Organization and Classification of

Cytochrome P450 Genes in Castor (Ricinus

communis L.)
Maryada Shailendar Kumar, Peram
Ravindra Babu, Khareedu Venkateswara
Rao & Vudem Dashavantha Reddy
Proceedings of the National
Academy of Sciences, India Section B:
Biological Sciences
ISSN 0369-8211
Volume 84
Number 1
Proc. Natl. Acad. Sci., India, Sect. B Biol.
Sci. (2014) 84:131-143
DOI 10.1007/s40011-013-0192-8

1 23

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Author's personal copy

Proc. Natl. Acad. Sci., India, Sect. B Biol. Sci. (JanMar 2014) 84(1):131143
DOI 10.1007/s40011-013-0192-8

RESEARCH ARTICLE

Organization and Classification of Cytochrome P450 Genes

in 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 the
largest 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 nomenclature these genes have been classified into 45 families representing 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. Maximum 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

M. S. Kumar  P. R. Babu  K. V. Rao  V. D. Reddy (&)

Centre for Plant Molecular Biology, Osmania University,
Hyderabad 500007, India
e-mail: vdreddycpmb@yahoo.com

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 acid
present 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 antifreeze fuels and lubricants for space rockets. The sequence
analysis established genome size of the castor as *320 Mb
with 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, flavonoids, terpenoids, lignin and signalling molecules etc.
Cytochrome P450s catalyze oxidation of various substrates
using oxygen and NAD (P) H [8, 9]. Furthermore, these

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132

proteins represent *1 % protein coding genes of any given

organism [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 exogenous 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 nucleotide (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 carried
out based on similarity with the gene orthologs of Arabidopsis. 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 NeighbourJoining (NJ) tree method by P-distance in MEGA5 [13]
was used to construct the phylogenetic tree. The significance 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 represented 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

123

M. S. Kumar et al.

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 containing 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,
CYP77, CYP79, CYP82, CYP84, CYP86, CYP89, CYP94,
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 containing 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).

RcCYP72A15

RcCYP72A16

RcCYP72A17

RcCYP72A18

RcCYP709B2

RcCYP714A1

RcCYP714A2

RcCYP714A3

RcCYP714A4

RcCYP714A5

RcCYP715A1

RcCYP721A1

RcCYP734A1

RcCYP734A2

RcCYP734A3

RcCYP734A4

RcCYP734A5

RcCYP734A6

RcCYP735A1

29983.m003136

29739.m003779

29983.m003138

30076.m004534

29848.m004472

29794.m003364

27955.m000386

29907.m000622

27955.m000385

30169.m006256

30170.m014009

28320.m001078

30174.m009065

30174.m009066

30174.m009067

30174.m009070

30174.m009068

30205.m001577

RcCYP74B2

RcCYPN

29901.m000415

30910.m000018

RcCYP87A4

27985.m000878

RcCYP87A5

RcCYP87A2

30190.m011135

30147.m014292

RcCYP85A1

29790.m000806

CYP85 clan

RcCYP74A1

30170.m013972

CYP74 clan

RcCYP72A14

29633.m000932

RcCYP51G1

CYP
gene name

29739.m003612

CYP72 clan

30128.m008568

CYP51 clan

Castor gene ID

8,540

2,516

2,519

3,182

1,251

6,105

1,796

3,533

2,135

2,196

2,162

1,884

1,917

3,291

4,529

1,942

4,996

2,165

2,893

3,507

3,644

3,868

2,096

1,899

1,919

1,797

2,055

2,442

Length of
genomic
seqs (bp)

Table 1 Organisation of Cytochrome P450 genes in castor

No. of
Intron (s)

197,325,150,252,
90,79,107,128,94

215,340,150,249,93,79,
118,126,94

194,322,150,252,90,79,
107,128,256,57

104,322,150,246,87,
79,107,125,88

1,251

471,382,638

1,557

274,227,242,379,426

280,224,233,379,429

94,224,233,379,429

169,221,233,376,429

289,224,233,376,429

274,224,236,379,429

295,224,242,376,453

492,245,364,385,356

606,426

301,159,95,168,88,417,
227,251,369,340

286,227,245,355,426

210, 267, 248, 388, 369

286,227,251,349,426

295,227,254,370,426

280,173,251,376,432

259,218,251,379,423

103,81,221,245,391,426

274,218,245,379,414

14,181,245,376,426

277,221,245,364,426

462,999

Exon(s)
size (bp)

84. 1,493, 101, 5,056,

110, 91, 95, 88

96, 89, 290, 87, 78, 94,

216, 102

114, 84, 232, 100, 82,

110, 78, 58, 26

461, 122, 92, 82, 147,

738, 141, 91

4,265, 262

120, 186, 564, 1,115

98, 166, 116, 210

343, 112, 225, 157

159, 265, 116, 194

91, 77, 88, 77

99, 73, 121, 82

1,206, 86, 131, 278

1,002, 222, 93, 1,370

910

217, 217, 172, 46, 523, 632,

364, 219, 191

192, 182, 92,160

112, 126, 109, 235

1,063, 578, 101, 226

1,227, 352, 219, 274

2,035, 151, 88, 82

210, 102, 153, 101

89, 95, 92, 72, 84

80, 99, 109, 101

211,104, 100,140

79, 207, 161, 75

402

Intron (s)
size (bp)

2,0,0,0,0,1,0,2

2,0,0,0,0,1,2,2

2,0,0,0,0,1,0,2,0

2,0,0,0,0,1,0,2

0,1

1,0,2,0

1,0,2,0

1,0,2,0

1,0,2,0

1,0,2,0

1,0,2,0

1,0,2,0

0,2,0,1

1,1,0,0,1,1,0,2,2

1,0,2,0

0,0,2,0

1,0,2,0

1,0,2,0

1,0,2,0

1,0,2,0

1,1,0,2,0

1,0,0,1

2,0,2,0

1,0,2,0

Intron (s)
phase

7,118

1,052

884

1,874

4,527

1,985

590

837

734

333

375

1,701

2,687

910

2,581

626

582

1,968

2,072

2,356

566

432

389

555

522

402

Sum of
intron
length
(bp)

