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Molecular Evidence for Occurrence of Tomato leaf curl New Delhi virus in Ash Gourd (Benincasa hispida) Germplasm Showing a Severe Yellow Stunt Disease in India

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Page 1: Molecular Evidence for Occurrence of Tomato leaf curl New Delhi virus in Ash Gourd (Benincasa hispida) Germplasm Showing a Severe Yellow Stunt Disease in India

Dear Author,Here are the proofs of your article.

• You can submit your corrections online, via e-mail or by fax.• For online submission please insert your corrections in the online correction form. Always

indicate the line number to which the correction refers.• You can also insert your corrections in the proof PDF and email the annotated PDF.• For fax submission, please ensure that your corrections are clearly legible. Use a fine black

pen and write the correction in the margin, not too close to the edge of the page.• Remember to note the journal title, article number, and your name when sending your

response via e-mail or fax.• Check the metadata sheet to make sure that the header information, especially author names

and the corresponding affiliations are correctly shown.• Check the questions that may have arisen during copy editing and insert your answers/

corrections.• Check that the text is complete and that all figures, tables and their legends are included. Also

check the accuracy of special characters, equations, and electronic supplementary material ifapplicable. If necessary refer to the Edited manuscript.

• The publication of inaccurate data such as dosages and units can have serious consequences.Please take particular care that all such details are correct.

• Please do not make changes that involve only matters of style. We have generally introducedforms that follow the journal’s style.Substantial changes in content, e.g., new results, corrected values, title and authorship are notallowed without the approval of the responsible editor. In such a case, please contact theEditorial Office and return his/her consent together with the proof.

• If we do not receive your corrections within 48 hours, we will send you a reminder.• Your article will be published Online First approximately one week after receipt of your

corrected proofs. This is the official first publication citable with the DOI. Further changesare, therefore, not possible.

• The printed version will follow in a forthcoming issue.

Please noteAfter online publication, subscribers (personal/institutional) to this journal will have access to thecomplete article via the DOI using the URL: http://dx.doi.org/[DOI].If you would like to know when your article has been published online, take advantage of our freealert service. For registration and further information go to: http://www.springerlink.com.Due to the electronic nature of the procedure, the manuscript and the original figures will only bereturned to you on special request. When you return your corrections, please inform us if you wouldlike to have these documents returned.

Page 2: Molecular Evidence for Occurrence of Tomato leaf curl New Delhi virus in Ash Gourd (Benincasa hispida) Germplasm Showing a Severe Yellow Stunt Disease in India

Metadata of the article that will be visualized in OnlineFirst

Please note: Images will appear in color online but will be printed in black and white.ArticleTitle Molecular Evidence for Occurrence of Tomato Leaf Curl New Delhi Virus in Ash Gourd (Benincasa

hispida) Germplasm Showing a Severe Yellow Stunt Disease in IndiaArticle Sub-Title

Article CopyRight Indian Virological Society(This will be the copyright line in the final PDF)

Journal Name Indian Journal of Virology

Corresponding Author Family Name RoyParticle

Given Name AnirbanSuffix

Division Germplasm Evaluation Division

Organization National Bureau of Plant Genetic Resources

Address 110012, New Delhi, India

Email [email protected]

Author Family Name SpoorthiParticle

Given Name P.Suffix

Division Germplasm Evaluation Division

Organization National Bureau of Plant Genetic Resources

Address 110012, New Delhi, India

Email

Author Family Name PanwarParticle

Given Name G.Suffix

Division Germplasm Evaluation Division

Organization National Bureau of Plant Genetic Resources

Address 110012, New Delhi, India

Email

Author Family Name BagParticle

Given Name Manas KumarSuffix

Division Germplasm Evaluation Division

Organization National Bureau of Plant Genetic Resources

Address 110012, New Delhi, India

Email

Author Family Name PrasadParticle

Given Name T. V.

