Reference strains




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Supplementary material.
Table S1. Reference strains and accession numbers used.


Reference strains

Genus/species

Host plant

Origin

dnaK

ITS

recA

glnII

atpD

USDA110

B. japonicum

Glycine max

USA

NC004463

AF338865

NC_004463

NC_004463

NC_004463

ARC403

B. japonicum

Lupinus albus

Egypt

AJ431134













USDA122

B. japonicum bv. glycinearum

Glycine max

USA




AF208503

AY591562

AY386777

AY653767

NC92

B. japonicum

Arachis hypogaea

USA

AJ431144













WM9

B. japonicum

Lupinus albus

Poland

AF222752













USDA3505

B. japonicum

Lupinus montanus

USA

AJ431150













ANU289

B. elkanii

Parasponia sp.

USA

AJ431133













USDA94

B. elkanii

Glycine max

USA

AY328393

AF338868

AY591569

AY59911

AY386759

USDA76

B. elkanii

Glycine max

USA

AJ431152

U35000

AY591568

AY599117

AY386758

CGA009

R. palustris

Non-symbiotic







AJ534609










BTA-1

B. canariense bv. genistearum

Chamaecytisus proliferus

Canary Islands, Spain




AY591553


AY591553


AY386765

AY386739

BC-C2

B. canariense bv. genistearum

Chamaecytisus proliferus

Canary Islands, Spain

AJ431135

AY386704

AY591541

AY386762

AY386736

BES-1

B. canariense bv. genistearum

Chamaecytisus proliferus

Canary Islands, Spain




AY386707

AY591548

AY386764




BES-2

B. canariense bv. genistearum

Chamaecytisus proliferus

Canary Islands, Spain




AY599096

AY591549

AY599109

AY653753

ISLU16

B. canariense bv. genistearum

Ornithopus sp.