473

487

544

435

416

496

518

515

514

452

475

516

513

529

613

343

445

512

493

512

523

503

509

488

509

413

510

486

No. of
amino
acids

Author's personal copy

Organization and Classification of Cytochrome P450

133

123

123

RcCYP87A6

RcCYP87A7

RcCYP87A8

RcCYP87A9

RcCYP87A10

RcCYP88A4

RcCYP90B1

RcCYP90C1

RcCYP90D1

RcCYP707A1

RcCYP707A2

RcCYP707A3

RcCYP707A4

RcCYP716A1

RcCYP716A2

RcCYP716A3

RcCYP716A4

RcCYP716A5

RcCYP716B1

RcCYP716C1

RcCYP716C2

RcCYP716D1

RcCYP716E1

RcCYP716F1

RcCYP718A1

RcCYP720A1

30138.m003878

30170.m014356

27985.m000880

29609.m000602

29709.m001228

29634.m002158

29634.m002059

28694.m000680

30115.m001196

29801.m003223

30170.m013873

29801.m003183

28226.m000875

30018.m000548

30152.m002401

29728.m000795

30074.m001374

28226.m000853

29776.m000481

29776.m000483

30063.m001421

28842.m000941

29666.m001453

29993.m001052

30172.m000208

CYP
gene name

28448.m000359

Castor gene ID

Table 1 continued

2,014

1,805

2,302

2,914

No. of
Intron (s)

135,234,84,79,
122,128,115

961,179

501,442,188,306

502,372,188,306

88,456,189,179

931,188,303

940,188,297

946,188,309

958,188,306

961,188,294

943,188,303

451,504,188,300

928,188,300

206,322,150,249,87,
79,107,119,97

194,322,150,204,90,
79,107,119,103

206,319,387,175,
107,119,94

182,322,153,249,90,
79,107,119,112

221,325,150,246,90,
186,122,109

245,325,150,273,97,
125,128,100

203,325,153,234,93,
79,119,234

233,478,270,90,79,
107,122,100

200,331,150,249,87,
79,107,132

321,150,249,90,76,
107,128,100

212,331,150,249,90,
79,107,128,94

200,328,153,249,90,
79,107,128,94

197,325,150,252,90,
79,108,128,91

Exon(s)
size (bp)

111, 141, 87,

581, 116, 81

665

387, 384, 94

233, 667, 646

78, 100, 213

329, 241

166, 142

183, 85

402, 81

108, 98

97, 86

102, 1,358, 211

94, 93

127, 190, 95, 94, 106,

105, 178, 98

96, 164, 103, 158, 107,

482, 96, 216

106, 159, 94, 129,

105, 163

93, 728, 136, 84, 98,

384, 145, 88

358, 614, 96, 1,021,

86, 144, 1,121

1,779, 254, 263, 1,424,

642, 420, 283

97, 101, 82, 96, 103,

96, 1,343

1,279, 137, 87, 87,

198, 91, 90

516, 106, 212, 203,

102, 297, 354

184, 200, 99, 538,89,

147,88

182, 121, 117, 154,

113, 120, 152, 100

205, 96, 96, 108, 88,

86, 124, 85

100, 159, 103, 96,

91, 84, 107, 67

Intron (s)
size (bp)

0,0,0,1,0,2

0,1,0

1,1,0

1,1,1

1,0

1,0

1,0

1,0

1,0

1,0

1,1,0

1,0

2,0,0,0,0,1,0,2

2,0,0,0,0,1,0,2

2,0,0,1,0,2

2,0,0,0,0,1,0,2

0,1,0,0,0,0,2

2,0,0,0,1,0,2

2,0,0,0,0,1,0

2,0,0,0,1,0,2

2,0,0,0,0,1,0

0,0,0,0,1,0,2

2,0,0,0,0,1,0,2

2,0,0,0,0,1,0,2

2,0,0,0,0,1,0,2

Intron (s)
phase

1,117

665

865

1,546

391

570

308

268

483

206

183

1,671

187

994

1,422

756

1,756

3,444

5,065

1,918

1,969

1,790

1,345

1,059

888

807

Sum of
intron
length
(bp)

298

379

478

455

303

473

474

480

483

480

477

480

471

471

455

468

470

482

480

479

492

444

406

479

475

472

No. of
amino
acids

134

1,303

1,992

1,733

1,711

1,935

1,649

1,617

3,114

1,603

2,410

2,790

2,163

3,710

4,893

6,508

3,358

3,448

3,125

2,566

2,499

2,316

2,227

Length of
genomic
seqs (bp)

Author's personal copy

M. S. Kumar et al.

RcCYP722A2

RcCYP722A3

RcCYP722B1

RcCYP724A1

RcCYP724A2

29634.m002092

29863.m001089

29982.m000224

29633.m000931

30005.m001270

RcCYP86A3

RcCYP86B1

RcCYP86C1

RcCYP94B1

RcCYP94B2

RcCYP94B3

RcCYP94B4

RcCYP94C1

RcCYP94C2

RcCYP94D1

RcCYP94D2

RcCYP96A1

RcCYP96A2

RcCYP96B1

RcCYP96B2

RcCYP704A2

RcCYP704A3

RcCYP704A4

30174.m008617

30094.m000683

29929.m004790

30147.m014517

29883.m002015

30190.m010938

29883.m002017

29791.m000529

28779.m000137

29811.m000531

30078.m002275

29917.m002008

29917.m002010

29409.m000268

29660.m000772

30174.m008914

30174.m008915

30194.m000057

RcCYP704B1

RcCYP86A2

30190.m011234

29813.m001518

RcCYP86A1

29681.m001310

CYP86 clan

RcCYP722A1

CYP
gene name

30170.m014078

Castor gene ID

Table 1 continued

2,345

2,680

1,555

2,046

1,613

1,518

1,518

1,530

1,521

1,563

1,506

1,500

1,873

1,530

1,494

1,443

1,563

3,062

2,045

1,921

1,536

3,404

3,569

2,305

2,867

4,067

4,063

Length of
genomic
seqs (bp)

