775568) / 100 / Mucorales / Soil
S16 / Alternaria sp. L2334
(KC288115) / 99 / Pleosporales / Clinical isolate from
subcutaneous
S17 / Aureobasidium pullulansBLE6
(FN868454) / 99 / Dothideales / Pinus halepensis
S18 / Aspergillus unguisCaLm 17
(AB259861) / 94 / Eurotiales / Croton oblongifolius
leaf
R01 / Fusarium sp. 2 TMS-2011
voucher MS6p50-29
(HQ630976) / 100 / Hypocreales / Miscanthus giganteus
R02 / Fusarium redolens strain Ppf2
(EF495234) / 99 / Hypocreales / The Rhizomes of Paris
polyphylla var.
yunnanensis
R03 / Amanita sp. 2(HE814194) / 98 / Agaricales / Root tips
R04 / Uncultured Ceratobasidiaceae
isolate 173(HM141034) / 95 / Cantharellales / Mycorrhizal root
R05 / Sebacina sp. F1143128 isolate
AFTOL-ID 1517(DQ911617) / 89 / Sebacinales / Not mentioned
R06 / Hygrocybe virginea var.
virginea(FM208869) / 92 / Agaricales / Not mentioned
R07 / Inocybe sp. OTU288
(HQ215787) / 100 / Agaricales / Soil
R08 / Spizellomyces lactosolyticus
voucher DAOM BR 277
(FJ827724) / 93 / Spizellomycetales / Crop soil
R09 / Xylaria sp. BLD10(FN868478) / 93 / Xylariales / Pinus halepensis
R10 / Pleosporales sp. 418H
(HE653990) / 98 / Pleosporales / Tallgrass
R11 / Phoma sp. MA 4621
(AJ972865) / 90 / Pleosporales / Antique marbles
R12 / Uncultured Phomabee12
(FN539075) / 95 / Pleosporales / Beech sapwood
R13 / Phoma herbarumBLE15
(FN868459) / 99 / Pleosporales / Pinus halepensis
R14 / Phomopsis sp. G26(EF432256) / 99 / Diaporthales / Garlic mustard (Alliaria
petiolata)
R15 / Uncultured Alternaria clone
d73_4_29(JQ346899) / 100 / Pleosporales / Roots of herbs
R16 / Uncultured Tetracladium clone
TI00097D10(JX545196) / 99 / Ascomycota / Soil
R17 / Pezizales sp. P10(AJ969618) / 89 / Pezizales / Fagus sylvatica
R18 / Arthrinium sp. LH52
(HQ832803) / 99 / Xylariales / Camellia sinensis
R19 / Fusarium sp. Papochf 05
(HQ731633) / 98 / Hypocreales / Paris polyphylla
R20 / Fusarium sp. 5/97-45
(AJ279478) / 97 / Hypocreales / Common reed
R21 / Cylindrocarpon sp. FKI-4602
(AB725901) / 99 / Hypocreales / Soil
R22 / Cladosporium sp. TMS-2011
voucher SC8d50p14-1
(HQ631003) / 99 / Capnodiales / Saccharum officinarum
R23 / Cladosporium sp. AF13
(JX173100) / 96 / Capnodiales / Agar wood trunk
R24 / Uncultured Ascomycota clone
1.8(GU392000) / 92 / Ascomycota / Sarcochilus weinthalii
R25 / Penicillium sp. s060
(HQ649932) / 97 / Eurotiales / Rhizosphere soil
R26 / Penicillium brevicompactum
strain P1.19(EU833211) / 98 / Eurotiales / Leaf litter from cave
R27 / Penicillium sp. RfereqUK-1
(HM222629) / 98 / Eurotiales / Rhinolophus
ferrumequinum
R28 / Penicillium sp. H10
(GU566279) / 99 / Eurotiales / The rhizosphereof
Phalaris arundinacea
R29 / Ascomycete sp. ZGZII03175
(DQ124116) / 91 / Ascomycota / Not mentioned
R30 / Capronia pilosella isolate
AFTOL-ID 657(DQ826737) / 90 / Chaetothyriales / Not mentioned
R31 / Capronia sp. POPeuph62
(FR865030) / 88 / Chaetothyriales / Populus euphratica
R32 / Ascomycota sp. 1 LX-2012
(JX145388) / 87 / Ascomycota / Mycorrhizal root
R33 / Penicillium olsonii strain QH48
(JF911768) / 88 / Eurotiales / Qinghai Lake
R34 / Penicillium sp. IV(FJ471606) / 92 / Eurotiales / Corn bread
R35 / Penicillium granulatum strain
P4.6(EU833219) / 98 / Eurotiales / Cave soil
R36 / Hypocreales sp. SN-2008 clone
o26_ITS1F(EU754933) / 98 / Hypocreales / Soil and roots of oilseed rape