Page 3: Molecular Evidence for Occurrence of Tomato leaf curl New Delhi virus in Ash Gourd (Benincasa hispida) Germplasm Showing a Severe Yellow Stunt Disease in India

Suffix

Division Germplasm Evaluation Division

Organization National Bureau of Plant Genetic Resources

Address 110012, New Delhi, India

Email

Author Family Name KumarParticle

Given Name GunjeetSuffix

Division Germplasm Evaluation Division

Organization National Bureau of Plant Genetic Resources

Address 110012, New Delhi, India

Email

Author Family Name GangopadhyayParticle

Given Name K. K.Suffix

Division Germplasm Evaluation Division

Organization National Bureau of Plant Genetic Resources

Address 110012, New Delhi, India

Email

Author Family Name DuttaParticle

Given Name M.Suffix

Division Germplasm Evaluation Division

Organization National Bureau of Plant Genetic Resources

Address 110012, New Delhi, India

Email

Schedule

Received 23 August 2012

Revised

Accepted 10 September 2012

Abstract An evaluation of 70 accessions of ash gourd germplasm grown at National Bureau of Plant Genetic Resources,New Delhi, India during Kharif season (2010) showed natural occurrence of a yellow stunt disease in threeaccessions (IC554690, IC036330 and Pusa Ujjwal). A set of begomovirus specific primers used in PCR gaveexpected amplicon from all the symptomatic plants; however no betasatellite was detected. Complete genomeof the begomovirus (DNA-A and DNA-B), amplified through rolling circle amplification, was cloned andsequenced. The begomovirus under study shared high sequence identities to different isolates of Tomato leafcurl New Delhi virus (ToLCNDV) and clustered with them. Among those isolates, the DNA-A and DNA-Bof the present begomovirus isolate showed highest 99.6 and 96.8 % sequence identities, respectively with anisolate reported on pumpkin from India (DNA-A: AM286433, DNA-B: AM286435). Based on the sequenceanalysis, the begomovirus obtained from ash gourd was considered as an isolate of ToLCNDV. Thus, thepresent findings constitute the first report of occurrence of a new yellow stunt disease in ash gourd from Indiaand demonstrated the association of ToLCNDV with the symptomatic samples. Occurrence of ToLCNDVin ash gourd germplasm not only adds up a new cucurbitaceous host of this virus but also raises the concernabout the perpetuation of this virus in absence of its main host tomato and thus has an epidemiologicalrelevance for understanding the rapid spread of this virus in tomato and other hosts in Indian sub-continent.

Keywords (separated by '-') Benincasa hispida - Begomovirus - Tomato leaf curl New Delhi virus - Rolling circle amplification

Page 4: Molecular Evidence for Occurrence of Tomato leaf curl New Delhi virus in Ash Gourd (Benincasa hispida) Germplasm Showing a Severe Yellow Stunt Disease in India

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Page 6: Molecular Evidence for Occurrence of Tomato leaf curl New Delhi virus in Ash Gourd (Benincasa hispida) Germplasm Showing a Severe Yellow Stunt Disease in India

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SHORT COMMUNICATION1

2 Molecular Evidence for Occurrence of Tomato Leaf Curl New

3 Delhi Virus in Ash Gourd (Benincasa hispida) Germplasm

4 Showing a Severe Yellow Stunt Disease in India

5 Anirban Roy • P. Spoorthi • G. Panwar •

6 Manas Kumar Bag • T. V. Prasad • Gunjeet Kumar •

7 K. K. Gangopadhyay • M. Dutta

8 Received: 23 August 2012 / Accepted: 10 September 20129 � Indian Virological Society 2012

10 Abstract An evaluation of 70 accessions of ash gourd

11 germplasm grown at National Bureau of Plant Genetic

12 Resources, New Delhi, India during Kharif season (2010)

13 showed natural occurrence of a yellow stunt disease in three

14 accessions (IC554690, IC036330 and Pusa Ujjwal). A set of

15 begomovirus specific primers used in PCR gave expected

16 amplicon from all the symptomatic plants; however no

17 betasatellite was detected. Complete genome of the be-

18 gomovirus (DNA-A and DNA-B), amplified through rolling

19 circle amplification, was cloned and sequenced. The be-

20 gomovirus under study shared high sequence identities to

21 different isolates of Tomato leaf curl New Delhi virus

22 (ToLCNDV) and clustered with them. Among those iso-

23 lates, the DNA-A and DNA-B of the present begomovirus

24 isolate showed highest 99.6 and 96.8 % sequence identities,

25 respectively with an isolate reported on pumpkin from India

26 (DNA-A: AM286433, DNA-B: AM286435). Based on the

27 sequence analysis, the begomovirus obtained from ash gourd

28 was considered as an isolate of ToLCNDV. Thus, the

29 present findings constitute the first report of occurrence of a

30 new yellow stunt disease in ash gourd from India and

31 demonstrated the association of ToLCNDV with the symp-

32 tomatic samples. Occurrence of ToLCNDV in ash gourd

33 germplasm not only adds up a new cucurbitaceous host of

34 this virus but also raises the concern about the perpetuation

35 of this virus in absence of its main host tomato and thus has

36 an epidemiological relevance for understanding the rapid

37spread of this virus in tomato and other hosts in Indian sub-

38continent.