No. of
Intron (s)

330,216,297,
387,201,180

309,216,291,
321,45

277,26,144,92,
337,168

522,285,339,
201,192

1,086,324

1,518

1,518

1,530

1,521

1563

1506

1,500

1,524

1,530

1,494

1,443

1,563

1260,393

256,1313

1,638

1,536

221,325,153,246,87,
79,107,122,76,156

200,325,153,243,87,
79,111,136,115

209,319,153,267,
87,79,107,119,91

248,325,150,252,84,
79,107,119,112

260,325,150,252,87,
79,107,119,100

146,322,150,184,80,90,
79,107,119,100

Exon(s)
size (bp)

179, 104, 99, 219, 133

325, 87, 107, 979

149, 129, 51, 98, 84

85, 121, 206, 95

203

1,409

110

129, 89, 213, 185,

244, 256, 388, 33, 295

187, 227, 86, 183,

99, 158, 831, 349

111, 94, 93, 84,

89, 88, 89, 226

257, 109, 76, 90,

95, 562, 105, 97

217, 628, 289, 87,

455, 106, 95, 723

108, 1,550, 101, 91,

111,178, 116, 288, 143

Intron (s)
size (bp)

0,0,0,0,0

0,0,0,0

1,0,0,2,0

0,0,0,0

2,0,0,0,0,1,0,2,0

2,0,0,0,0,1,1,2

2,0,0,0,0,1,0,2

2,0,0,0,0,1,0,2

2,0,0,0,0,1,0,2,

2,0,0,1,0,0,1,0,2

Intron (s)
phase

734

1,498

511

507

203

1,409

110

1,832

2,120

874

1,391

2,588

2,686

Sum of
intron
length
(bp)

536

394

347

512

469

505

505

509

506

520

501

499

507

509

497

480

520

550

522

545

511

523

482

476

491

492

458

No. of
amino
acids

Author's personal copy

Organization and Classification of Cytochrome P450

135

123

123

RcCYP97C1

30078.m002224

28223.m000100

RcCYP71A24

RcCYP71A25

RcCYP71A26

RcCYP71A27

RcCYP71A28

RcCYP71B1

RcCYP71B4

RcCYP71B8

RcCYP71B9

RcCYP71B10

RcCYP71B11

RcCYP71B13

RcCYP71B14

RcCYP71B22

RcCYP71B23

RcCYP71B24

RcCYP71B25

RcCYP71B26

RcCYP71B27

RcCYP71B28

30147.m013842

30147.m013843

30147.m013847

30147.m013848

30129.m000355

29724.m000821

30169.m006288

29785.m000965

29785.m000959

29785.m000962

29826.m000757

30169.m006277

29887.m000239

29910.m000943

29878.m000239

29887.m000240

29887.m000241

30169.m006273

30169.m006275

RcCYP727A1

RcCYP711A1

30147.m013846

CYP71 clan

29686.m000867

CYP727 clan

29739.m003566

CYP711 clan

RcCYP710A1

RcCYP97B3

29724.m000853

CYP710 clan

RcCYP97A3

CYP
gene name

30128.m009010

CYP97 clan

Castor gene ID

Table 1 continued

1,608

1,616

1,647

1,754

1,810

13

15

No. of
Intron (s)

891,615

906,615

894,621

882,621

477,26,199,615

897,627

882,621

996,609

945,654

906,624

906,624

666,153,624

157,638,627

123,466,359

942,615

963,621

945,621

915,612

915,618

915,612

208,200,642,
148,127,136,78

248,153,784,
96,330

903,615

501,297,198,102,
141,108,83,163,66

71,178,108,85,239,
174,48,60,87,89,
92,62,150,225

139,163,217,72,111,
192,162,96,102,33,
81,83,132,61,66,189

Exon(s)
size (bp)

102

95

132

251

101, 137, 255

268

112

129

79

892

856

79, 611

39, 99

117, 97

88

477

975

338

187

918

255, 1,101, 592,

671, 400, 328

630, 593,290, 77

143

0, 2, 0

0,0

1,0

0,1

1,0,0,1,2,0

2,2,0,0

0,0,0,0,0,0,2,0

2,0,0,1,0,0,0,
0,0,2,1,0,0

445, 213, 486, 10,665, 1,559,

1,623, 1,029, 192,151, 462,
681, 200, 105
559, 64, 549, 390, 154,
587, 165, 202

1,2,0,0,0,0,0,
0,0,0,0,2,2,0,0

Intron (s)
phase

81, 107, 111, 89, 581,

128, 276, 68, 328,
116, 100, 713, 233,
148, 168

Intron (s)
size (bp)

102

95

132

251

493

268

112

129

79

892

856

690

138

214

88

477

975

338

187

918

3,347

1,590

143

2,670

17,801

3,247

Sum of
intron
length
(bp)

501

506

504

500

438

507

500

534

532

509

509

480

473

315

518

527

521

508

510

508

512

536

159

552

555

632

No. of
amino
acids

136

1,792

1,615

1,734

1,678

2,475

2,501

2,185

1,560

1,662

1,645

2,061

2,541

1,865

1,720

2,445

4,886

3,201

480

4,329

19,469

5,146

Length of
genomic
seqs (bp)

