PNAS Shailender

1 23

Proceedings of the NationalAcademy of Sciences, India Section B:Biological Sciences ISSN 0369-8211Volume 84Number 1 Proc. Natl. Acad. Sci., India, Sect. B Biol.Sci. (2014) 84:131-143DOI 10.1007/s40011-013-0192-8

Organization and Classification ofCytochrome P450 Genes in Castor (Ricinuscommunis L.)

Maryada Shailendar Kumar, PeramRavindra Babu, Khareedu VenkateswaraRao & Vudem Dashavantha Reddy

1 23

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RESEARCH ARTICLE

Organization and Classification of Cytochrome P450 Genesin Castor (Ricinus communis L.)

Maryada Shailendar Kumar Peram Ravindra Babu

Khareedu Venkateswara Rao Vudem Dashavantha Reddy

Received: 3 December 2012 / Revised: 13 April 2013 / Accepted: 7 May 2013 / Published online: 12 June 2013

The National Academy of Sciences, India 2013

Abstract Castor is an important non-edible oilseed crop

with several industrial applications. Cytochrome P450s

represent*1 % of plant proteome and constitutes one of thelargest family of enzymes controlling primary and secondary

metabolism. Analysis of castor genomic resources identified

210 putative Cytochrome P450 genes. Based on sequence

similarity with Arabidopsis orthologs and CYP nomencla-

ture these genes have been classified into 45 families rep-

resenting 77 subfamilies and grouped into ten clans. Genes

pertaining to ten CYP families (CYP80, CYP92, CYP702,

CYP705, CYP708, CYP728, CYP729, CYP733, CYP736

and CYP749) are not present in the castor genome. Maxi-

mum number (92) of CYP450 genes possessed single intron

followed by intron less genes(35),two intron containing

genes (25) and four intron containing genes (20). Deduced

CYP proteins of castor on an average exhibited 485 amino

acid residues. In general, among the subfamily members

conserved sequences as well as length of exons and phasing

of introns have been observed. However, variable intron

length(s) recorded was attributed to continuous genome

expansion. Distinctive phylogenetic groups of castor CYPs

showed varying levels of conserved gene organization. A

novel gene RcCYPN could be identified in the present study.

Keywords Cytochrome P450 Ricinus communis L. Exonintron phasing Arabidopsis

Introduction

Castor (Ricinus communis L) is an important non-edible oil

seed crop belonging to the family Euphorbiaceae. The

genus Ricinus is monotypic with R. communis as the only

species [1]. Castor is diploid (2n = 20) and is presumed to

be a secondary-balanced polyploid with basic number of

chromosomes x = 5 [2]. The crop is extensively grown in

tropics and sub-tropics as well as temperate regions. Castor

is predominantly cultivated in India, China, Brazil, USSR,

the EEC and Japan. India accounts for nearly 60 % castor

production [3]. Castor bean oil besides its use as vegetable

and medicinal oil has several industrial applications.

Dehydrated castor oil is used in the paint and varnish

industry, manufacture of a wide range of products like

nylon fibre, jet engine lubricants, hydraulic fluids, plastics,

artificial leather, fibre optics, bullet proof glass and bone

prostheses [35]. High level (*90 %) of ricinoleic acidpresent in castor oil contributes to the stable viscosity index

and high lubricity even under low temperature conditions

and hence castor oil is used in the manufacture of anti-

freeze fuels and lubricants for space rockets. The sequence

analysis established genome size of the castor as *320 Mbwith an estimated number of 31,000 genes [6].

Cytochrome P450s(CYPs) represents a large class of

enzymes which mediate diverse metabolic reactions in

almost all organisms such as bacteria, fungi, animals and

plants. Cytochrome P450s have been found to play vital

role in the metabolism and detoxification [7]. CYPs in

various plants are known to perform reactions of both

primary and secondary metabolism and are involved in the

production of fatty acids, sterols, plant hormones, flavo-

noids, terpenoids, lignin and signalling molecules etc.

Cytochrome P450s catalyze oxidation of various substrates

using oxygen and NAD (P) H [8, 9]. Furthermore, these

M. S. Kumar P. R. Babu K. V. Rao V. D. Reddy (&)Centre for Plant Molecular Biology, Osmania University,

Hyderabad 500007, India

e-mail: [email protected]

123

Proc. Natl. Acad. Sci., India, Sect. B Biol. Sci. (JanMar 2014) 84(1):131143

DOI 10.1007/s40011-013-0192-8

Author's personal copy

proteins represent *1 % protein coding genes of any givenorganism [10]. The chemical diversity across plant species

is well correlated with the diversity of CYPs. CYPs are also

responsible for the degradation of endogenous and exoge-

nous compounds which are harmful to plants [11]. In view

of economic importance of castor and the central role of

CYPs in the plant metabolism, the present study has been

mainly focused on structural analysis of CYP genes from

castor and their classification, besides identifying novel

CYP coding genes, if any.

Material and Methods

Castor genome at phytozome v 8.0 database (http://www.

phytozome.net/) was searched for putative Cytochrome

P450 genes and retrieved the predicted protein and nucleo-

tide (CDs and Genomic) sequences. The CYP proteins which

are below 300 and above 600 amino acids were validated by

using Softberry gene prediction tool (http://linux1.softberry.

com/berry.phtml) by increasing the scaffold size to 2,000 bp

upstream of 50 end. Naming of castor CYP genes was carriedout based on similarity with the gene orthologs of Arabid-

opsis. BLASTP analysis of castor proteome with retrieved

CYP protein orthologs was carried out to identify diversified

paralogs, if any.

Multiple sequence alignment of castor CYP proteins

was performed using the UPGMB clustering (Gap opening

-2.9 and gap extension penalty 0), in the MUSCLE

module [12] from the Mega5 software. The Neighbour-

Joining (NJ) tree method by P-distance in MEGA5 [13]

was used to construct the phylogenetic tree. The signifi-

cance level for the NJ analysis of phylogenetic tree using

bootstrap testing with 1,000 replications was carried out.

The alignment of predicted amino acid sequences of

CYPs from the castor with genomic DNA sequence using

Wise2 program (http://www.ebi.ac.uk/Wise2/) was carried

out to identify positions of introns and exons and their

phases. Use of the generated alignments computed the

lengths of introns. Alignment of CYP coding sequences to

genomic sequences using BLAT program was carried out

predicting the number of introns, exonic lengths and total

length of intronic sequences.

Results

Sequence analysis of castor genome disclosed 210 putative

CYP coding genes grouped into ten clans (CYP51, 71, 72, 74,

85, 86, 97, 710,711 and 727) consisting of 45 families rep-

resented by 77 subfamilies (Table 1). The highest number

(123) of the CYP genes are present in the CYP71 clan which

represents the whole set of A-type CYP genes belonging to

18 families, CYP71, CYP73,CYP75, CYP76, CYP77,

CYP78, CYP79, CYP81, CYP82, CYP83, CYP84, CYP89,

CYP93, CYP98, CYP701, CYP703, CYP706, CYP712 and

distributed into 33 subfamilies(Fig. 1). The non-A type CYP

genes (87) are distributed in the other nine clans. Of these, six

clans are single family clans, CYP51, CYP74, CYP97,

CYP710, CYP711 and CYP727. While, remaining three

clans, CYP72, CYP85, and CYP86 are multi-family clans.

The non-A type CYP genes are distributed into 27 families

consisting of 44 subfamilies (Fig. 2). The clan CYP72 con-

taining seven families viz., CYP72, CYP709, CYP714,

CYP715, CYP721, CYP734, and CYP735, possessed 20

genes. The clan CYP85 comprising of 36 genes represent

CYP85, CYP87, CYP88, CYP90, CYP707, CYP716,

CYP718, CYP720, CYP722, and CYP724 families. The clan

86 with CYP86, CYP94, CYP96, and CYP704 families

contain 21 genes. The clan CYP727 present in castor is

absent in the Arabidopsis genome.

