Pseudomonas fluorescens SBW25 - PLOS

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BWA LCA: Pseudomonas fluorescens SBW25. Blast LCA: Pseudomonas fluorescens SBW25. P_fluorescens_Pf0_1. Pseudomonas_poae_RE*1-1-14.
A

BWA LCA: Pseudomonas fluorescens SBW25 Blast LCA: Pseudomonas fluorescens SBW25

Pse udo mo nas _po ae_ RE *1-1 -14

P_fluorescens_Pf0-1

32 274 845 484 R05 SR

69% % 70

52 %

*P _flu ore sc en s_ SB W 25

6 19 tig n co p_ Ar 29 f _P ns ce s ore flu s_ a on om ud W4 e Ps sp_U P

% 19

Pfluore scens _A506

4%

98%

96%

13 _F1 1 ens FM42 c s e _N luor P_f cearum a ic ass _br rum a e c sica ras P_b

0.03

P_aeruginosa_PAO1 P_aeruginosa_M18 P_aeruginosa_LESB58 P_aeruginosa_PtxR P_aeruginosa_DK2

B BWA LCA: Pseudomonas fluorescens SBW25 Blast LCA: Pseudomonas fluorescens SBW25

Ps eu do m on as _p oa e_ RE *1 -1 -1 4

06 A5 s_ en sc re uo _fl as on m do eu Ps 29%

*P se ud om on as _fl uo re sc en s_ SB W 25

8 89 04 89 7.3 14 03 R2 SR

0.0050

C Ps ulico eu ide do s_ m so on no as re _p ns ro is_ teg cl en one s_ _C Pf -5 ssg 00 03 1

C BWA LCA: Pseudomonas fluorescens Blast LCA: Pseudomonas fluorescens SBW25

% 65

a

Cottus_gobio_Bullhead_contig_24818 (fish) Pseudomonas_poae_RE*1-1-14 *Pseudomonas_fluorescens Pseudomonas_stutzeri_DSM_10701 *Pseudomonas_fluorescens_SBW25 Pseudomonas_sp_UW4 SRR20315.825397602 *Pseudomonas_fluorescens_A506

f0-1 escens_P onas_fluor *Pseudom

a

0.0040

D

BWA LCA: Pseudomonas Blast LCA: Pseudomonas cina nas_mendo 01 *Pseudomo 07 _1 M DS ri_ ze tut _s as on om ud se *P

c

36%

b

Marinomonas_mediterranea_MMB-1

40%

54%

a a

1 o-18 IA-P V I ica_ idon s o s_p ona m o n i Mar Marinomonas_sp_MWYL1

42%

*P se ud om on as _e nto mo ph ila_ str _L 48

98%

0.03

*Pseudomonas_syringae_pv_syringae_B728a *Pseudomonas_syringae_pv_syringae_strain_UMAF0158

b

*Pseudomonas_perfectomarina *Pseudomonas_stutzeri

*Pseudomonas_putida_GB-1

*Pseudomonas_stutzeri_A1501

*Pseudomonas_putida_W619

*Pseudomonas_stutzeri_CCUG_29243

*Pseudomonas_fluorescens_SBW25

*Pseudomonas_stutzeri_RCH2

*Pseudomonas_fluorescens_Pf0-1 *Pseudomonas_putida_BIRD-1 *Pseudomonas_putida_S16 *Pseudomonas_fluorescens_F113 *Pseudomonas_fluorescens_A506 *Pseudomonas_putida_ND6 *Pseudomonas_putida_DOT-T1E *Pseudomonas_sp_UW4 *Pseudomonas_putida_HB3267 *Pseudomonas_poae_RE-1-1-14 *Pseudomonas_fluorescens_Pf29Arp *Pseudomonas_putida_KT2440 *Pseudomonas_syringae_pv_tomato_str_DC3000 *Pseudomonas_syringae_pv_phaseolicola_1448A *Pseudomonas_protegens_Pf-5 *Pseudomonas_putida_F1 *Pseudomonas_brassicacearum_NFM421 SRR06183721207268

c

*Pseudomonas_stutzeri_DSM_4166 *Pseudomonas_mendocina_NK-01 *Pseudomonas_stutzeri_ATCC_17588 *Pseudomonas_fulva_12-X