Author's personal copy

M. S. Kumar et al.

RcCYP71B29

RcCYP71B30

RcCYP71B31

RcCYP71B36

RcCYP71B37

RcCYP71B38

RcCYP71B39

RcCYP71B40

RcCYP71B41

RcCYP71B42

RcCYP71C1

RcCYP71C2

RcCYP71C3

RcCYP71D1

RcCYP73A5

RcCYP73A6

RcCYP75B1

RcCYP75B2

RcCYP75B3

RcCYP75B4

RcCYP76C3

RcCYP76C4

RcCYP76D1

RcCYP76D2

RcCYP76D3

RcCYP76D4

RcCYP76E1

RcCYP76G1

RcCYP76G2

RcCYP76H1

RcCYP76H2

RcCYP76I1

RcCYP76I2

RcCYP76I3

RcCYP76I4

RcCYP77A4

RcCYP77B1

30169.m006282

30169.m006285

29792.m000625

29929.m004561

29629.m001350

29629.m001392

29929.m004562

29792.m000626

30142.m000643

29792.m000624

30206.m000783

29785.m000966

29929.m004748

29976.m000504

43540.m000048

30138.m003983

30146.m003563

29706.m001271

29739.m003754

30190.m011068

30190.m011069

30147.m014296

30169.m006290

30169.m006295

30169.m006291

30190.m011130

29815.m000508

29815.m000509

29815.m000510

29815.m000512

29815.m000515

29815.m000516

29815.m000519

29815.m000520

29428.m000318

29842.m003625

CYP
gene name

30169.m006279

Castor gene ID

Table 1 continued

1,518

No. of
Intron (s)

1,518

1,596

930,615

930,618

939,591

960,615

473,445,621

900,609

915,630

927,651

879,627

391, 285, 605

906,51

885,606

882,609

900,606

889,245

942,624

906,630

942,624

282,453,651

875, 736

785, 134, 599

927,636

903, 510, 87

903,12

906,618

894,174,21

906,609

951,624

900,624

891,609

903,612

862,63,614

990,612

885,609

957,615

Exon(s)
size (bp)

128

153

149

107

93, 312

556

468

1,037

176

97, 113

499

142

121

84

179

156

547

573

891, 853

362

176, 1,525

723

280, 1,035

66

1,472

250, 52

824

150

108

132

269

124, 84

93

122

157

Intron (s)
size (bp)

2,0

1,1

0,0

2,1

0,0

0,0

1,1

Intron (s)
phase

128

153

149

107

405

556

468

1,037

176

210

499

142

121

84

179

156

547

573

1,744

362

1,701

723

1,315

66

1,472

302

824

150

108

132

269

208

93

122

157

Sum of
intron
length
(bp)

505

531

514

515

509

524

512

502

514

525

501

426

318

496

496

501

377

521

511

521

461

536

505

520

499

304

507

362

504

524

507

499

504

512

533

497

523

No. of
amino
acids

Organization and Classification of Cytochrome P450

1,596

1,673

1,701

1,679

1,682

1,944

2,065

2,013

2,615

1,682

1,491

1,456

1,633

1,612

1,794

1,313

1,722

2,210

2,139

3,130

1,973

3,576

2,399

2,815

981

2,996

1,391

2,339

1,725

1,632

1,632

1,784

1,747

1,695

1,616

1,729

Length of
genomic
seqs (bp)

Author's personal copy

137

123

123

RcCYP77B2

RcCYP78A6

RcCYP78A7

RcCYP78A8

RcCYP78A9

RcCYP78A10

RcCYP78A11

RcCYP79A2

RcCYP79B3

RcCYP79B4

RcCYP79B7

RcCYP81D2

RcCYP81D3

RcCYP81D4

RcCYP81D8

RcCYP81D9

RcCYP81D10

RcCYP81D11

RcCYP81H1

RcCYP81K1

RcCYP82C2

RcCYP82C3

RcCYP82C4

RcCYP82C5

RcCYP82C6

RcCYP82C7

RcCYP82C8

RcCYP82C9

RcCYP82C10

RcCYP82C11

RcCYP82C12

RcCYP82C13

RcCYP82G1

RcCYP83B1

RcCYP83B3

RcCYP83B4

RcCYP84A1

28014.m000118

28256.m000134

28644.m000933

30068.m002578

30138.m003950

29929.m004656

29910.m000911

29910.m000917

29910.m000914

28438.m000050

29970.m001003

29910.m000948

30170.m014208

29970.m001002

30170.m013774

30170.m013773

30170.m013780

29970.m000998

30170.m014207

29851.m002485

30170.m013958

30170.m013953

30120.m000372

30170.m013957

30170.m013963

29676.m001679

30170.m013949

30170.m013950

30170.m013960

30170.m013964

30170.m013965

30120.m000371

30170.m014153

30170.m014151

30174.m009168

30131.m007121

CYP
gene name

29842.m003626

Castor gene ID

Table 1 continued

942

2,331

1,797

1,611

2,684

No. of
Intron (s)

942

714,612

879,612

885,609

942,630

963,624

939,630

945,621

948,624

948,633

939,627

945,621

927,666

951,627

400,464,624

954,633

963

897,621

327,633

903,612

882,621

903,627

891,621

930,615

918,636

272,469,618

1,017

1,113

981,9

1,173

963,597

783,606

960,636

996,618

999,603

405,618

1,518

Exon(s)
size (bp)

1,005

306

117

1,112

145

654

1,542

122

267

721

580

53

1,158

90, 207

112

187

12,217

158

624

406

1,072

766

1,472

149, 1,745

81

1,166

533

349

94

92

157

Intron (s)
size (bp)

1,0

2,0

Intron (s)
phase

1,005

306

117

1,112

145

654

1,542

122

267

721

580

53

1,158

297

112

187

12,217

158

624

406

1,072

766

1,472

1,894

81

1,166

533

349

94

92

157

Sum of
intron
length
(bp)

313

441

496

497

523

528

522

521

523

526

521

521

530

525

495

528

320

505

319

504

500

509

503

514

517

452

338

370

329

390

519

462

531

537

533

340

505

No. of
amino
acids

138

1,732

2,223

3,108

1,694

1,848

2,287

2,146

1,646

2,736

1,785

1,699

963

1,790

13,177

1,673

2,127

1,936

2,584

2,311

3,026

3,253

1,017

1,113

1,071

1,173

2,726

2,045

1,950

1,708

1,694

1,180

1,529

Length of
genomic
seqs (bp)