The CYP genes in castor code for proteins in the range of

298632 amino acids with an average of 485 residues.

Among the 210 CYP genes, 175 genes are split genes and the

remaining 35 genes are intron less and are present in CYP74,


CYP96 and CYP98 families. Maximum number of ten intron

less genes are seen in the family CYP89 followed by eight

genes in the family CYP94. Only one of the 13 genes in the

CYP82 family is intron less and 11 genes are with single

intron. Maximum number (92) of CYP genes are with single

intron. Except for 8, all single intron containing CYP genes

(84) are grouped into A-type families.

Among the genes (83) with multiple introns, 25 genes

are with two introns followed by 20 with four introns, 14

with eight introns, 7 with seven introns, 5 with three

introns, 4 with nine introns, 3 each with five and six

introns, and single genes each with 13 and 15 introns,

respectively. Among the intron containing genes a total of

670 exons with varied length from 9 to 1,313 bp and a

mean of 385 bp were observed. However the intron length

varied from 26 to 12,217 bp with an average of 328 bp. A

total of 495 introns were recorded in all 175 intron con-

taining CYP genes. Out of them 327 introns exhibited

phase zero. While, an equal number of introns represent

phase one (88) and phase two (80) organization. All the

introns showed canonical GTAG splice sites. About 44 %

castor CYP genes are with single intron. Of the 92 single

intron containing genes majority (87) of them exhibited

phase 0 introns, followed by four genes with phase 1

introns and one gene with phase 2 intron. A-type CYP

genes (123) possessed 130 introns, of which 104 are with

phase zero followed by 18 with phase one and 8 with phase

2. On the other hand non-A-type genes (87) contained 365

introns of which 223 with phase zero, 70 with phase 1 and

72 with phase 2 (Table 1).

132 M. S. Kumar et al.

123


Ta

ble

1O

rgan

isat

ion

of

Cy

toch

rom

eP

45

0g

enes

inca

sto

r

Cas

tor

gen

eID

CY

P

gen

enam

e

Len

gth

of

gen

om

ic

seqs

(bp)

No.

of

Intr

on

(s)

Exon(s

)

size

(bp)

Intr

on

(s)

size

(bp)

Intr

on

(s)

phas

e

Sum

of

intr

on

length

(bp)

No.

of

amin

o

acid

s

CY

P51

clan

30128.m

008568

RcC

YP

51G

12,4

42

1462,9

99

402

0402

486

CY

P72

clan

29739.m

003612

RcC

YP

72A

14

2,0

55

4277,2

21,2

45,3

64,4

26

79,

207,

161,

75

1,0

,2,0

522

510

29633.m

000932

RcC

YP

72A

15

1,7

97

414,1

81,2

45,3

76,4

26

211,1

04,

100,1

40

2,0

,2,0

555

413

29983.m

003136

RcC

YP

72A

16

1,9

19

4274,2

18,2

45,3

79,4

14

80,

99,

109,

101

1,0

,0,1

389

509

29739.m

003779

RcC

YP

72A

17

1,8

99

5103,8

1,2

21,2

45,3

91,4

26

89,

95,

92,

72,

84

1,1

,0,2

,0432

488

29983.m

003138

RcC

YP

72A

18

2,0

96

4259,2

18,2

51,3

79,4

23

210,

102,

153,

101

1,0

,2,0

566

509

30076.m

004534

RcC

YP

709B

23,8

68

4280,1

73,2

51,3

76,4

32

2,0

35,

151,

88,

82

1,0

,2,0

2,3

56

503

29848.m

004472

RcC

YP

714A

13,6

44

4295,2

27,2

54,3

70,4

26

1,2

27,

352,

219,

274

1,0

,2,0

2,0

72

523

29794.m

003364

RcC

YP

714A

23,5

07

4286,2

27,2

51,3

49,4

26

1,0

63,

578,

101,

226

1,0

,2,0

1,9

68

512

27955.m

000386

RcC

YP

714A

32,8

93

4210,

267,

248,

388,

369

112,

126,

109,

235

0,0

,2,0

582

493

29907.m

000622

RcC

YP

714A

42,1

65

4286,2

27,2

45,3

55,4

26

192,

182,

92,1

60

1,0

,2,0

626

512

27955.m

000385

RcC

YP

714A

54,9

96

9301,1

59,9

5,1

68,8

8,4

17,

227,2

51,3

69,3

40

217,

217,

172,

46,

523,

632,

364,

219,

191

1,1

,0,0

,1,1

,0,2

,22,5

81

445

30169.m

006256

RcC

YP

715A

11,9

42

1606,4

26

910

0910

343

30170.m

014009

RcC

YP

721A

14,5

29

4492,2

45,3

64,3

85,3

56

1,0

02,

222,

93,

1,3

70

0,2

,0,1

2,6

87

613

28320.m

001078

RcC

YP

734A

13,2

91

4295,2

24,2

42,3

76,4

53

1,2

06,

86,

131,

278

1,0

,2,0

1,7

01

529

30174.m

009065

RcC

YP

734A

21,9

17

4274,2

24,2

36,3

79,4

29

99,

73,

121,

82

1,0

,2,0

375

513

30174.m

009066

RcC

YP

734A

31,8

84

4289,2

24,2

33,3

76,4

29

91,

77,

88,

77

1,0

,2,0

333

516

30174.m

009067

RcC

YP

734A

42,1

62

4169,2

21,2

33,3

76,4

29

159,

265,

116,

194

1,0

,2,0

734

475

30174.m

009070

RcC

YP

734A

52,1

96

494,2

24,2

33,3

79,4

29

343,

112,

225,

157

1,0

,2,0

837

452

30174.m

009068

RcC

YP

734A

62,1

35

4280,2

24,2

33,3

79,4

29

98,

166,

116,

210

1,0

,2,0

590

514

30205.m

001577

RcC

YP

735A

13,5

33

4274,2

27,2

42,3

79,4

26

120,

186,

564,

1,1

15

1,0

,2,0

1,9

85

515

CY

P74

clan

30170.m

013972

RcC

YP

74A

11,7

96

01,5

57

00

518

29901.m

000415

RcC

YP

74B

26,1

05

2471,3

82,6

38

4,2

65,

262

0,1

4,5

27

496

30910.m

000018

RcC

YP

N1,2

51

01,2

51

00

416

CY

P85

clan

29790.m

000806

RcC

YP

85A

13,1

82

8104,3

22,1

50,2

46,8

7,

79,1

07,1

25,8

8

461,

122,

92,

82,

147,

738,

141,

91

2,0

,0,0

,0,1

,0,2

1,8

74

435

30190.m

011135

RcC

YP

87A

22,5

19

9194,3

22,1

50,2

52,9

0,7

9,

107,1

28,2

56,5

7

114,

84,

232,

100,

82,

110,

78,

58,

26

2,0

,0,0

,0,1

,0,2

,0884

544

27985.m

000878

RcC

YP

87A

42,5

16

8215,3

40,1

50,2

49,9

3,7

9,

118,1

26,9

4

96,

89,

290,

87,

78,

94,

216,

102

2,0

,0,0

,0,1

,2,2

1,0

52

487

30147.m

014292

RcC

YP

87A

58,5

40

8197,3

25,1

50,2

52,

90,7

9,1

07,1

28,9

4

84.

