Additional File 3: Comparative genome organization of the B genome of B. juncea (B1-B8; present study) and B.nigra (G1-G8) [18].

G7At1g08730Y37bAt1g38230At1g55545UM711bAt4g13590mi291a

0.0

UM711aAgave45a At3g12450At4g34890

2.0

ve39b At3g188105.3At3g03930At3g0474011.0At2g1879011.2At3g28170At5g2774016.0ve53c16.2At2g3708021.0UM711d29.1At3g0581034.0At5g3591437.2At1g5768039.0pO79b40.6At2g26300At3g2329043.1ve39a At1g62670UM611aAt3g1860045.6

pW142b47.6y37a51.2ve45b At3g1245056.6

At3g0702068.6At3g0412069.2At5g15150At3g0220072.6

F

F

Q

D

At C1At C2

At C3At C4At C5

e34t74h7190.0

At3g064838.8

p58m39h4059.9

At1g03910 At3g1312013.2

e45t66v716At3g10572a19.1

At3g17300b At3g15190b26.9e44m38v420At3g18600*27.9

At3g2092030.1

e34m47h10535.1

At5g47890 e47m38h13044.6At5g28750b46.4

At5g2783047.2

At5g2508048.0

At5g6629051.2

At1g57680a53.9At1g58220*a55.3e44m39h13156.7

At3g2398061.6

e35t63v14465.3

p53m42h18869.8

At3g14850*74.3

At3g12260b84.9p33m32h14885.7

At3g09050 At3g08690b*90.7

e58m40h8595.6

At3g13062*109.4

B1

x

F

F

D

Q

v

a

pW180b0.0At1g209605.1ve50a m453a19.1mi185a20.1At1g6978020.6At1g6612021.6pW104a23.6At1g67170 UM511eUM413a25.0

ve3a2 At3g46610y29a d104aL8e7b

26.8

UM573a At5g21170At5g22555 At5g58710At5g57870 At5g58000

27.2

At3g07020 At5g0622028.7At5g14120 At5g07790UM518b At3g30703y33c

29.2

y34b30.9pR115a33.1pN180c35.0At5g1348043.4At5g1378046.3Chs2a47.0c1211a R6C3ave29b48.4

At5g1547048.5At5g1630050.7

L9F10bAt5g1515052.1At3g51070 ve24aAt4g1521053.6

At4g15236 At4g1643055.8At4g1779059.5At4g1933060.2At4g1969062.4At4g2140064.6ve30a66.8At4g2416069.0At3g03600 PG11aAt2g02430 pCeria74.2

At4g3216082.3At2g14810 UM555aUM173a91.0

At4g3489091.3

G5

U

E

R

W

M

N890.0

e62t65h1478.8At1g7598010.5

e62t65h44216.0

N18327.5

At1g68310*b35.2e45m34v19236.6

At4g11790a46.5N1949.0At3g48100*50.0

At3g48540a51.1

GA-N1At4g02425a51.6

At5g1963054.6

e31m62v19956.8At5g2107059.2At4g17050b63.5

e51t78h33566.5

At4g1874068.0

At4g24680 At4g15910a69.3

At5g10460 At4g18150*At4g20410 At3g45100At4g23860 At4g19400At4g21720b At4g16180

At5g07910*At4g16280*

69.8

A19175.3

At4g2749079.4e34m47h309At4g2966083.0

At4g30790a88.0At4g30950*88.9

At4g3113089.7

p33t65v19992.3

p64t66h390At4g33140At4g33100

97.4

At4g33925100.0At4g34140a103.5

At4g34412105.3

At4g34700b e34m62v219106.1At4g36960*a At4g37280*be31m50h174

115.7

At4g39350*b120.7e35t69h736125.9

B2

U

R

M

E

rm

o

p

G8xx0.0pW205a10.0At2g2630015.6ve14a18.0pW130b22.0At2g29320 tai224bAt3g51070At3g46610At3g07460 y29bAt4g04460At4g03490At4g03310ve23aAt4g11800