Author's personal copy

M. S. Kumar et al.

RcCYP84A2

RcCYP84A3

RcCYP84A4

RcCYP89A4

RcCYP89A5

RcCYP89A6

RcCYP89A7

RcCYP89A8

RcCYP89A9

RcCYP89A10

RcCYP89A11

RcCYP89A12

RcCYP89B1

RcCYP93D1

RcCYP93D2

RcCYP93D3

RcCYP93D4

RcCYP93D5

RcCYP98A3

RcCYP98A4

RcCYP98A5

RcCYP701A3

RcCYP703A2

RcCYP706A4

RcCYP706A5

RcCYP706A7

RcCYP712A1

RcCYP712A2

RcCYP712B1

30138.m003926

30174.m008711

29827.m002605

30148.m001481

30073.m002236

30148.m001477

30148.m001478

30148.m001476

30148.m001482

30148.m001475

30148.m001483

29083.m000045

29216.m000256

29216.m000255

30152.m002423

29788.m000321

29788.m000323

29940.m000401

30147.m014117

29940.m000400

30170.m013942

29742.m001406

30190.m011008

30190.m011007

30147.m014189

29216.m000258

27647.m000174

29216.m000257

CYP
gene name

28196.m000205

Castor gene ID

Table 1 continued

2,151

3,153

1,967

1,694

3,820

1,705

1,888

2,988

4,472

1,536

3,583

2,230

1,296

3,031

2,434

2,380

1,738

1,545

1,503

1,568

1,551

1,542

1,575

1,601

1,551

1,551

1,783

2,629

1,661

Length of
genomic
seqs (bp)

No. of
Intron (s)

921,630

939,618

912,630

894,235,347

936,621

960,633

909,639

154, 160, 163,140,

258, 158, 195, 314

178,398,612

1,536

493,398,645

609,231,681

891,111

16,959,666

802,428

811,671

1,173

1,545

1,503

1,557

1,545

1,542

1,575

1,563

1,551

1,551

675,828

714,822

903,615

Exon(s)
size (bp)

600

1,281

425

172, 46

2,116

112

340

185, 824, 102, 93,

85, 84, 83

2,311, 973

1,574, 335

70, 639

294

157, 1,233

1,204

898

277

1,093

143

Intron (s)
size (bp)

0,1

1,2,0,2,2,1,1

1,0

1,0

0,0

1,0

Intron (s)
phase

600

1,281

425

218

2,116

112

340

1,456

3,284

1,909

709

294

1,390

1,204

898

277

1,093

143

Sum of
intron
length
(bp)

516

518

513

491

518

530

515

513

395

511

511

506

333

546

409

493

390

514

500

518

514

513

524

520

516

516

501

511

505

No. of
amino
acids

Author's personal copy

Organization and Classification of Cytochrome P450

139

123

Author's personal copy

140

M. S. Kumar et al.
914 1 7
000
9
000
10.m
-299 9910.m
9B 4
-2
911
YP7
9B3
000 00050
RcC
YP7
0.m
0
RcC 2-2991 438.m
79A B7-28
YP
79
YP
RcC

CY

2
79A
YP 3
AtC P79B 2
06 2
14 A
Y 9B
00 703
AtC YP7
.m P
42 Y
AtC 2
97 AtC
9F
2-2
P7 F1
3A
1
CY 79
At CYP 79C2 79C P70
At YP CYP cCY
C
R
At At

0.1

AtCYP71B21
AtCYP71B22
AtCYP71B38P
AtCYP71B5
AtCYP71B30P
AtCYP71B
AtCYP71B 32
31
AtCYP7 AtCYP71B8
1B23
AtCYP7
1B7
AtCY AtCYP7
1B15
P71B
AtCY AtCYP71 28
P71
B29
AtC B2
YP7
1
A
AtC tCYP7 B27
AtC YP71B 1B16
17
Y
AtCAtCYP P71B1
9
Y
7
AtC P71B 1B20
AtC AtC YP71 24
YP YP7 B3
71 1B
A B4 25
A tCY
A t tCYP P 7 1 B
CY 71 11
A P B
A t 71 12
A tC CY B1
A tC YP P71 3
At tCY YP7 71B B14
At CY P71 1B2 6
B 6
C P
A Y 71 33
At At tCY P71 B34
B
At CY CY P71 35
P P
R CY 71B 71B B9
cC P7 3 3
Y 1B 7 6
P7 1
1B 0
36
-2
97
92
.m
00
06
25

Rc C

76
14
00 78 7
.m 014 147 1
8
48
36
01 .m0 00 14
22
9-3 48 8.m 00
00
9A 301 014 8.m 3
P8
8-3 14 48 3.m 75
CY 9A A7 -30 01 07 14
Rc YP8 P89 A5 .m0 6-30 00 482
C CY P89 148 A 8.m 01
9
4
0
Rc
c
0
R
P8 301 .m
CY 2-3
Rc A1 cCY 11- 148
9
R 9A -30
P8
P8 A10
CY 89
Rc YP
cC
R

Rc

A AtC
At tCY YP
Rc
At CY P8 89
P 9 A
Rc CY
C
P8
At YP 89A A2 3
C
Rc
CY YP8 9A4
At At CYP 89A 7
9
P7
7B B1-2 2982 CYP CYP 89A 6
1
9
8
7
8
0
.
9
Rc
29
9 5
84 83.m m00 A9 A4
CY
2.m
P
0 26
Rc 77B
At 003 0004 05
CY
2
C
P7 -298 YP 625 5
4
7A
7
4-2 2.m0 7B1
9
0
AtC 428.m 362
RcC
YP
00 6
YP
701
AtC AtC 77A9 0318
A3-3
YP YP7
017
7A
77
A
0.m
7
013 tCYP A6
77A
AtC 942
4
Y
RcC P701A
YP7
3
3A5
-299
RcC
76.m
YP7
000
3A6
A
5
-435
40.m tCYP7 04
0000 3A5
48