1,4

93,

101,

5,0

56,

110,

91,

95,

88

2,0

,0,0

,0,1

,0,2

7,1

18

473

Organization and Classification of Cytochrome P450 133

123


Ta

ble

1co

nti

nu

ed

Cas

tor

gen

eID

CY

P

gen

enam

e

Len

gth

of

gen

om

ic

seqs

(bp)

No.

of

Intr

on

(s)

Exon(s

)

size

(bp)

Intr

on

(s)

size

(bp)

Intr

on

(s)

phas

e

Sum

of

intr

on

length

(bp)

No.

of

amin

o

acid

s

28448.m

000359

RcC

YP

87A

62,2

27

8197,3

25,1

50,2

52,9

0,

79,1

08,1

28,9

1

100,

159,

103,

96,

91,

84,

107,

67

2,0

,0,0

,0,1

,0,2

807

472

30138.m

003878

RcC

YP

87A

72,3

16

8200,3

28,1

53,2

49,9

0,

79,1

07,1

28,9

4

205,

96,

96,

108,

88,

86,

124,

85

2,0

,0,0

,0,1

,0,2

888

475

30170.m

014356

RcC

YP

87A

82,4

99

8212,3

31,1

50,2

49,9

0,

79,1

07,1

28,9

4

182,

121,

117,

154,

113,

120,

152,

100

2,0

,0,0

,0,1

,0,2

1,0

59

479

27985.m

000880

RcC

YP

87A

92,5

66

7321,1

50,2

49,9

0,7

6,

107,1

28,1

00

184,

200,

99,

538,8

9,

147,8

8

0,0

,0,0

,1,0

,21,3

45

406

29609.m

000602

RcC

YP

87A

10

3,1

25

7200,3

31,1

50,2

49,8

7,

79,1

07,1

32

516,

106,

212,

203,

102,

297,

354

2,0

,0,0

,0,1

,01,7

90

444

29709.m

001228

RcC

YP

88A

43,4

48

7233,4

78,2

70,9

0,7

9,

107,1

22,1

00

1,2

79,

137,

87,

87,

198,

91,

90

2,0

,0,0

,1,0

,21,9

69

492

29634.m

002158

RcC

YP

90B

13,3

58

7203,3

25,1

53,2

34,9

3,

79,1

19,2

34

97,

101,

82,

96,

103,

96,

1,3

43

2,0

,0,0

,0,1

,01,9

18

479

29634.m

002059

RcC

YP

90C

16,5

08

7245,3

25,1

50,2

73,9

7,

125,1

28,1

00

1,7

79,

254,

263,

1,4

24,

642,

420,

283

2,0

,0,0

,1,0

,25,0

65

480

28694.m

000680

RcC

YP

90D

14,8

93

7221,3

25,1

50,2

46,9

0,

186,1

22,1

09

358,

614,

96,

1,0

21,

86,

144,

1,1

21

0,1

,0,0

,0,0

,23,4

44

482

30115.m

001196

RcC

YP

707A

13,7

10

8182,3

22,1

53,2

49,9

0,

79,1

07,1

19,1

12

93,

728,

136,

84,

98,

384,

145,

88

2,0

,0,0

,0,1

,0,2

1,7

56

470

29801.m

003223

RcC

YP

707A

22,1

63

6206,3

19,3

87,1

75,

107,1

19,9

4

106,

159,

94,

129,

105,

163

2,0

,0,1

,0,2

756

468

30170.m

013873

RcC

YP

707A

32,7

90

8194,3

22,1

50,2

04,9

0,

79,1

07,1

19,1

03

96,

164,

103,

158,

107,

482,

96,

216

2,0

,0,0

,0,1

,0,2

1,4

22

455

29801.m

003183

RcC

YP

707A

42,4

10

8206,3

22,1

50,2

49,8

7,

79,1

07,1

19,9

7

127,

190,

95,

94,

106,

105,

178,

98

2,0

,0,0

,0,1

,0,2

994

471

28226.m

000875

RcC

YP

716A

11,6

03

2928,1

88,3

00

94,

93

1,0

187

471

30018.m

000548

RcC

YP

716A

23,1

14

3451,5

04,1

88,3

00

102,

1,3

58,

211

1,1

,01,6

71

480

30152.m

002401

RcC

YP

716A

31,6

17

2943,1

88,3

03

97,

86

1,0

183

477

29728.m

000795

RcC

YP

716A

41,6

49

2961,1

88,2

94

108,

98

1,0

206

480

30074.m

001374

RcC

YP

716A

51,9

35

2958,1

88,3

06

402,

81

1,0

483

483

28226.m

000853

RcC

YP

716B

11,7

11

2946,1

88,3

09

183,

85

1,0

268

480

29776.m

000481

RcC

YP

716C

11,7

33

2940,1

88,2

97

166,

142

1,0

308

474

29776.m

000483

RcC

YP

716C

21,9

92

2931,1

88,3

03

329,

241

1,0

570

473

30063.m

001421

RcC

YP

716D

11,3

03

388,4

56,1

89,1

79

78,

100,

213

1,1

,1391

303

28842.m

000941

RcC

YP

716E

12,9

14

3502,3

72,1

88,3

06

233,

667,

646

1,1

,01,5

46

455

29666.m

001453

RcC

YP

716F

12,3

02

3501,4

42,1

88,3

06

387,

384,

94

0,1

,0865

478

29993.m

001052

RcC

YP

718A

11,8

05

1961,1

79

665

1665

379

30172.m

000208

RcC

YP

720A

12,0

14

6135,2

34,8

4,7

9,

122,1

28,1

15

111,

141,

87,

581,

116,

81

0,0

,0,1

,0,2

1,1

17

298


123


Ta

ble

1co

nti

nu

ed

Cas

tor

gen

eID

CY

P

gen

enam

e

Len

gth

of

gen

om

ic

seqs

(bp)

No.

of

Intr

on

(s)

Exon(s

)

size

(bp)

Intr

on

(s)

size

(bp)

Intr

on

(s)

phas

e

Sum

of

intr

on

length

(bp)

No.