28.0

At4g02780UM415bAt4g00450At4g0023430.8

ve31cAt2g4762033.0UM165b34.0pDesa UM574f34.4

ve18bAt2g3708039.0pR95bve15ay22b41.1

At4g3263043.2At5g57035pN180dN46.1At5g3926049.0At5g22555At5g59350UM573b55.0

pR115c55.1pN180c58.1

UM559dAt5g1741065.1L21F12a66.5c339a68.6

CHS2bAt5g1378070.1L6G7bAt5g1348074.1

UM177b76.5UM518c78.3y33d79.0At5g0622079.1

O/P

J

W

R

M,N

e47m43h2580.0

At3g54670*a14.6

At3g55005*a e31m47v235h15.6At3g5413017.3

e55t63h137h22.2

At4g0419029.8e34m43v140h32.6

At3g4761036.1

At3g45620*37.4

At3g4361038.8

At4g03150b40.5e46m59v40242.0At4g00585a44.5At4g0131047.3p53m48v22748.3

At4g01897b50.9

At4g1093055.9

At2g26590a At4g1018058.8At4g1005059.6e31m61v23561.2At2g3486062.9

At1g14620a At2g43360At2g44050

68.1

p33m67v370At2g40765a70.7

At2g4153073.2At2g45690b At2g36530*a78.3e50t70v23882.5

At2g0734088.5

At3g47370*90.0

e44m50h29893.1

At4g09820*93.7At4g07666b94.2At5g59140a99.8

e31m42h150103.6At5g17410*108.3

At5g17840108.8

At5g15750110.1p87t77v400113.3At5g13480*113.8At5g13030115.0

p65t71h400125.3

At5g09310a126.9

At5g01220 At5g02120p53t82h195

131.8

B3

N

M

O

P

J

W

R

o

i

a

g

p

m

G6

101.3

102.7

At1g79800 m132bpW130cAt3g52200

0.0

pW180c2.1tai224a3.6UM574b6.4

pW107a17.8

At1g10290At5g39760At5g3926027.0

At5g3584029.1

At5g3543036.2

pW130a50.4At4g1523653.2UM415d pW205b54.0At5g1666057.5ve32a At5g62810UM177a ve2am132a At1g79800UM511f At1g61240At1g07745 At1g50150At1g55545 UM175by22a At3g30703UM710a ve39cve14a ve15bAt2g34150 At1g75130

61.0

pR6a64.5pR95a UM178e68.0At2g3554069.4At2g3708073.0UM173d83.6UM555d83.7pDesc98.5UM574cNAt2g46680 m551aAt4g18050

N

S

X

J

E

A

B4

e31m60v1710.0At1g804601.0At4g137202.7

At4g14110 At4g13940*a4.1

At3g52990*8.6

e31m47v96At3g55430*bAt3g55440*a

12.7

At3g63420*a20.9

At3g53190*b26.5

At3g55005*b27.6

e49m35h803At3g57650*31.2

p48t67h42043.7

p33t65h27554.6

At2g21620b58.5

e31m50v95At1g1674063.5

At1g1537065.9

At2g3208071.9p32m66v12773.2

e44m39v340v82.5At5g6522083.2

At5g63760*90.2

p53t76h342*v97.2

e51t78v71At1g47570105.9

At2g38130*109.9At2g37560111.6

e47m33v212120.4

At2g36930b124.9

wg6d7b133.7

c

T

N

i

A

J

E

X

G1

F

J

C

At3g022000.0At3g03260 At3g039302.0At3g047404.0At3g041206.0

At3g0702017.0y34a21.5pO123a26.0At5g0597034.3pSLG29a35.0At3g13000 y37d42.7pW142a45.3At3g18290 At4g0202054.0At3g1860054.3At5g35430 At4g01580mi2a UM571aAt3g23290 At3g18810At3g22650 m560bY35a At2g23460At2g26300 At1g49750mi291

57.0

At3g5167063.0At1g55545 y36a63.9pN99b64.7At2g29320 ve57a68.0pR95c69.1UM178d71.0va16a At2g3554072.2UM579c pSLR2-5a78.0

pR113a96.0

pDesc106.8At2g46680 At5g50950108.7

B5

p87m38v9120.0

At3g02860 At3g02420b5.7

e48m34v83813.5

At3g12260a21.3

At3g12120*b22.2

At3g15190a28.3

p58t68v30436.1

e60t65h39042.6

e48m34v83749.9

At2g29980*b54.3

e55t73h21557.4

At2g31490c58.1

At2g33400*63.1

p61m44h14564.8

At1g78560*b71.1

e62m33h10774.5

J

F

pUM711c At3g151200.0At5g25330 At5g274701.8At5g277405.3ve53b pW176a6.8At5g2719012.0pO5a20.3At3g2585521.1UM579b23.3ve28a30.0At2g02990 At5g4297030.5At2g03710 At5g46910ve27a