E

_UW 4

BWA LCA: Pseudomonas Blast LCA: Pseudomonas

na

ns

mo 65

_P

f0-

u

b

on

a

f s_

lu

ace rass ic

or

e

arum

ns

_

9A

_NFM

rp

421

%

1

*Pseu

25%

sce

as_ * % omon 7 0 * Pseud

_L48 67 32

ore

HB

flu

a_

s_

tid

na

pu

mo

omophila

s_

do

se

m do

udo

mo

eu

*P

Pse

do

on as _e nt

eu

*P s

nas

Ps

*

_sp

P se ud om

*

e sc

2 Pf

domo

nas_

pu tid

a_S1

6

*Pseudomonas_protegens_Pf-5 48

escens_S onas_fluor Pseudom

11E* _R ae po s_ na

5

mo

467

do

432

eu

4.1

Ps

315

BW25

6

14

o

re

50

R20

om

uo

_A

SR

ud

_fl

ns

%

*

e Ps

s na

sce

*

*

*Ps

0.02

eu

do

m

on

as

_p

ut

id

a_

W

61

9

F

nas

_po

ae_

RE

*1-

1-1

4

71

a_

id

_p

ut

_BI

on

as

tida

do

m

_pu

eu

nas

Ps

mo

%

*

*

46

%

33

ring

BW25 escens_S

46

onas_f luor

6 4 1%

50

_A

ns

ce

es or

lu

*Pseudom

_sy

_f

_pv

as

gae

on

yrin

*P

B72

se

ae_

om

s_s

421

ona

s_s

p_B

G3

3R

8a

0.03

_P f2 9A rp

*P *P se *P s e u u d o se d o m ud m o n om o n a s on a s _ _ s y as f l r i n _s u o g a p_ r e e UWsc e _pv 4 ns_ _to Pf ma 0- to _s 1

ona

um_NFM

ud

om

15

sicacear

25

eud

84

20

*Ps

S

RR

1 06

3 63

*P se ud om 6 3 on as _f lu or es ce ns %

nas_bras

%

o

13

%

om

_F1

22

eud

lu

ens

o *Pseudom

* Ps

_f nas

sc ore

%

%

M _1 07 01

31

%

40% 18%

9

46

id a_ W 61

om

er i_ D S as _s tu tz

*Ps eud

*P

se ud om on

on as _p ut

72

1 a_F D 6 1E utid _N T-T s_pput idaa_D O a n _ o d om nas pu ti eud mo as_ * Psseudoomon % d 2 6 * P seu *P % 72

%

*P se ud om

udo

mo

* *

Pse

udo

7 d a _ H B 3 2S616 onas_puti P s e u d o m omonas_putida_ G B - 1 tida_ Pseud onas_pu Pseudom

*P s e

*

*

1 -0 NK p a_ _ym cin na do ci en ndo _m e as _m on as m on do m eu udo Ps se P

*

RD

-1

KT

24

40

BWA LCA: Pseudomonas Blast LCA: Pseudomonas

tr_

DC

30

00

1 70_ _10 SM ri_D t ze _stu nas omo eud *Ps

G

BWA LCA: Pseudomonadaceae Blast LCA: Pseudomonas

*Pseudomonas_syringae_pv__syringae *Pseudomonas_aeruginosa_PAO1 *Pseudomonas_aeruginosa_UCBPP-PA14 *Pseudomonas_aeruginoas_PA7

b

*Pseudomonas_aeruginosa_LESB58 *Pseudomonas_fluorescens_SBW25 *Pseudomonas_aeruginosa_DB3 *Pseudomonas_brassicacearum

48 %

*Pseudomonas_fluorescens_F113 % 39

*Pseudomonas_fluorescens_A506

% 18

Spodoptera_exigua_comp1146_c0_seq1 (moth) *Pseudomonas_brassicacearum_NFM421 SRR203141.1048355 10%

*Pseudomonas_syringae_pv__tomato *Pseudomonas_poae_RE*1-1-14 *Pseudomonas_aeruginosa_M18 *Pseudomonas_aeruginosa_DK2 *Pseudomonas_fluorescens_Pf29Arp

*Pseudom onas_sp_ _UW4 *Pseudomonas_fluorescens_ Pf0-1

*Azotobacter_vinelandii_DJ

44% 45%

a

*Pseudomonas_perfectomarina_23S *P_stutzeri_23S_rRNA_gene

do m on *P as _c _a ich er ori ug i_2 3S ino sa _s *P_ fluor tra 4 esce 8% in_ ns_ AU 23S _rR B2 NA

b

45%

*Pseudomonas_aeruginosa_B136-33

*Pseudomonas_stutzeri *Pseudomonas_stutzeri_A1501-1 *Pseudomonas_stutzeri_DSM_4166 *Pseudomonas_stutzeri_ATCC_17588 *Pseudomonas_stutzeri_CCUG_29243