of

amin

o

acid

s

30170.m

014078

RcC

YP

722A

14,0

63

9146,3

22,1

50,1

84,8

0,9

0,

79,1

07,1

19,1

00

108,

1,5

50,

101,

91,

111,1

78,

116,

288,

143

2,0

,0,1

,0,0

,1,0

,22,6

86

458

29634.m

002092

RcC

YP

722A

24,0

67

8260,3

25,1

50,2

52,8

7,

79,1

07,1

19,1

00

217,

628,

289,

87,

455,

106,

95,

723

2,0

,0,0

,0,1

,0,2

,2,5

88

492

29863.m

001089

RcC

YP

722A

32,8

67

8248,3

25,1

50,2

52,8

4,

79,1

07,1

19,1

12

257,

109,

76,

90,

95,

562,

105,

97

2,0

,0,0

,0,1

,0,2

1,3

91

491

29982.m

000224

RcC

YP

722B

12,3

05

8209,3

19,1

53,2

67,

87,7

9,1

07,1

19,9

1

111,

94,

93,

84,

89,

88,

89,

226

2,0

,0,0

,0,1

,0,2

874

476

29633.m

000931

RcC

YP

724A

13,5

69

8200,3

25,1

53,2

43,8

7,

79,1

11,1

36,1

15

187,

227,

86,

183,

99,

158,

831,

349

2,0

,0,0

,0,1

,1,2

2,1

20

482

30005.m

001270

RcC

YP

724A

23,4

04

9221,3

25,1

53,2

46,8

7,

79,1

07,1

22,7

6,1

56

129,

89,

213,

185,

244,

256,

388,

33,

295

2,0

,0,0

,0,1

,0,2

,01,8

32

523

CY

P86

clan

29681.m

001310

RcC

YP

86A

11,5

36

01,5

36

00

511

30190.m

011234

RcC

YP

86A

21,9

21

01,6

38

00

545

30174.m

008617

RcC

YP

86A

32,0

45

1256,1

313

110

1110

522

30094.m

000683

RcC

YP

86B

13,0

62

11260,3

93

1,4

09

01,4

09

550

29929.m

004790

RcC

YP

86C

11,5

63

01,5

63

00

520

30147.m

014517

RcC

YP

94B

11,4

43

01,4

43

00

480

29883.m

002015

RcC

YP

94B

21,4

94

01,4

94

00

497

30190.m

010938

RcC

YP

94B

31,5

30

01,5

30

00

509

29883.m

002017

RcC

YP

94B

41,8

73

01,5

24

00

507

29791.m

000529

RcC

YP

94C

11,5

00

01,5

00

00

499

28779.m

000137

RcC

YP

94C

21,5

06

01506

00

501

29811.m

000531

RcC

YP

94D

11,5

63

01563

00

520

30078.m

002275

RcC

YP

94D

21,5

21

01,5

21

00

506

29917.m

002008

RcC

YP

96A

11,5

30

01,5

30

00

509

29917.m

002010

RcC

YP

96A

21,5

18

01,5

18

00

505

29409.m

000268

RcC

YP

96B

11,5

18

01,5

18

00

505

29660.m

000772

RcC

YP

96B

21,6

13

11,0

86,3

24

203

0203

469

30174.m

008914

RcC

YP

704A

22,0

46

4522,2

85,3

39,

201,1

92

85,

121,

206,

95

0,0

,0,0

507

512

30174.m

008915

RcC

YP

704A

31,5

55

5277,2

6,1

44,9

2,

337,1

68

149,

129,

51,

98,

84

1,0

,0,2

,0511

347

30194.m

000057

RcC

YP

704A

42,6

80

4309,2

16,2

91,

321,4

5

325,

87,

107,

979

0,0

,0,0

1,4

98

394

29813.m

001518

RcC

YP

704B

12,3

45

5330,2

16,2

97,

387,2

01,1

80

179,

104,

99,

219,

133

0,0

,0,0

,0734

536


123


Ta

ble

1co

nti

nu

ed

Cas

tor

gen

eID

CY

P

gen

enam

e

Len

gth

of

gen

om

ic

seqs

(bp)

No.

of

Intr

on

(s)

Exon(s

)

size

(bp)

Intr

on

(s)

size

(bp)

Intr

on

(s)

phas

e

Sum

of

intr

on

length

(bp)

No.

of

amin

o

acid

s

CY

P97

clan

30128.m

009010

RcC

YP

97A

35,1

46

15

139,1

63,2

17,7

2,1

11,

192,1

62,9

6,1

02,3

3,

81,8

3,1

32,6

1,6

6,1

89

81,

107,

111,

89,

581,

128,

276,

68,

328,

116,

100,

713,

233,

148,

168

1,2

,0,0

,0,0

,0,

0,0

,0,0

,2,2

,0,0

3,2

47

632

29724.m

000853

RcC

YP

97B

319,4

69

13

71,1

78,1

08,8

5,2

39,

174,4

8,6

0,8

7,8

9,

92,6

2,1

50,2

25

445,

213,

486,

10,6

65,

1,5

59,

1,6

23,

1,0

29,

192,1

51,

462,

681,

200,

105

2,0

,0,1

,0,0

,0,

0,0

,2,1

,0,0

17,8

01

555

30078.m

002224

RcC

YP

97C

14,3

29

8501,2

97,1

98,1

02,

141,1

08,8

3,1

63,6

6

559,

64,

549,

390,

154,

587,

165,

202

0,0

,0,0

,0,0

,2,0

2,6

70

552

CY

P710

clan

28223.m

000100

RcC

YP

710A

1480

1903,6

15

143

0143

159

CY

P711

clan

29739.m

003566

RcC

YP

711A

13,2

01

4248,1

53,7

84,

96,3

30

630,

593,2

90,

77

2,2

,0,0

1,5

90

536

CY

P727

clan

29686.m

000867

RcC

YP

727A

14,8

86

6208,2

00,6

42,

148,1

27,1

36,7

8

255,

1,1

01,

592,

671,

400,

328

1,0

,0,1

,2,0

3,3

47

512

CY

P71

clan

30147.m

013846

RcC

YP

71A

24

2,4

45

1915,6

12

918

0918

508

30147.m

013842

RcC

YP

71A

25

1,7

20

1915,6

18

187

0187

510

30147.m

013843

RcC

YP

71A

26

1,8

65

1915,6

12

338

0338

508

30147.m

013847

RcC

YP

71A

27

2,5

41

1945,6

21

975

0975

521

30147.m

013848

RcC

YP

71A

28

2,0

61

1963,6

21

477

0477

527

30129.m

000355

RcC

YP

71B

11,6

45

1942,6

15

88

088

518

29724.m

000821

RcC

YP

71B

41,6

62

2123,4

66,3

59

117,

97

0,1

214

315

30169.m

006288

RcC

YP

71B

81,5

60

2157,6

38,6

27

39,

99

1,0

138

473

29785.m

000965

RcC

YP

71B

92,1

85

2666,1

53,6

24

79,

611

0,0

690

480

29785.m

000959

RcC

YP

71B

10

2,5

01

1906,6

24

856

0856

509

29785.m

000962

RcC

YP

71B

11

2,4

75

1906,6

24

892

0892

509

29826.m

000757

RcC

YP

71B

13

1,6

78

1945,6

54

79

079

532

30169.m

006277

RcC

YP

71B

14

1,7

34

1996,6

09

129

0129

534

29887.m

000239

RcC

YP

71B

22

1,6

15

1882,6

21

112

0112

500

29910.m

000943

RcC

YP

71B

23

1,7

92

1897,6

27

268

0268

507

29878.m

000239

RcC

YP

71B

24

1,8

10

3477,2

6,1

99,6

15

101,

137,

255

0,

2,

0493

438

29887.m

000240

RcC

YP

71B

25

1,7

54

1882,6

21

251

0251

500

29887.m

000241

RcC

YP

71B

26

1,6

47

1894,6

21

132

0132

504

30169.m

006273

RcC

YP

71B

27

1,6

16

1906,6

15

95

095

506

30169.m

006275

RcC

YP

71B

28

1,6

08

1891,6

15

102

0102

501


123


Ta

ble

1co

nti

nu

ed

Cas

tor

gen

eID

CY

P

gen

enam

e

Len

gth

of

gen

om

ic

seqs

(bp)

No.

of

Intr

on

(s)

Exon(s

)

size

(bp)

Intr

on

(s)

size

(bp)

Intr

on

(s)

phas

e

Sum

of

intr

on

length

(bp)

No.