33.8

At1g5768036.8At5g48545 ve31bve23c At1g6124037.0

mi116a40.1UM178a At1g55545At1g49750 UM413c46.5

m241a47.1pW199a At1g09570At1g0951057.0

At1g0957058.5

At1g1696071.3At1g74820 mi203aAt1g1985074.2

y22c80.2At3g07460 m560ave13a At1g31540mi103a At1g70610

82.4

G4

B, A

, C, D

Q

l

V

K

GE-N10.0

e31m62h28811.3

At2g01940*19.4

e31m49v9420.0

At5g5475023.4

At1g6043026.6At1g6178028.3

e62m33h24133.6

At2g20490a34.2

At1g1084041.7

At1g12840b e34m50v205At2g15290

42.5

At2g15430*a43.8

p53t91h25252.6At1g18340b54.5GP-N255.5

At1g18270*56.1

At1g1924056.9p62t78v26560.9

At1g2041063.4

e55t63v22469.1

p48t67v37080.2

At1g49340*b89.3

B6

C

B

A

D

K

w

h

h

At4g18050 pN170a0.0At1g071101.4AtRASa At1g102906.4A322Aa8.5At1g087309.5At1g118709.6pUM511c12.2At1g1578015.8At1g1680018.0pW131b21.8At1g19850 At1g7482023.2At4g3216025.3y33a At2g02430At4g27415 At4g39970UM596a pCerib

29.5

UM413e35.1At3g0396036.5UM178c36.7At1g2797039.3ve16b43.5At4g1969047.7At1g0968050.5At1g2096051.9pUM556b54.7pUM173c m551bAt3g0702058.9

At1g16800At4g23540At4g15210 m51b65.9

UM571cAt1g15020At1g2096068.7

UM178b At3g0396073.0UM413b ve3c

mi2bAt1g7061084.5

UM559bAt1g65730UM515aAt1g67170

86.6

pUM511bAt1g6978088.0UM611c89.0ve50b90.0At1g74820 At1g75130100.7

UM177cAt2g18900102.1At4g18050At2g19030

At2g03710103.1

UM518a104.2At2g14810 pW194b105.2

G3

E

A

B

U

H

UA

B7

At1g02410a0.0

At1g05850*2.4

At1g03330 e31m50v273At1g03180a

3.4

At1g05055 At1g05720a4.3At1g087807.3

At1g0976010.0

p62m59h40011.8

e47m43v84621.9

p64m32v32838.3At1g28530a At1g28560a39.8

At1g2618044.5e50m39h15846.7At1g23180b48.0

At4g34520*b At4g34700a54.6

At1g02090b58.9

At4g20150a62.3

p62t78h18564.3

GP-N171.7

e50m32h20975.7

At1g02090a83.4

At1g01910*85.2e46t65v70885.9

At1g73530*93.2

At1g7186593.9At1g70610*95.7

p79t78v127At1g6866097.4

At1g67170*a102.0At1g67280* At1g79150102.9

p32m66v270108.0

At1g72380b111.1

e39m55h163*v118.5

At1g78560*a121.6

At2g20320*a125.5

a

B

E

A

U

A

H

G2

A

W

R

U

ve2b At1g059100.0

ve6a At1g0711014.0At1g09570 At1g0957019.7At1g1187025.4UM511a At1g6124030.2At1g66120 At4g00234UM571b pR115b32.6

UM515b At5g5703534.1At5g59350 pN180a35.0At5g1741036.6UM573c38.6UM559c L8e7aAt5g17820 At5g17310At5g16300 ve29ac339bN c141a

40.7

L9F10a41.0R17B5a45.6R6C3b46.8Chs2c48.0At5g15470 At5g1378049.0L6G7a At5g1412050.6At5g1147058.1At5g0779070.8At5g0622071.1UM515d76.8At1g5768079.3

ve23bAt5g4412080.1At5g0231082.6At5g4321086.7At3g2585590.1ve27b UM579dAt2g0371091.6

pO5b94.5At4g16430 At4g34460At1g66120 At3g28170At4g19690

99.0

At3g51070 mi271bAt4g17790100.0

ve28b At5g25330At4g21400101.0

At5g27740110.0At3g15120119.0At4g24160119.8At5g27920123.9At4g23250 At5g27190124.0UM555c133.7

V

Q

n

e50m32v292At1g05720b0.0

p33t66v20016.1

At4g15520c23.5

p53t82v36027.5

At2g07690*29.1

At2g1771032.6At2g20760*a33.6At2g22000b36.3

At2g21620a37.7

At2g23090a38.8

e39t74v73340.6

At5g5873043.9e35t63h280At5g2264047.3

At5g1820057.7

At5g15400b64.7

p64m32h25865.8

At5g09310b76.5

p53m42v13977.2

At5g10070 At5g08280b77.7

At5g0492083.6p62m59v465At5g0377085.1

p33m38v26099.7At4g21720a103.8At5g28750a104.7At5g49510 At4g20150cAt4g19140

105.2

At4g18230 e44m39v89106.0

At4g16060a106.6At4g15530107.2At3g51260*b111.6

At3g51010112.8

p48m67h295117.1

GE-N2119.0

At4g07666a120.4At5g24314 At5g24490b122.6e62m32v179126.5At5g27380128.9

At4g25140*b137.6

At4g26240a e44m50h105139.5

p63t78h267149.8

B8

A

t

G

H

I

W

R

q/w

pU

Q

N