*P se u

*Pseudomonas_stutzeri_RCH2 *Pseudomonas_stutzeri_A1501 *Pseudomonas_putida_KT2440 Rubrobacter_radiotolerans_23S *Pseudomonas_entomophila_L48 *Pseudomonas_putida_F1 *Pseudomonas_putida_W619 *Pseudomonas_putida_BIRD-1 *Pseudomonas_putida_S16 *Pseudomonas_putida_ND6 *Pseudomonas_putida_DOT-T1E *Pseudomonas_putida_HB3267

*P_ chlo rora phi s_2 3S

c

57%

% 74

23%

*Pseudomonas_aeruginosa_NCGM2_S1

ida

*Pseudomonas_syringae_pv__phaseolicola

*Ps eud om ona s_p ut

*Pseudomonas_syringae_pv__tomato_DC3000 *Pseudomonas_aeruginosa_DSM_50071T

*Pse udom onas _prote gens _Pf-5

*Pseudomonas_fluorescens_rrnC

_G B-1

*Pseudomonas_aeruginosa_23S *Pseudomonas_fluorescens_rrnB

*Pseud omona s_me n d o c in *Pseudomon a as_m docin _ymp en a_NKATCC_1386 7 _denitrificans_ *Pseudomonas A S_rRN -X 60% es_23 a_12 lcalign eudoa _fulv *P_ps onas udom *Pse

a

0.02

c

H

BWA LCA: Pseudomonadaceae Blast LCA: Cellular Organism eud

om

ona

s_d

eni

trifi

can

s_A

TC

C_

67

61

138

d %

os

om

as

_s

I p_

55%

s7

3

9A

la s_vio cysti Thio 9 8 %

scen

s

co hylo Met 8 _19 _DSM

ccu

s_

su cap

latu

s_s

tr_B

at h

to sa e as _v en yn th ia e H al om on _h al oc Ha lo m on as

39%

%

J

dii_D

27

elan

%

_v in

36

c ter

%

*A

ba zoto

b

57

85%

N

c

itr

on

*P * Pseu se d o ud mo om na on s_s a s tu _p tze er ri_ fe DS ct om M_ ar 107 in a 01

*Ps

37% cla s tic us_

LW8 P1 is_J sp_ obil ra_m _ 3 01 tene _ v e r s a t i l i s a hylo Met h y l o t e n e r Met

a

SRR061837.18908151 *Pseudomonas_brassicacearum_NFM421 *Pseudomonas_stutzeri_A1501 *Pseudomonas_protegens_Pf-5 *Pseudomonas_syringae_pv_phaseolicola_1448A *Pseudomonas_syringae_pv_tomato_str_DC3000 *Pseudomonas_fluorescens_Pf29Arp *Pseudomonas_poae_RE*1-1-14 *Pseudomonas_stutzeri_RCH2 *Pseudomonas_sp_UW4 *Pseudomonas_stutzeri_CCUG_29243 *Pseudomonas_stutzeri_23S i *Pseudomonas_fluorescens *Pseudomonas_syringae_pv_syringae_B728a *Pseudomonas_fluorescens_SBW25 *Pseudomonas_fluorescens_Pf0-1 Albugo_laibachii_Nc14 (oomycete) *Pseudomonas_stutzeri_DSM_4166 Albugo_laibachii_Alem1 (oomycete) *Pseudomonas_stutzeri_ATCC_17588 *Pseudomonas_fluorescens_F113 *Pseudomonas_fluorescens_A506

clo

0.03

Cy

86%

5 6 % Methylomicrobium_alcaliphilum_20Z

49%

a

b c

d

*Pseudomonas_entomophila_str_L48 *Pseudomonas_mendocina_NK-01 *Pseudomonas_mendocina_ymp *Pseudomonas_fulva_12-X *Pseudomonas_putida_F1 *Pseudomonas_putida_KT2440 *Pseudomonas_putida_HB3267 *Pseudomonas_putida_DOT-T1E *Pseudomonas_putida_ND6 *Pseudomonas_putida_S16 *Pseudomonas_putida_BIRD-1 *Pseudomonas_putida_W619 *Pseudomonas_putida_GB-1 *Pseudomonas_aeruginosa *Pseudomonas_aeruginosa_strain_ATCC_1014 5 *Pseudomonas_aeruginosa_UCBPP-PA14 *Pseudomonas_aeruginosa_PA7 *Pseudomonas_aeruginosa_LESB58 *Pseudomonas_aeruginosa_strain_DB3 *Pseudomonas_aeruginosa_strain_AUB2 *Pseudomonas_aeruginosa_M18 *Pseudomonas_aeruginosa_NCGM2S1 *Pseudomonas_aeruginosa_DK2 *Pseudomonas_aeruginosa_PAO1 *Pseudomonas_aeruginosa_B136-33