of

amin

o

acid

s

30169.m

006279

RcC

YP

71B

29

1,7

29

1957,6

15

157

0157

523

30169.m

006282

RcC

YP

71B

30

1,6

16

1885,6

09

122

0122

497

30169.m

006285

RcC

YP

71B

31

1,6

95

1990,6

12

93

093

533

29792.m

000625

RcC

YP

71B

36

1,7

47

2862,6

3,6

14

124,

84

1,1

208

512

29929.m

004561

RcC

YP

71B

37

1,7

84

1903,6

12

269

0269

504

29629.m

001350

RcC

YP

71B

38

1,6

32

1891,6

09

132

0132

499

29629.m

001392

RcC

YP

71B

39

1,6

32

1900,6

24

108

0108

507

29929.m

004562

RcC

YP

71B

40

1,7

25

1951,6

24

150

0150

524

29792.m

000626

RcC

YP

71B

41

2,3

39

1906,6

09

824

0824

504

30142.m

000643

RcC

YP

71B

42

1,3

91

2894,1

74,2

1250,

52

0,0

302

362

29792.m

000624

RcC

YP

71C

12,9

96

1906,6

18

1,4

72

01,4

72

507

30206.m

000783

RcC

YP

71C

2981

1903,1

266

066

304

29785.m

000966

RcC

YP

71C

32,8

15

2903,

510,

87

280,

1,0

35

0,0

1,3

15

499

29929.m

004748

RcC

YP

71D

12,3

99

1927,6

36

723

0723

520

29976.m

000504

RcC

YP

73A

53,5

76

2785,

134,

599

176,

1,5

25

2,1

1,7

01

505

43540.m

000048

RcC

YP

73A

61,9

73

1875,

736

362

2362

536

30138.m

003983

RcC

YP

75B

13,1

30

2282,4

53,6

51

891,

853

0,0

1,7

44

461

30146.m

003563

RcC

YP

75B

22,1

39

1942,6

24

573

0573

521

29706.m

001271

RcC

YP

75B

32,2

10

1906,6

30

547

0547

511

29739.m

003754

RcC

YP

75B

41,7

22

1942,6

24

156

0156

521

30190.m

011068

RcC

YP

76C

31,3

13

1889,2

45

179

1179

377

30190.m

011069

RcC

YP

76C

41,7

94

1900,6

06

84

084

501

30147.m

014296

RcC

YP

76D

11,6

12

1882,6

09

121

0121

496

30169.m

006290

RcC

YP

76D

21,6

33

1885,6

06

142

0142

496

30169.m

006295

RcC

YP

76D

31,4

56

1906,5

1499

0499

318

30169.m

006291

RcC

YP

76D

41,4

91

2391,

285,

605

97,

113

1,1

210

426

30190.m

011130

RcC

YP

76E

11,6

82

1879,6

27

176

0176

501

29815.m

000508

RcC

YP

76G

12,6

15

1927,6

51

1,0

37

01,0

37

525

29815.m

000509

RcC

YP

76G

22,0

13

1915,6

30

468

0468

514

29815.m

000510

RcC

YP

76H

12,0

65

1900,6

09

556

0556

502

29815.m

000512

RcC

YP

76H

21,9

44

2473,4

45,6

21

93,

312

2,0

405

512

29815.m

000515

RcC

YP

76I1

1,6

82

1960,6

15

107

0107

524

29815.m

000516

RcC

YP

76I2

1,6

79

1939,5

91

149

0149

509

29815.m

000519

RcC

YP

76I3

1,7

01

1930,6

18

153

0153

515

29815.m

000520

RcC

YP

76I4

1,6

73

1930,6

15

128

0128

514

29428.m

000318

RcC

YP

77A

41,5

96

01,5

96

00

531

29842.m

003625

RcC

YP

77B

11,5

18

01,5

18

00

505


123


Ta

ble

1co

nti

nu

ed

Cas

tor

gen

eID

CY

P

gen

enam

e

Len

gth

of

gen

om

ic

seqs

(bp)

No.

of

Intr

on

(s)

Exon(s

)

size

(bp)

Intr

on

(s)

size

(bp)

Intr

on

(s)

phas

e

Sum

of

intr

on

length

(bp)

No.

of

amin

o

acid

s

29842.m

003626

RcC

YP

77B

21,5

29

01,5

18

00

505

28014.m

000118

RcC

YP

78A

61,1

80

1405,6

18

157

0157

340

28256.m

000134

RcC

YP

78A

71,6

94

1999,6

03

92

092

533

28644.m

000933

RcC

YP

78A

81,7

08

1996,6

18

94

094

537

30068.m

002578

RcC

YP

78A

91,9

50

1960,6

36

349

0349

531

30138.m

003950

RcC

YP

78A

10

2,0

45

1783,6

06

533

0533

462

29929.m

004656

RcC

YP

78A

11

2,7

26

1963,5

97

1,1

66

01,1

66

519

29910.m

000911

RcC

YP

79A

21,1

73

01,1

73

00

390

29910.m

000917

RcC

YP

79B

31,0

71

1981,9

81

081

329

29910.m

000914

RcC

YP

79B

41,1

13

01,1

13

00

370

28438.m

000050

RcC

YP

79B

71,0

17

01,0

17

00

338

29970.m

001003

RcC

YP

81D

23,2

53

2272,4

69,6

18

149,

1,7

45

2,0

1,8

94

452

29910.m

000948

RcC

YP

81D

33,0

26

1918,6

36

1,4

72

01,4

72

517

30170.m

014208

RcC

YP

81D

42,3

11

1930,6

15

766

0766

514

29970.m

001002

RcC

YP

81D

82,5

84

1891,6

21

1,0

72

01,0

72

503

30170.m

013774

RcC

YP

81D

91,9

36

1903,6

27

406

0406

509

30170.m

013773

RcC

YP

81D

10

2,1

27

1882,6

21

624

0624

500

30170.m

013780

RcC

YP

81D

11

1,6

73

1903,6

12

158

0158

504

29970.m

000998

RcC

YP

81H

113,1

77

1327,6

33

12,2

17

012,2

17

319

30170.m

014207

RcC

YP

81K

11,7

90

1897,6

21

187

0187

505

29851.m

002485

RcC

YP

82C

2963

0963

00

320

30170.m

013958

RcC

YP

82C

31,6

99

1954,6

33

112

0112

528

30170.m

013953

RcC

YP

82C

41,7

85

2400,4

64,6

24

90,

207

1,0

297

495

30120.m

000372

RcC

YP

82C

52,7

36

1951,6

27

1,1

58

01,1

58

525

30170.m

013957

RcC

YP

82C

61,6

46

1927,6

66

53

053

530

30170.m

013963

RcC

YP

82C

72,1

46

1945,6

21

580

0580

521

29676.m

001679

RcC

YP

82C

82,2

87

1939,6

27

721

0721

521

30170.m

013949

RcC

YP

82C

91,8

48

1948,6

33

267

0267

526

30170.m

013950

RcC

YP

82C

10

1,6

94

1948,6

24

122

0122

523

30170.m

013960

RcC

YP

82C

11

3,1

08

1945,6

21

1,5

42

01,5

42

521

30170.m

013964

RcC

YP

82C

12

2,2

23

1939,6

30

654

0654

522

30170.m

013965

RcC

YP

82C

13

1,7

32

1963,6

24

145

0145

528

30120.m

000371

RcC

YP

82G

12,6

84

1942,6

30

1,1

12

01,1

12

523

30170.m

014153

RcC

YP

83B

11,6

11

1885,6

09

117

0117

497

30170.m

014151

RcC

YP

83B

31,7

97

1879,6

12

306

0306

496

30174.m

009168

RcC

YP

83B

42,3

31

1714,6

12

1,0

05

01,0

05

441

30131.m

007121

RcC

YP

84A

1942

0942

00

313


123


Ta

ble

1co

nti

nu

ed

Cas

tor

gen

eID

CY

P

gen

enam

e

Len

gth

of

gen

om

ic

seqs

(bp)

No.

of

Intr

on

(s)

Exon(s

)

size

(bp)

Intr

on

(s)

size

(bp)

Intr

on

(s)

phas

e

Sum

of

intr

on

length

(bp)

No.