RcCY

AtC
Y
4-3014 AtCYP P98A9
98A8
RcC 7.m0141
RcCY YP98A5- 17
P98A329
29940. 940.m0004
m
00
00
RcCYP7
AtCYP90401
8A8-286
8A3
RcCYP7
44.m00
09
8A7-282
56.m0001 33
34
RcCYP78A1 AtCYP78A7
0-30138.m0
03950
AtCYP78A10
AtCYP78A5
RcCYP78A11-29929.m004656
RcCYP78A9-30068.m002578
RcCYP78A6-28014.m000118
AtCYP78A8
AtCYP78A9
AtCYP78A6
29815.m000520
6I4RcCYP7
5.m000519
981
3-2
RcCYP76I
000516
-29815.m
15
RcCYP76I2 6I1-29815.m0005 000512
815.m
RcCYP7
6H2-29
10
RcCYP7 815.m0005 6G1
29
tCYP7 09
P76H1A
Y
cC
R
0005 08
05
815.m
G2-29 815.m00
76
P
30
RcCY P76G1-290.m0111 006291
RcCY E1-3019 0169.m 96
-3
4
76
6D
0142
YP
7.m
YP7
RcC
RcC 1-3014
6D
069
290
YP7
006 .m011
.m
RcC
169 0190
C7
2-30 4-3
P76 3
76D P76C 8
CY P76C
295
t
P
6
Y
0
A
Y
6
0
Y C6
RcC RcC 0110
9.m
AtC P76 C5 6C1
016
.m
Y 76 P7
190
D3-3
C
t
6
0
7
P
A Y tCY 6C4 6C2
3-3
YP
C A P7 7
76C
RcC
At
P
YP
CY Y
RcC
At AtC
89
41
A2
01
.m 1008 706 A1 07
7
14 01 YP 06 0
-30 .m tC P7 011
A7 0190 A tCY 0.m A7 A3 A4
6
0
A 19 706 706 706 6
P7 4-3
30 P P P
CY 6A
5- Y Y Y 06A 5
Rc P70
6A AtC AtC AtC P7 6A
70
CY
0
CY 7
Rc
YP
C
At YP
Rc
tC
A

2
2
A A3 28
05 05 5A 30
P7 P7 0 5A
Y Y P7 70 2
tC tC Y P A2
A A AtC tCY 705 3
A P 5A
0
CY P7 A6 8
At CY 705 5A1 33
At CYP P70 05A 3
At tCY YP7 5A1 2
24
A AtC P70 A1 A1
5
5 705A
CY 70 70
At CYP YP CYP
At AtC At 25
05A
258 00257
P7 A27
000
0
CY 05
321
At YP7 A1 216.m 216.m
000
2 -29
-29
AtC 71
88.m
74
YP 2A1 12B1
001
-297
AtC YP71 CYP7 712A2 647.m0 P93D4
P
RcC Rc AtCY 2A2-27 RcCY
1
YP7
RcC
3
2
0003
88.m 02423
-297
0
3D5 0152.m
YP9
-3
56
RcC P93D3 D1
m0002
Y
93
0255
RcC AtCYP D1-29216. 216.m00
P93
D2-29
RcCYRcCYP93

cC
Y
P7
5B
At
130
C
A
13
A tC YP
8.
At tCY YP 81D
m
At CY P8 81D 3 At 00
CY 3
CY P8 1D 2
1D 8
P
P7 983
At AtC AtC 81D 10
5B
At CY YP YP 5 P
1
Rc
C
P
8
8
YP 81 1D 1D
C
Rc
81 D7 11 4
CY YP8
D
1
P8
1D H1-2 AtCY AtC 6
3-2
997 P8 YP
Rc
9
C
1
RcC YP 910 0.m H 81
D1
YP 81D .m0 000 1
81D 8-2 00
9
2-2 997 948 98
997 0.m
0
0
AtC .m001 0100
YP 00 2
AtC 81F4 3
YP
A
RcC
AtC tCYP8 81F3
YP8
YP8 1F2
1D
RcC 4-30170 AtCYP 1F1
Y
.m
8
RcCY P81D11-3 014208 1G1
P81D
0170
9-30
.m01
R
RcCY cCYP81D10 170.m01 3780
37
P81K
1-3017 -30170.m 74
01
0.
AtCYP8 m014207 3773
1K2
AtCY
RcCYP8
2C8-296 P81K1
76.m00
AtCYP82F 1679
1
RcCYP82C5
RcCYP82C2-298
-30120.m000
51.m002485
372
RcCYP82G1-30120.m0
00371
AtCYP82G1
RcCYP82C13-30170.m013965
RcCYP82C12-30170.m013964
RcCYP82C7-30170.m013963
RcCYP82C11-30170.m013960
13957
RcCYP82C6-30170.m0
70.m013958
RcCYP82C3-301 0170.m013949
9-3
RcCYP82C
m013950
10-30170.
RcCYP82C 0170.m013953
2C4
2C4-3
AtCYP83
RcCYP8
2C
AtCYP8 2C2
P8
AtCY