I

M_10

44 % 35%

nas_c

a_G

B -1

domo

s_p

utid

*P s e u

ona

b

7 01

om

ri _ D S

eud

s tu tz e

c

*Ps

nas_

8 7 % *Ps eud

domo

39

71

60

%

d

%

16%

%

48%

*P s e u

om ona s_p rot

ege ns_ Pf-5

h lo ro ra

p h is

BWA LCA: Pseudomonadaceae Blast LCA: Pseudomonadaceae

*Pseudom onas_sp_UW 4 *Pseudomonas_fluorescens_Pf0-1

38%

61

*A

zo

t

a ob

ct

er

_v

i

l ne

an

di

i_

%

a

*Pseudom onas_aerugin

osa_ATCC_10145

DJ

0.02

a

*Pseudomonas_aeruginosa_AUB2 *Pseudomonas_fluorescens *Pseudomonas_aeruginosa *Pseudomonas_aeruginosa_UCBPP-PA14 *Pseudomonas_aeruginosa_DB3 *Pseudomonas_fluorescens_A506 *Pseudomonas_aeruginosa_DK2 *Pseudomonas_fluorescens_F113 *Pseudomonas_fluorescens_SBW25 *Pseudomonas_syringae_pv_syringae_UMAF0158 *Pseudomonas_syringae_pv_syringae_B728a *Pseudomonas_cichori i *Pseudomonas_fluorescens *Pseudomonas_poae_RE*1-1-14 SRR061897.14995429 *Pseudomonas_aeruginosa_B136-33 *Pseudomonas_brassicacearum_NFM421 *Pseudomonas_syringae_pv_phaseolicola_1448A *Pseudomonas_syringae_pv_tomato_str_DC3000 *Pseudomonas_aeruginosa_PAO1

b

c

*Pseudomonas_fulva_12-X *Pseudomonas_perfectomarina *Pseudomonas_stutzeri *Pseudomonas_stutzeri_D SM_4166 *Pseudomonas_stutzeri_ATCC_17588 *Pseudomonas_stutzeri_CCUG_29243 *Pseudomonas_stutzeri_RCH2 *Pseudomonas_stutzeri_A1501

d

*Pseudomonas_mendocina_NK-01 *Pseudomonas_mendocina_ymp *Pseudomonas_pseudoalcaligenes *Pseudomonas_denitrificans_ATCC_13867

Rubrobacter_radiotolerans *Pseudomonas_entomophila_str_L4 8 *Pseudomonas_putida_W619 *Pseudomonas_putida_BIRD-1 *Pseudomonas_putida_S16 *Pseudomonas_putida_ND6 *Pseudomonas_putida_DOT-T1E *Pseudomonas_putida_HB3267 *Pseudomonas_putida_KT2440 *Pseudomonas_putida_F1

J

BWA LCA: Pseudomonas Blast LCA: Pseudomonas

Pseudomonas_fluorescens_S BW25 P Aerom Ps seudo o P n s a eudo s_salm eud m m o on om na onas ona s_s _puti icida_sub Ps sp_sa da_H s_s tutz eu lmon B32 tutz eri_ do icida_ 67 eri_ A1 mo A449 AT 501 na C s_ C_ fluo 175 res 88_ ce =_L ns _P MG f29 _11 Arp 199 _c on tig0 96 Ge 16 ob % ac ter _s p_ Az M os 18 pir illu m_ bra sile ns e_ Sp 24 5_ pla sm id_ AZ OB R_ p2

Pseudomonas_putida_GB-1 H2 8 s_stutzeri_RC 000 4 048 Pseudomona C3 str_L _ 6 6 ila rp_contig 9 r_D _Pf29A 3867 ntomophATCC_74166 _st CC_1 e orescens _ _ ato ns_AT nas_ drophila _DSM onas_flu tom ri y omo e nitrifica Pseudom pv_ seud bsp_h stutz as_de P ae_ omon ila_su onas_ Pseud ring droph dom _sy s_hy Pseu mona nas Aero mo udo Pse