of

amin

o

acid

s

28196.m

000205

RcC

YP

84A

21,6

61

1903,6

15

143

0143

505

30138.m

003926

RcC

YP

84A

32,6

29

1714,8

22

1,0

93

01,0

93

511

30174.m

008711

RcC

YP

84A

41,7

83

1675,8

28

277

0277

501

29827.m

002605

RcC

YP

89A

41,5

51

01,5

51

00

516

30148.m

001481

RcC

YP

89A

51,5

51

01,5

51

00

516

30073.m

002236

RcC

YP

89A

61,6

01

01,5

63

00

520

30148.m

001477

RcC

YP

89A

71,5

75

01,5

75

00

524

30148.m

001478

RcC

YP

89A

81,5

42

01,5

42

00

513

30148.m

001476

RcC

YP

89A

91,5

51

01,5

45

00

514

30148.m

001482

RcC

YP

89A

10

1,5

68

01,5

57

00

518

30148.m

001475

RcC

YP

89A

11

1,5

03

01,5

03

00

500

30148.m

001483

RcC

YP

89A

12

1,5

45

01,5

45

00

514

29083.m

000045

RcC

YP

89B

11,7

38

01,1

73

00

390

29216.m

000256

RcC

YP

93D

12,3

80

1811,6

71

898

1898

493

29216.m

000255

RcC

YP

93D

22,4

34

1802,4

28

1,2

04

11,2

04

409

30152.m

002423

RcC

YP

93D

33,0

31

216,9

59,6

66

157,

1,2

33

1,0

1,3

90

546

29788.m

000321

RcC

YP

93D

41,2

96

1891,1

11

294

0294

333

29788.m

000323

RcC

YP

93D

52,2

30

2609,2

31,6

81

70,

639

0,0

709

506

29940.m

000401

RcC

YP

98A

33,5

83

2493,3

98,6

45

1,5

74,

335

1,0

1,9

09

511

30147.m

014117

RcC

YP

98A

41,5

36

01,5

36

00

511

29940.m

000400

RcC

YP

98A

54,4

72

2178,3

98,6

12

2,3

11,

973

1,0

3,2

84

395

30170.m

013942

RcC

YP

701A

32,9

88

7154,

160,

163,1

40,

258,

158,

195,

314

185,

824,

102,

93,

85,

84,

83

1,2

,0,2

,2,1

,11,4

56

513

29742.m

001406

RcC

YP

703A

21,8

88

1909,6

39

340

0340

515

30190.m

011008

RcC

YP

706A

41,7

05

1960,6

33

112

0112

530

30190.m

011007

RcC

YP

706A

53,8

20

1936,6

21

2,1

16

02,1

16

518

30147.m

014189

RcC

YP

706A

71,6

94

2894,2

35,3

47

172,

46

0,1

218

491

29216.m

000258

RcC

YP

712A

11,9

67

1912,6

30

425

0425

513

27647.m

000174

RcC

YP

712A

23,1

53

1939,6

18

1,2

81

01,2

81

518

29216.m

000257

RcC

YP

712B

12,1

51

1921,6

30

600

0600

516


123


Comparative analysis of CYPs revealed that the families,


CYP707, CYP715, CYP718, CYP721, and CYP735 represent

conserved number of genes between the genomes of castor

and Arabidopsis. As compared to Arabidopsis, castor genome

exhibited an additional gene in the families CYP73, CYP704,

and CYP712.The families CYP83, and CYP84 exhibited two

additional genes in castor as compared to the Arabidopsis.

Similarly CYP93 family showed five genes against one in

Arabidopsis. Arabidopsis CYP716 family showed two genes

(A1 and A2) while castor displayed 11 genes viz., orthologs

A1, and A2, and nine paralogs (A3, A4, A5, B1, C1, C2, D1,

E1 and F1). The family CYP87 consist of 1 gene (A2) in

Arabidopsis whereas 8 genes (A2, A4, A5, A6, A7, A8, A9,

and A10) were recorded in the castor genome. About twofold

amplification of genes is observed in the families, CYP76,

AtC

YP7

1B21 22B17P

YCt

A AtC

YP7

1B38

PA

tCY

P71B

5A

tCY

P71B

30P

AtC

YP7

1B32

AtC

YP7

1B31

AtC

YP7

1B8

AtC

YP7

1B23

AtC

YP71

B7 AtCY

P71B

15A

tCYP

71B2

8A

tCYP

71B2

9A

tCYP

71B2

AtCY

P71B

27At

CYP7

1B16

AtCY

P71B

17At

CYP7

1B19

AtCY

P71B

20At

CYP7

1B24

AtCY

P71B

3At

CYP7

1B25

AtCY

P71B

4At

CYP7

1B11

AtCY

P71B

12At

CYP7

1B13

AtCY

P71B

14

AtCY

P71B

6

AtCY

P71B

26

AtCY

P71B

33

AtCY

P71B

34

AtCY

P71B

35

AtCY

P71B

9

AtCY

P71B

36

AtCY

P71B

37

AtCY

P71B

10

RcCY

P71B

36-29

792.m

0006

25

RcCY

P71B

41-297

92.m0

00626

RcCY

P71B

42-301

42.m0

00643

RcCY

P71C

1-2979

2.m000

624

RcCY

P71B

9-2978

5.m000

965

RcCY

P71B1

0-2978

5.m000

959

RcCY

P71B1

1-2978

5.m000

962

RcCY

P71C2

-30206

.m0007

83

RcCY

P71C3

-29785

.m0009

66

AtCYP

83A1

AtCYP

83B1

RcCYP8

3B1-301

70.m014

153

RcCYP8

3B3-301

70.m014

151

RcCYP8

3B4-301

74.m009

168

RcCYP7

1B1-301

29.m000

355

RcCYP7

1A25-30

147.m01

3842

RcCYP7

1A26-30

147.m01

3843

RcCYP7

1A24-30

147.m01

3846

RcCYP7

1A27-301

47.m0138

47

RcCYP71

A28-3014

7.m01384

8

AtCYP71A

21

AtCYP71A

22

AtCYP71A

24

AtCYP71A2

6

AtCYP71A23

AtCYP71A25

AtCYP71A12

AtCYP71A13

AtCYP71A18

AtCYP71A19

AtCYP71A20

AtCYP71A16AtCYP71A27

AtCYP71A28


RcCYP71D1-29929.m004748RcCYP71B13-29826.m000757

RcCYP71B38-29629.m001350RcCYP71B39-29629.m001392RcCYP71B23-29910.m000943RcCYP71B24-29878.m000239RcCYP71B8-30169.m006288RcCYP71B37-29929.m004561RcCYP71B40-29929.m004562

RcCYP71B27-30169.m006273RcCYP71B29-30169.m006279

RcCYP71B22-29887.m000239RcCYP71B25-29887.m000240

RcCYP71B26-29887.m000241RcCYP71B14-30169.m006277

RcCYP71B31-30169.m006285RcCYP71B4-29724.m000821

RcCYP71B28-30169.m006275

RcCYP71B30-30169.m006282

AtCYP84A1

RcCYP84A1-30131.m007121

AtCYP84A4

RcCYP84A2-28196.m000205

RcCYP84A3-30138.m003926

RcCYP84A4-30174.m008711

RcCYP75B3-29706.m001271

RcCYP75B2-30146.m003563

RcCYP75B4-29739.m003754

AtCYP705A16

AtCYP705A19

AtCYP705A23

AtCYP705A20


AtCYP705A4


AtCYP705A5

AtCYP705A2

AtCYP705A32

AtCYP705A28

AtCYP705A30

AtCYP705A22

AtCYP705A3

AtCYP705A6

AtCYP705A18

AtCYP705A33

AtCYP705A13

AtCYP705A12

AtCYP705A1

AtCYP705A24

AtCYP705A25

AtCYP705A27

AtCYP712A1

RcCYP712A1-29216.m000258

RcCYP712B1-29216.m000257

AtCYP712A2

RcCYP712A2-27647.m000174

RcCYP93D4-29788.m

000321

RcCYP93D5-29788.m

000323

RcCYP93D3-30152.m

002423

AtCYP93D1

RcCYP93D1-29216.m

000256

RcCYP93D2-29216.m

000255

AtC

YP82

C2A

tCYP

82C3

AtC

YP8

2C4

RcC

YP8

2C4-

3017

0.m

0139

53R

cCY

P82C

10-3

0170

.m01

3950

RcC

YP8

2C9-

3017

0.m

0139

49R

cCY

P82C

3-30

170.