Sevila, Spain




AY386712










BGA-1

B. japonicum bv. genistearum

Teline stenopetala

Canary Islands, Spain




AY386714

AY591558

AY386772




USDA6

B. liaoningense bv. glycinearum

Glycine max

Canary Islands, Spain




U69638




AF169582




LMG18230

B. liaoningense bv. glycinearum

Glycine max


China




AF345256

AY591564


AY386775

AY386752

CCBAU10071

B. yuanmingense


Lespedeza cuneata


Canary Islands, Spain




AY386734

AY591566

AY386780




LMG10690







Canary Islands, Spain




AJ534598










BRE-4

B. canariense bv. genistearum

Teline canariense

Canary Islands, Spain







AY591552




AY653755

BC-MAM1

B. canariense bv. genistearum

Chamaecytisus proliferus

Canary Islands, Spain







AY591546

AY386767





BC-MAM2

B. canariense bv. genistearum

Chamaecytisus proliferus

Morocco













AY653756

BC-MAM3

B. canariense bv. genistearum

Chamaecytisus proliferus

Morocco




AY386710







AY386768

BC-MAM5

B. canariense bv. genistearum

Chamaecytisus proliferus

Morocco




AY386711

AY591547

AY386769




BC-MAM6

B. canariense bv. genistearum

Chamaecytisus proliferus

Morocco













AY653757

BC-MAM8

B. canariense bv. genistearum

Chamaecytisus proliferus

Morocco







AY653746




AY653758

BC-MAM9

B. canariense bv. genistearum

Chamaecytisus proliferus

Morocco













AY653759

BC-MAM12

B. canariense bv. genistearum

Chamaecytisus proliferus

Morocco













AY653760

BC0-1

B. canariense bv. genistearum

Adenocarpus foliolosus

Canary Islands, Spain







AY591550




AY653754

BC-P5

B. canariense bv. genistearum

Chamaecytisus proliferus

Canary Islands, Spain







AY591542







BC-P22

B. canariense bv. genistearum

Chamaecytisus proliferus

Canary Islands, Spain




AY386706

AY591545

AY386766




BC-P24

B. canariense bv. genistearum

Chamaecytisus proliferus

Canary Islands, Spain













AY653752

USDA 62

Bradyrhizobium japonicum

Glycine max


USA




AF271642










USDA 92

B. japonicum bv. glycinearum

Glycine max

USA




AF293382










Blup MR1

B. japonicum bv. genistearum

Lupinus polyphylus


Germany




AY386717










FN13

B. japonicum bv. genistearum

Lupinus montanus


Mexico




AY386716










LMG 4271

Bradyrhizobium japonicum










AJ279307










LMG 21987

Bradyrhizobium betae

Non-symbiotic

Spain




AJ631967











LMG 6136

Bradyrhizobium japonicum

Glycine max

USA




AJ534589










LMG 11955

Bradyrhizobium genosp. V

Faidherbia albida

Senegal




AJ534590










LMG 11957

Bradyrhizobium genosp. V

Faidherbia albida

Senegal




AJ534591










LMG 10691

Bradyrhizobium genosp. IX

Faidherbia albida

Senegal




AJ534600










LMG 10690

Bradyrhizobium genosp. IX

Faidherbia albida

Senegal




AJ534598










LMG 15178

Bradyrhizobium genosp. VII

Tephrosia purpurea

Senegal




AJ534604










LMG 11706

Bradyrhizobium genosp. X

Faidherbia albida

Senegal




AJ534593










LMG 15261

Bradyrhizobium genosp. XI

Crotalaria glauccoïdes

Senegal




AJ534596










LMG 4265

Bradyrhizobium japonicum










AJ279306










LMG 6134

B. elkanii

Glycine max







AJ279308










LMG 12186

Bradyrhizobium genosp. VI

Aeschynomene sensitiva

Senegal




AJ534585










LMTR28

B. yuanmingense

Phaseolus lunatus

Peru




AY599094










BC-C1

B. genosp. alpha bv. genistearum


Chamaecytisus proliferus


Canary Islands, Spain




AY386703











Nep1

B. japonicum bv. glycinearum

Glycine max

Nepal




AY386718










BC-MK6

Bradyrhizobium genosp. beta

Chamaecytisus proliferus

Morocco




AY386722










BC-MK1

Bradyrhizobium genosp. beta

Chamaecytisus proliferus

Morocco




AY386721










BC-P6

Bradyrhizobium genosp. beta

Chamaecytisus proliferus

Canary Islands, Spain




AY599097












STATISTICAL TESTS:
1) Tests of congruence of tree topologies using Shimodaira-Hasegawa (SH) test implemented in PAUP.

Trees were compared one by one with each other for each marker, on restricted datasets of 13 strains for which all markers sequences were available (USDA94, USDA76, USDA110, WSM2150, WSM2154, WSM2157, WSM471, WSM2150, 3S16, BC-C2, WU425, 4S16 and 1S20). Trees used for the test were generated by Maximum Likelihood, using a gamma distribution of site substitutions, with 2 types of substitutions and estimating base frequencies.


Values shown indicate the probability than 2 trees exhibit the same topology. If P<0.05 (5%), the hypothesis that the trees have the same topology is rejected.





recA

atpD

dnaK

glnII

ITS

recA

-

0.110

0.022

0.007

0.026

atpD




-

0.176

0.008

0.147

dnaK







-

0.140

0.373

glnII










-

0.210

ITS













-

Bold values indicate values greater than 5% between two trees topologies, meaning the topologies are statistically congruent using the SH test.


In conclusion, topology congruence of trees was found on nearly all trees, except glnII and recA trees that did show significant incongruence with others trees.


2) Partition-homogeneity or ILD test (Incongruence Length Difference) (using PAUP)

Calculation of incongruence used to measure character congruence, allow a direct comparison of data partitions by separating the incongruence into between-, and within-data set incongruence. Rather than limiting the study of incongruence to a small number of data partitions that were then combined, a randomisation procedure (sometimes termed the ILD test) was used to divide the combined data into a large number of sets of the same size and number as the original data partitions (Farris et al., 1995). If the data partitions are significantly incongruent at the 95% significance level, then less than 5% of the randomly divided data sets should have trees with lengths longer than the original data partitions. PAUP* includes the Partition Homogeneity Test (PHT), which performs the ILD test with branch swapping, and has been used to test the significance of character congruence.

A partition of all markers (dnaK, recA, atpD, glnII, ITS) was made for 11 strains for which sequences were available. These strains are USDA94, USDA76, USDA110, WSM2150, WSM2154, WSM2157, WSM471, WSM2150, 3S16, BC-C2 and WU425. Strains 4S16 and 1S20 were excluded as their phylogenetic position differed in several trees and recombination was detected in several markers. Tests were performed under parsimony criteria.
Partition used: “ABCDE”

A: recA (position 1-485)

B: atpD (position 486-968)

C: dnaK (969-1246)

D: glnII (1247-1840)

E: ITS (1841-2708)


Number of repetition used (Nrep) was 1000.

P values obtained indicate homogeneity (or not) in the partition. A P value >5% indicates homogeneity in the phylogenetical signal between the markers used in the partition.


Partition P value

ABCDE 0.015

ABCD 0.031

BCDE 0.001

ABCE 0.001

ABC 0.136 (recA-atpD-dnaK)

ABD 0.018

BCD 0.060 (atpD-dnaK-glnII)

ACD 0.030

ACE 0.001

ADE 0.001

CDE 0.002

AB 0.1500 (recA-atpD)

AC 0.1950 (recA-dnaK)

AE 0.002

AD 0.023


BC 0.424 (atpD-dnaK)

BD 0.049


BE 0.001

CD 0.479 (dnaK-glnII)



CE 0.002

DE 0.029
Homogeneity could be found in small partitions of two to three markers, but not when including four or all markers.


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