R37 / Arthrographis kalrae
(AB506810) / 99 / Dothideomycetes
incertae sedis / Homo sapiens
fingernail
R38 / Arthrographis sp. 07MA20
(JX270420) / 97 / Dothideomycetes
incertae sedis / Soil from bat
hibernaculum
R39 / Claussenomyces sp. PDD
95741(HQ533008) / 92 / Helotiales / Not mentioned
R40 / Cryptosporiopsis californiae
culture-collection CBS:124819
(GU973504) / 90 / Helotiales / Eucalyptus leaves
R41 / Coniosporium sp. SL110414
(JQ354926) / 95 / Chaetothyriales / Rock
R42 / Uncultured Basidiomycota
clone 6_g06(HQ211760) / 91 / Basidiomycota / Soil
R43 / Geoglossum fallax strain
1131046 (AY789311) / 92 / Geoglossales / Not mentioned
R44 / Ascomycete sp. MA 4771
(AJ972828) / 97 / Ascomycota / Marble Monument
R45 / Uncultured glomeraceous AM
fungus isolate 1 clone 3
(AY896541) / 96 / Glomerales / Caltha palustris
(sporophyte)
R46 / Sebacina vermiferaCBS 572.83
(AF202728) / 98 / Sebacinales / Hexalectrisspicata
R47 / Uncultured Mortierellales2B12
(FN689675) / 98 / Mortierellales / Rhizosphere of tomato
plants
R48 / Mortierella sp. T12(JF439487) / 98 / Mortierellales / Zijin Mountain
R49 / Mortierella sp. TR065
(HQ608097) / 99 / Mortierellales / Trachymyrmex
septentrionalis nest
R50 / Uncultured Filobasidiales2B16(FN689678) / 97 / Filobasidiales / Rhizosphere of tomato
plants
R51 / Cryptococcus aerius strain CBS 4192(AF444376) / 100 / Filobasidiales / Soil
R52 / Mucor sp. TMS-2011 voucher MS3p_50-5(HQ630989) / 99 / Mucorales / Miscanthus giganteus
R53 / Hydnobolites sp. 3 RH-2012
voucher MIN:928504
(JN102453) / 88 / Pezizales / Truffle fruitbody
R54 / Trichocladium sp. 19VA02
(JX270543) / 99 / Ascomycota / Soil from bat
hibernaculum
R55 / Rhodosporidium azoricum
strain PYCC 4648(JN246556) / 91 / Sporidiobolales / Soil
R56 / Arthrobotrys vermicola isolate
125(EU977548) / 99 / Orbiliales / Decaying wood
R57 / Aureobasidium pullulans isolate
2679(EU272483) / 99 / Dothideales / An Andean Colombian
Paramo ecosystem
R58 / Uncultured Agaricales clone
fung4(JN000918) / 99 / Agaricales / Fungus comb
Closest known species with each fungal OTU were retrieved by GenBank database search
aRs, rhizosphere; L, leaf; S, stem; R, root
Figure Captions:
Fig. S1Phylogenetic trees based on neighbor-joining (NJ) analysis of the rDNA ITS sequences of the rhizosphere and endophytic fungal clones obtained from rhizosphere (a), leaf (b), stem (c) and root (d) of S. chamaejasme. OTUs were defined by MOTHUR using the furthest neighbor algorithm with a distance level of 3%. One representative clone of each OTU was used for phylogenetic analysis. Sequences from this study are by labeled their clone name followed by a GenBank accession number and numbers of clones. The phylotypes from which the sequences have been recovered from GenBank and used as reference sequences are indicated by species name and their accession number. Numbers on the nodes arethe bootstrap values (percentages) based on 1000 replicates and values of above 50% were presented.Clustersdelineated by braces indicate broader group designations and the numbers of the clones in these classes were shown in the parentheses, respectively.Evolutionary distance was based on the maximum composite likelihood method, and phylogenetic analysis was conducted in MEGA 5.0.