m01

3958

RcC

YP8

2C6-

3017

0.m

0139

57R

cCY

P82C

11-3

0170

.m01

3960369310

m. 07103

- 7C28P

YCc

R469310

m. 0 7103

-2 1C28P

YCc

R569310

m.07103

-31C28P

YCc

RA

tCY

P82G

1

RcC

YP8

2G1-

3012

0.m

0003

71

RcC

YP8

2C2-

2985

1.m

0024

85R

cCY

P82C

5-30

120.

m00

0372

AtC

YP8

2F1

RcC

YP8

2C8-

2967

6.m

0016

79

AtC

YP8

1K1

AtC

YP81

K2

RcC

YP81

K1-

3017

0.m

0142

07

RcC

YP81

D10-

3017

0.m

0137

73

RcC

YP81

D9-3

0170

.m01

3774

RcC

YP81

D11-

3017

0.m

0137

80

RcC

YP81

D4-3

0170

.m01

4208

AtCY

P81G

1

AtCY

P81F

1

AtCY

P81F

2

AtCY

P81F

3

AtCY

P81F

4

RcCY

P81D

2-29

970.m

0010

03

RcCY

P81D

8-29

970.m

0010

02

RcCY

P81D

3-29

910.m

0009

48

RcCY

P81H

1-29

970.m

0009

98

AtCY

P81H

1

AtCY

P81D

1

AtCY

P81D

6

AtCY

P81D

7

AtCY

P81D

11

AtCY

P81D

4

AtCY

P81D

5

AtCY

P81D

10P

AtCY

P81D

8

AtCY

P81D

2

AtCY

P81D

3At

CYP7

5B1

RcCY

P75B

1-301

38.m

0039

83

AtCY

P706A

5

AtCY

P706A

6

AtCY

P706A

4

AtCY

P706A

3

AtCYP

706A7

RcCY

P706A

5-3019

0.m011

007

AtCYP

706A1

AtCYP

706A2

RcCYP

706A4-

30190.

m0110

08

RcCYP

706A7-

30147.m

014189AtC

YP76C

2

AtCYP7

6C4AtCYP7

6C1

AtCYP7

6C5AtCYP7

6C6AtCYP7

6C3AtCYP7

6C7

RcCYP7

6C3-3019

0.m01106

8RcC

YP76C4-3

0190.m01

1069

RcCYP76D

2-30169.m

006290

RcCYP76D

3-30169.m0

06295RcCY

P76D1-301

47.m014296

RcCYP76D4

-30169.m006

291

RcCYP76E1

-30190.m011

130RcCYP

76G1-29815.m

000508

RcCYP76G2-2

9815.m000509

AtCYP76G1

RcCYP76H1-2981

5.m000510

RcCYP76H2-29815

.m000512RcCYP76I1-29815.m00

0515RcCYP76I2-29815.m0005

16RcCYP76I3-29815.m000519Rc

CYP76I4-29815.m000520

AtCYP78A6AtCYP78A9

AtCYP78A8RcCYP78A6-28014.m000118

RcCYP78A9-30068.m002578RcCYP78A11-29929.m004656

AtCYP78A5AtCYP78A10

RcCYP78A10-30138.m003950AtCYP78A7

RcCYP78A7-28256.m000134

RcCYP78A8-28644.m000933AtCYP98A3

RcCYP98A3-29940.m000401

RcCYP98A5-29940.m000400

RcCYP98A4-30147.m014117

AtCYP98A8

AtCYP98A9

RcCYP73A6-43540.m000048

AtCYP73A5

RcCYP73A5-29976.m000504

AtCYP701A3

RcCYP701A3-30170.m013942AtCYP77A4

AtCYP77A6

AtCYP77A7

AtCYP77A9

RcCYP77A4-29428.m000318

RcCYP77B2-29842.m003626

AtCYP77B1

RcCYP77B1-29842.m003625

RcCYP89B1-29083.m000045

RcCYP89A4-29827.m002605

AtCYP89A9

AtCYP89A4

AtCYP89A5

AtCYP89A6

AtCYP89A7

AtCYP89A2

AtCYP89A3

RcCYP89A10-30148.m001482

RcCYP89A11-30148.m001475

RcCYP89A6-30073.m002236

RcCYP89A12-30148.m001483

RcCYP89A5-30148.m001481

RcCYP89A7-30148.m001477

RcCYP89A8-30148.m001478

RcCYP89A9-30148.m001476

AtCYP703A2

RcCYP703A2-29742.m001406

AtCYP79C1

AtCYP79C2AtCYP79F1

AtCYP79F2AtCYP79B2

AtCYP79B3AtCYP79A2

RcCYP79B7-28438.m000050

RcCYP79A2-29910.m000911

RcCYP79B3-29910.m000917

RcCYP79B4-29910.m

000914

0.1

Fig. 1 Phylogenetic tree of A-type Cytochrome P450 proteins of castor and Arabidopsis. Rc and At represent CYP proteins of castor andArabidopsis, respectively


123


CYP82 and CYP89 of castor as compared to Arabidopsis. The

gene families CYP71, CYP72, CYP77, CYP79, CYP81,

CYP86, CYP90, CYP96, CYP706, CYP709, and CYP710 of

castor exhibited less number of genes as compared to Ara-

bidopsis. A single intron containing non-A-type castor gene

RcCYPN coding for 416 amino acids (Table 1) exhibited

42.5 % similarity and 30.8 % identity with RcCYP74A1

gene. However phylogenetic tree displayed distinct projection

of this gene from CYP74 family (Fig. 2).

Discussion

The present study on the genome analysis of castor revealed

the presence of 210 putative CYP genes belonging to 45

families, grouped into ten clans. CYP450 genes identified in

castor represent*0.68 % of the predicted*31,000 proteincoding genes. The observation is in conformity with CYPs

representing 0.571.07 % of the protein coding genes of

Arabidopsis (246/23,000), rice (356/37,544) [14], poplar

AtC

YP9

4B1

AtC

YP9

4B3

RcC

YP9

4B1-

3014

7.m

0145

17R

cCY

P94B

3-30

190.

m01

0938

AtC

YP9

4B2

RcC

YP9

4B2-

2988

3.m

0020

15R

cCYP

94B4

-298

83.m

0020

17A

tCYP

94C1

RcC

YP94

C1-2

9791

.m00

0529

RcC

YP94

C2-2

8779

.m00

0137

RcC

YP94

D1-2

9811

.m00

0531

RcCY

P94D

2-30

078.m

0022

75

AtCY

P94D

1At

CYP9

4D2

AtCY

P704

B1Rc

CYP7

04B1

-298

13.m

0015

18

RcCY

P704

A4-3

0194

.m00

0057

AtCY

P704

A1At

CYP7

04A2

RcCY

P704

A2-30

174.m

0089

14

RcCY

P704

A3-30

174.m

0089

15

AtCY

P86A

2

AtCY

P86A

4

AtCY

P86A

8

RcCY

P86A

3-3017

4.m008

617

RcCY

P86A

2-3019

0.m011

234

AtCYP

86A7

AtCYP

86A1

RcCY

P86A1

-29681

.m0013

10

AtCYP

86B1

AtCYP

86B2

RcCYP8

6B1-300

94.m000

683

AtCYP8

6C1

RcCYP8

6C1-299

29.m0047

90

AtCYP8

6C2

AtCYP86C

3

AtCYP86C

4

RcCYP96B

2-29660.m0

00772

RcCYP96A

1-29917.m0

02008

RcCYP96A2

-29917.m0020

10

RcCYP96B1-2

9409.m000268

AtCYP96A3

AtCYP96A4

AtCYP96A15

AtCYP96A10

AtCYP96A9

AtCYP96A1

AtCYP96A5

AtCYP96A7

AtCYP96A8AtCYP96A13

AtCYP96A12AtCYP96A11AtCYP96A2AtCYP97A3RcCYP97A3-30128.m009010AtCYP97B3RcCYP97B3-29724.m00085