P98A

3
64
00
6 m0
62 42.
0
83
00 01
07
m -3
00
2. 42 24
6.m
79 B 06
20
29 P71 00 65 9
0
3
41 Y 2.m 09 095
21B cC 79 00 00 962 71C 6
P7 R1-29 5.m 5.m 000 YP 096
Y
C 78 78 .m cC 00
cC
71 9-29 -29 785 R 5.m
R
P
0
8
9
1
B 1
97 A
CY 71 1B 1-2
3-2 83
Rc YP P7 1B1
3
1C YP
15
C Y 7
P7 AtC 3B1 014 4151
5
Rc RcC CYP
8
.m 1
8
CY
035
YP 0170 0.m0 0916 .m00
Rc
Rc
C
At 1-3 3017 4.m0 0129 842
B
3
3
7
3
3
P8 83B 4-301 71B1 7.m01 3843
Y
P B
01
4
C
P
Rc cCY P83 cCY 5-301 147.m 3846
1
R CY R A2 -30
.m0 13847 13848
1
Rc
P7 A26 147
0
0
7.m
CY 71 -30 7.m
Rc cCYP 1A24 -3014 8-3014
7
7
2
R YP A2
1
71A
C
7
P
c
P
Y
R CY
1
RcCP71A2 2
Rc
2
Y
AtC YP71A 4
AtC P71A2
Y
6
AtC P71A2
Y
AtC P71A23
AtCY P71A25
AtCY 71A12
P
AtCY YP71A13
AtC 1A18
AtCYP7 1A19
AtCYP7 20
1A
AtCYP7 YP71A16
AtC
27
AtCYP71A
AtCYP71A28
AtCYP71A14
AtCYP71A15
RcCYP71D1-29929.m004748
RcCYP71B13-29826.m000757
RcCYP71B38-29629.m001350
RcCYP71B39-29629.m001392
RcCYP71B
RcCYP71B24-29 23-29910.m000943
878.m000239
RcCYP71B
RcCYP71B 8-30169.m006288
37-29929.
RcCY
m0
RcCYP7 P71B40-29929.m 04561
1B
RcCYP7 27-30169.m 004562
006273
1B
RcCY 29-30169.m
P7
00
1B22
6279
RcC
RcCY YP71B25 -29887.m00
-2
P71B
0239
26-2 9887.m
R
RcC cCYP71 9887.m00 000240
B
YP7
1B31 14-30169 0241
-3
.m
RcC RcCY RcCY 0169.m0 006277
P
0
AtCYP71B 71B28 P71B4-2 6285
YP 30-3 -301
9724
84A
6
016
Rc
1
9.m 9.m006 .m00082
C
2
006
AtC
1
282 75
R YP
Rc Rc cCY 84A2 YP84
CY CY P8 -28 A4
Rc P75B P84 4A3- 196.m
CY 3- A4 301 00
RcC
Rc P75 297 -301 38.m 0205
YP
CY B2 06.m 74.m 00
84A
P7 -30 00 00 3926
1-3
5B 14 12 87
013
4-2 6.m 71 11
1.m
97 00
007
121
At 39.m 3563
C
At YP 0037
C
5
7
A
4
0
Y
At A tCY P7 5A1
CY tC P7 05A 6
Y
0
P P
5 19
A 705 705 A23
At At tCY A21 A20
CY CY P7
A
P P7 05
tC
Y At 705 05A A15
P7 C A
05 YP 8 4
A 70
5
5A
9

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

Comparative analysis of CYPs revealed that the families,

CYP51, CYP74, CYP78, CYP97, CYP98, CYP701, CYP703,
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.

123

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,

Author's personal copy

CY

P8

P8

Rc

0.m

7A

P8

7A

10

8-3

-29

01

CY

P8

70

9.m

42

11

At

60

014517
RcCYP94B3
-30190.m010
938
AtCYP94B
2

AtCYP94B1

RcCYP94B1-30147.m

03

59

92

35

CY

7A

CY

CY

P8

P87

-27

01

9-2

P8

0C1

00

.m

94

00

-3
B1

790
004
1
9.m
992
1-2
6C
8
P
2
CY
86C
Rc
YP
3
AtC
772
86C
000
YP
60.m
AtC
C4
-296
P86
6B2
Y
08
YP9
0020
AtC
.m
RcC
7
1
-299
6A1
10
YP9
0020
RcC
917.m
A2-29
68
YP96
m0002
RcC
29409.
96B1P
Y
RcC
3
P96A
AtCY
6A4
AtCYP9
6A15
AtCYP9

P8

CY

6C

P8

CY

At

AtCYP9

B2

86

P
CY

At

83

06

6B

P8

Rc

798

.m

81

96

-2
A1

CY

At

10

13

00

A1

86

YP

C
At

CY

7-3

7A

A4

A7

86

Rc

P8

7A
.m
00
01
2
06
43
02
56
38
.m
00
38
5.m
7
8
985
000
.m0
880
008
78
AtC
YP
RcC
85A
YP8
AtC
2
5A1
YP
-297
85A
90.m
1
RcC
000
YP7
806
20A
1-30
172.m
RcCY
AtC
P90D
0002
YP7
1-2869
08
20A1
4.m00
0680
AtCY
RcCY
P90D
P90C11
29634.
m0020
59
Rc

Rc

6A

P
CY

At

0.

19

0
-3

P8

CY

Rc

00

01

01

P8

CY

Rc

8.m

7.m

34

12

01

cC

A2

44

14

19

CY

08

28

30

30

3-

6
P8

P7

6-

5-

2-

17

86

00

4.

7
01

CY

7A

7A

7A

Rc

P8

0.2

RcCYP9
4B2-298
83.m00
2015
RcCY
P94B429883.
m0020
AtCY
17
P94C
1
RcCY
P94C
1-2979
1.m00
RcC
05
29
YP9
4C2
RcC
-287
YP9
79.m
4D1
RcC
0001
-298
YP9
37
11.m
4D2
AtC
0005
-3
007
YP
31
8.m
94D
AtC
002
1
275
YP
94D
A tC
2
YP
704
Rc
B1
CY
P7
04B
1-2
At
981
CY
Rc
3.m
CY
P7
001
At
04
P7
518
CY
A1
04
A4
P
70
Rc
-30
4A
CY
19
2
4.m
P7
At
00
04
00
CY
A2
At
57
-30
P8
CY
Rc
6A
At
17
CY
4.m
CY P86
2
P7
A4
00
04
P8
89
A3
6A
1
4
30
8
17
4.m
00
89
15

Rc

At

CY

CY

415
000
01.m
4B2
-299
YP7
4B2
AtC
YP 7
RcC
972
013
74A
0.m
YP
017
6
A tC
018
1-3
02 A
000
74A
P7
5
YP
10.m
CY
2A
2
R cC
At
70
309
A
P
02
PN
CY
P7
CY
At
A1
Rc
CY
02
8
At
P7
2A
CY P7 0
3
At
A1
8
A
CY
70
02
At
P7
YP
A4
CY AtC
08
At
P7
3
CY 8A
0
At
P7
Y
tC
A