K2 8 8 _D 1 5 sa _M SB O1 ino osa _LE PA rug in sa a_ ae rug o os s_ ae gin gin na s_ eru eru mo na _a _a do o as as eu dom on on Ps seu dom om P seu eud P Ps

34 %

Pse Geobudomonas_ flu acter_ sp_M orescens_P Pse f29Arp 21 udo _contig mo 186 nas _fu lva_ 1235 X %

Ps eu do m on as _s yri ng ae De _p su v_ lfo ph vib as rio eo _a lic las ola ke _1 ns is_ 44 P G2 8A se 0 ud om on as _flu ore sc P en Pseudom seudomonas s_ _p on utida_B as_fluor Pseudomona A5 IR es D ce s_stutzeri_DS ns_SBW -1 0 SRR M_10701 25_wsp 061 13% 6 _operon 779 .226 042 37

10% % 10

Geobacter_sulfurreducens_P CA Oceanimonas_sp_GK1

11%

% 17

Des ulfo vibr io_d esu lfuric ans Ha _su hell bsp a_c _de heju sulf ens uric ans is_ _str KC _AT TC CC _23 _27 96 774

ria sicato v_ve tris_p 10331 s e C p A K CF_311018 _cam F ryzae_ onas _pv_ooryzae_MAO99A m e o za th ry Xan omonas_o ryzae_pv__oryzae_PX LS256 o Xanth omonas__o zicola_B zae_pv nth onas ry zae_pv_ory Xaan X thomonas_ory Xanthom

10%

0.04

AzAzos o p A sp iril Br zor irillu lum_ ad hiz m_ bra yrh ob lipo sile izo ium fer nse biu _ca um _Sp m ulin _4B 245 _s o p_ da _pla _main BT ns_ sm _ch OR id_ Ai rom 1 S_ AZO oso 57 _p me 1 5

A7 _P sa ino ug crA A d er DN or_ _a -1_ ept as 472 on _12 RS orec m s_ CC do eticu chem _AT _ um 32C eu n lace H ag aris Ps _vio s_sp_K _m ulg u ium rio _v cter Azoarc vib rio lfo vib oba su ulfo om Chr DeDes 46%

Pseudomonas_fluorescens_Pf29Arp_contig087 acearum_NFM421 cearum_subsp_brassic Pseudomonas_brassica 43 _292 CUG eri_C K9 02 _stutz 2 s a tig n n HLH 0% _co omo sis_ 9 f29Arp seud gen P P n _ s o n k e ng oresc r_ho as_flu te n o c m a b do Lari Pseu RS G6 S J-D E7R S S H _ SJ-D 12RRS e n F lo e_H -B 15 RS S J J e_c _sit _clon _HS SJ-E F1822R e NotI ite -B ing_ otI_s _clon ne_H HSJ 1-H d n P N g_ tI_site _clo ne_ SJ rrou _su o ite lo _H ndin nce rrou ing_N otI_s ite_c one que _su d cl e _se n _s _N c ic n m ou ding NotI ite_ e r o r u n su ge _s seq un ing_ ns_ ic_ otI ce_ urro ie n d m p N e a o n _s qu g_ o_s ou gen ce _se urr din ns_ Hom en _s pie mic un qu ce no se _sa rro e n o _ g u e ic m _s qu Ho ns_ om ce se pie en en ic_ _g _sa qu ns om mo e ie o n s p H e a ic_ _g _s m ns mo no pie Ho ge sa _ _ s n mo pie Ho sa o_ m Ho

07 SI pP m id_ m las 29 ap 16 eg 03m 0 _ 0 07 0 SI tig_ 03 _P n tig1 m _co u con 306 r 4 rp_i_str_ ea R2 A c f29 citr 9 na gii_ s_P pv_ 29-1 287 ola zy _s sy cen is_ ac w1 niania_ oresopoddis_Xcitri_A o t ls to _flu xon opo p_ Ra als onaass_aaxon subs R om n s_ itri_ o a 31% seudthommonnas_c P an tho mo X an ho % t X 6 n 4 56% 43% Xa

52%

% 64

Ps eu do m on as _a er ug ino sa Ps _B eu 13 d Ps omo 6eu na 33 do s_ mo me na nd s_p oc utidina_ Pse a_ NK udo W6 -01 mo 19 nas _flu Pseud ore omona sce 43 Pseudom s_putida_ ns_ % ND Candidatus Pseudom onas_p Pf0 _Accumuli ida_F16 -1 bacter_pho onas_putida_utKT sphatis_clad 2440 6 5 % e_IIA_str_UW -1