AtCYP97C1RcCYP97C1-30078.m002224RcCYP710A1-28223.m000100

AtCYP711A1RcCYP711A1-29739.m003566

RcCYP727A1-29686.m000867


RcCYP714A1-29848.m004472

RcCYP714A2-29794.m003364

RcCYP714A4-29907.m000622

RcCYP714A3-27955.m000386RcCYP714A5-27955.m000385

AtCYP715A1

RcCYP715A1-30169.m006256

AtCYP735A1

AtCYP735A2

RcCYP735A1-30205.m001577

AtCYP709B1

AtCYP709B2

AtCYP709B3

RcCYP709B2-30076.m004534

RcCYP734A4-30174.m009067

RcCYP734A6-30174.m009068

RcCYP734A5-30174.m009070

RcCYP734A2-30174.m009065

RcCYP734A3-30174.m

009066

AtCYP721A1

RcCYP721A1-30170.m

014009

AtCYP734A1

RcCYP734A1-28320.m

001078

RcCYP72A16-29983.m

003136

RcC

YP72A

18-29983.m003138

AtC

YP72C

1

RcC

YP72A

14-29739.m003612

RcC

YP72A

17-29739.m003779

2390

00m.

3369

2-51

A27P

YCc

R8

A27P

YCt

AAtC

YP72A

7A

tCY

P72A9

AtC

YP72A

14A

tCY

P72A10

AtC

YP72A

15A

tCYP72A11A

tCYP72A13AtCY

P710

A1

AtCY

P710

A2

AtCY

P710

A3

AtCY

P710

A4

AtCY

P51G

2

AtCY

P51G

1

RcCY

P51G

1-30

128.m

0085

68

RcCY

P716

A1-2

8226

.m00

0875

RcCY

P716

A2-3

0018

.m00

0548

RcCY

P716

A3-30

152.m

0024

01

AtCY

P716

A1

AtCY

P716

A2

RcCY

P716

A4-29

728.m

0007

95

RcCY

P716

A5-30

074.m

0013

74

RcCY

P716

B1-28

226.m

0008

53

RcCY

P716

C2-29

776.m

0004

83

RcCY

P716C

1-2977

6.m000

481

RcCY

P716D

1-3006

3.m001

421

RcCY

P716E

1-2884

2.m000

941

RcCY

P716F1

-29666

.m0014

53AtC

YP718

RcCYP

718A1-

29993.m

001052

AtCYP

707A1AtC

YP707A

3

RcCYP7

07A2-29

801.m0

03223

AtCYP7

07A2

RcCYP7

07A1-30

115.m00

1196AtCYP

707A4

RcCYP707

A3-30170

.m013873

RcCYP707A

4-29801.m0

03183

RcCYP88A4

-29709.m001

228AtCYP

88A3AtCYP

88A4RcCYP722B1

-29982.m000224

AtCYP722A1RcCYP722A

1-30170.m014078Rc

CYP722A2-29634.m002092

RcCYP722A3-29863.m001089

AtCYP724A1RcCYP724A1-29633.m000931

RcCYP724A2-30005.m001270

AtCYP90B1

RcCYP90B1-29634.m002158

AtCYP90A1

AtCYP90C1

RcCYP90C1-29634.m002059

AtCYP90D1

RcCYP90D1-28694.m000680

AtCYP720A1

RcCYP720A1-30172.m000208

RcCYP85A1-29790.m000806

AtCYP85A1

AtCYP85A2

RcCYP87A4-27985.m000878

RcCYP87A9-27985.m000880

RcCYP87A7-30138.m003878

RcCYP87A8-30170.m014356

RcCYP87A10-29609.m000602

AtCYP87A2

RcCYP87A2-30190.m011135

RcCYP87A5-30147.m014292

RcCYP87A6-28448.m000359

AtCYP708A2

AtCYP708A3AtCYP708A4AtCYP708A1




RcCYPN-30910.m000018

AtCYP74A

RcCYP74A1-30170.m013972 AtCYP74B2

RcCYP74B2-29901.m

000415

0.2

Fig. 2 Phylogenetic tree of non-A-type Cytochrome P450 proteins of castor and Arabidopsis. Rc and At represent CYP proteins of castor andArabidopsis, respectively


123


(310/45,654) [15], grape (315/30,434), papaya (142/24,746)

[16], soybean (332/46,500) [17] and flax (334/47,900) [18].

After excluding CYP702 and CYP708 genes which are

specific to model plant, the remaining CYP genes in Ara-

bidopsis are comparable to the number of CYP genes in

castor. Most of the CYP450 families in castor possessed

basic set of genes indicating the absence of gene amplifica-

tion which is prevalent in other plant systems. These results

are in conformity with the earlier report indicating the

absence of whole genome duplication in castor. However,

morphological differences observed between the polymor-

phic forms were attributed to differences in genes, cryptic

inversions, etc., rather than to changes in the whole chro-

mosome complement [19]. About 83 % of both A-type and

non-A-type CYP genes are split genes, while remaining

17 % sans introns indicate that the ancestral CYP gene

contains intron(s). Occurrence of more number of A-type

(123) CYP genes as compared to non-A-type (87) in castor

implicates to the rapid expansion of A-type CYP genes over

non-A-type. About *66 % of the introns of castor CYPgenes exhibited zero phase suggesting the plausible evolu-

tion of split genes by the inclusion of functional domain

coding sequences into single transcription unit. Prevalence

of single intron containing genes observed in A-type (68 %)

over non-A-type (9 %) support the possibility of rapid evo-

lution of A-type genes. Besides the presence of multiple

introns, a three-fold representation of phase 2 introns in non-

A-type (19 %) over A-type (6 %) might contribute to the

slower expansion of non-A-type genes. Earlier studies

speculate that non-A-type CYP genes are ancient than

A-type families and their organisation requires more time for

gene duplication and rearrangement contributing to their

slow evolution [17]. Single-family clans CYP51, 97, 710,

711 and 727 represented with a few (1-3) genes are plausibly

ancient and may code for enzymes associated with essential

functions, thereby limiting their diversification. Further,

presence of orthologs, CYP51, 97, 710 and 711 in green

algae [15] confirms their ancient nature. As compared to

Arabidopsis, castor CYP716, CYP87, CYP82 and CYP76

families recorded extensive amplification of genes plausibly

pertaining to oil and terpenoid metabolism. Distinct pro-

jection of RcCYPN gene of castor from CYP74 family genes

in the phylogenetic tree, indicate it as a novel gene. The gene

might have diversified from RcCYP74A1 gene. Functional

characterization of this gene is essential to confirm the same.

Conclusion

Castor genome disclosed 210 putative CYP coding genes

grouped into 10 clans consisting of 45 families represented

by 77 subfamilies. The highest number (123) of the CYP

genes are A-type and the remaining 87 genes are non-A

type suggesting the rapid expansion of A-type CYP genes.

About 83 % of CYP genes are split genes indicating their

origin from an ancestral CYP gene with intron. Extensive

amplification of genes was observed in CYP716, CYP87,

CYP82 and CYP76 families and functional analysis of

these paralogs might be of great help in understanding the

oil and terpenoid metabolism in castor.

Acknowledgments The authors thank to Prof. T. Papi Reddy for-mer Head, Department of Genetics, Osmania University for the

critical evaluation of the manuscript.

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Organization and Classification of Cytochrome P450 Genes in Castor (Ricinus communis L.)AbstractIntroductionMaterial and MethodsResultsDiscussionConclusionAcknowledgmentsReferences

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