Rc

Rc

141

AtCYP94B3

Organization and Classification of Cytochrome P450

10

AtCYP90A
1
-29634.m002
158

AtCYP96A

RcCYP90B1

AtCYP96A9

AtCYP90B1

AtCYP96A1

RcCYP724A2-30005.m001270

AtCYP96A5

RcCYP724A1-29633.m000931

AtCYP96A7

AtCYP724A1

AtCYP96A8

AtCYP96A13

AtCYP96A

12

AtCYP9

AtCY
P97A
3
P97A
3-3012
8.m00
AtC
9010
YP9
7B3
RcC
YP9
7B3
-297
24.m
AtC
0008
YP9
5
7C1
RcC
YP
97C
1-3
007
8.m
AtC
RcC
002
YP
224
YP
711
Rc
710
A1
CY
A1-2
P7
822
11A
3.m
At
1-2
000
CY
973
100
P7
9.m
At
Rc
003
CY 14A1
CY
566
P7
P
Rc
Rc
727
14
CY
CY
A2
A
1-2
Rc
P7
P7
Rc
968
14
CY
14
A1
6.m
P7
A3 CYP
-29
000
14
-2
71
84
867
A2
79
4A
8.m
-2
55
A
4
9
00
-2
tC
.m
79
99
4
4
00
Y
4
.m
72
07
Rc
P7
03
0
.
m
0
86
CY
15
33
00
A
64
06
P7
1
22
14
A5
-2
79
55
.m
00
03
85

53

07
00

A3

8.m

-30

16

A2

16

16A

P7

P7

CY

CY

Rc

Rc

Rc
C

YP
5

P7
CY
Rc

01

-30

15

At

At

CY

.m

28

97

-2

A4
16

P7
CY

Rc

003779

RcCYP72A17-29739.m

AtCYP72A7

AtCYP72A8

AtCYP72A9
AtCYP72A
14
AtCYP7
2A10
AtCY
P7
2A
15
AtCY
P72A11
AtCY
P72A
13

RcCYP72A1

95
P
CY 716A
P7
2
2.m 16A
1
00
24
01
1-2
1G
00
1-3
822
05
012
48
6.m
8.m
000
008
875
568
AtC
YP
51G
AtC
1
YP
AtC
51G
YP7
2
10A
AtC
4
YP7
10A
3
AtC
YP7
10A
2
AtCY
P710A
1

74

13

00

00

.m

74

00

-3

A5

16

16

P7

CY

Rc

CY

P7

cC

B1

P7

-2

16

82

26

2-

29

.m

77

6.

08

00

04

83

RcCY

RcCYP72A15-29633.m000932

Rc

6A11
AtCYP9
6A2

56
62
00
.m
77
69
15
01
00
-3
.m
A1 5A1 A2
05
3
15
5
02
-3
P7 YP7 P73
A1
CY tC tCY
35
B1
A
Rc
A
P7
09
CY YP7
534
B2
Rc
C
004
09
67
0
At
P7
3
6.m
009
CY 709B
007
.m
At
2-3
P
068
174
009
-30
CY
09B
A4
At
P7
4.m
4
3
017
CY
P7
70
6-3
Rc
090
CY
4A
Rc
.m0
P73
174
CY
65
-30
Rc
A5
090
.m0
734
4
6
6
YP
017
090
RcC
A2-3
.m0
174
734
YP
3-30
34A
RcC
1
YP7
21A
9
0
RcC
YP7
0140
AtC
70.m
-301
21A1
YP7
RcC
1
78
10
P734A
0.m00
AtCY
1-2832
P734A
003136
RcCY
9983.m
2A16-2
3138
RcCYP7
983.m00
2A18-29
RcCYP7
1
AtCYP72C
12
4-29739.m0036

.m001089
RcCYP722A3-29863
092
29634.m002
RcCYP722A20.m014078
22A1-3017
RcCYP7
22A1
AtCYP7
000224
9982.m
22B1-2
P7
Y
RcC
88A4
P
Y
AtC
3
P88A
AtCY
1228
83
.m00
9
0
7
0031
-29
73
801.m
8A4
138
YP8
4-29
.m0
RcC
07A
7A4
170
YP7
P70
3-30
Y
A
RcC
7
6
AtC
P70
119
Y
0
C
Rc
.m0 7A2
5
1
1
70
223
-30
YP
A1
003 7A3
AtC
.m
707
1
P
70
0
Y
98
YP
1
2
C
RcC
t
7A
A
A2
70
707
YP
YP
C
t
C
A
Rc
18
P7
3
52
CY 145
10
At
00
00
21
m
.
m
.
6
41 014
3
66
99
09
0
9
9
0
0
-2
.m
1-2
.m
F1
63
8A
42 300
16
71
8
7
P
8
P
1
-2
CY
D1 048
CY
E1
Rc
16
Rc
00
16
P7
.m
P7
CY 776
CY
9
Rc
Rc
2
1C
16
P7
Y
cC
R

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

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 Arabidopsis. 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 protein
coding 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

123

Author's personal copy

142

(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 Arabidopsis 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 amplification 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 polymorphic forms were attributed to differences in genes, cryptic
inversions, etc., rather than to changes in the whole chromosome 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 CYP
genes exhibited zero phase suggesting the plausible evolution 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 evolution of A-type genes. Besides the presence of multiple
introns, a three-fold representation of phase 2 introns in nonA-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 projection 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

123

M. S. Kumar et al.

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 former Head, Department of Genetics, Osmania University for the
critical evaluation of the manuscript.

References
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3. Sujatha M, Reddy TP, Mahasi MJ (2008) Role of biotechnological interventions in the improvement of castor (Ricinus communis L.) and Jatropha curcas L. Biotechnol Adv 26:424435
4. Ogunniyi DS (2006) Castor oil: a vital industrial raw material.
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5. Scarpa A, Guerci A (1982) Various uses of the castor oil plant
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