39

40Keywords Benincasa hispida � Begomovirus � Tomato

41leaf curl New Delhi virus � Rolling circle amplification

42Ash gourd (Benincasa hispida), also known as wax gourd,

43white gourd or winter melon; the only member of the genus

44Benincasa belonging to family Cucurbitaceae, is an

45important vegetable crop in India. In northern India and

46Pakistan, the vegetable is widely used to prepare a popular

47candy called Petha. In Ayurvedic remedies, it is believed to

48increase appetite and its fresh juice is used to cure kidney

49stones.

50Begomoviruses (family Geminiviridae) are characterized

51by their tween-quasiisometric virion of 20 9 30 nm and are

52exclusively transmitted by whitefly (Bemisia tabaci) in a

53persistent manner. Genome of begomoviruses is either

54bipartite i.e. consisted of two circular single stranded DNA

55molecules designated as DNA-A and DNA-B or monopar-

56tite having only one component homologous to that of

57DNA-A of bipartite begomoviruses. In India, first begomo-

58virus disease of cucurbits was recorded as yellow vein

59mosaic disease of pumpkin during 1955. Later, it was

60established that Squash leaf curl China virus was responsi-

61ble for the disease [9]. Begomovirus disease problem in

62cucurbits emerged in India during 1980s onward. Only two

63begomovirus species, Squash leaf curl China virus

64(SLCCNV) and Tomato leaf curl New Delhi virus (ToL-

65CNDV) are known to affect different cucurbits in India [8].

66In case of ash gourd, a yellow leaf disease was reported

67from Thailand and partial characterization of the associated

68virus indicated presence of a begomovirus with the disease

69[13]. However, the exact identity of the begomovirus

A1 A. Roy (&) � P. Spoorthi � G. Panwar � M. K. Bag �

A2 T. V. Prasad � G. Kumar � K. K. Gangopadhyay � M. Dutta

A3 Germplasm Evaluation Division, National Bureau of Plant

A4 Genetic Resources, New Delhi 110012, India

A5 e-mail: [email protected]

123Journal : Large 13337 Dispatch : 15-9-2012 Pages : 4

Article No. : 115h LE h TYPESET

MS Code : INJV-D-12-00126 h CP h DISK4 4

Indian J. Virol.

DOI 10.1007/s13337-012-0115-y

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70 associated with such disease was not confirmed due to

71 unavailability of full length sequence of the begomovirus,

72 which is essential for nomenclature of any begomovirus.

73 Another begomovirus associated disease of ash gourd was

74 reported from central Thailand where the infected plants

75 exhibited yellow leaf curl symptom [14]. An isolate of

76 SLCCNV was reported to be associated with such disease.

77 Prior to this report, neither any begomovirus associated

78 disease nor was any begomovirus reported from ash gourd

79 in India.

80 In the evaluation experiment on 70 accessions of ash gourd

81 germplasm, during Kharif season (2010) at National Bureau

82 of Plant Genetic Resources, New Delhi, India, seven plants of

83 three accessions (IC554690, IC036330 and Pusa Ujjwal)

84 showed a yellow stunt disease. The leaves of the diseased

85 plants became small, rough and brittle and exhibited yel-

86 lowing, puckering and vein thickening symptoms (Fig. 1a).

87 Overall the infected plants appeared severely stunted. Con-

88 siderable population of whiteflies (Bemisia tabaci) was

89 noticed on the field, however, the number of adult whiteflies

90 was more (average 30–50 per plant) in the symptomatic

91 plants than the asymptomatic one (average 5–15 per plant).

92 Based on the symptoms and the association of more whiteflies

93 with the diseased plants, a begomovirus infection was sus-

94 pected. Therefore, attempt was made to detect the begomo-

95 virus through PCR using begomovirus specific primers

96 PAL1v722/PAL1c1960 [2]. The PCR conditions for ampli-

97 fication were denaturation at 94 �C for 3 min, followed by 30

98 cycles each consists of denaturation for 30 s at 94 �C,

99 annealing for 30 s at 52 �C and synthesis for 80 s at 72 �C

100 with final extension for 10 min at 72 �C. All the seven

101 symptomatic samples yielded an expected 1.2 kb amplicon

102 (Fig. 1b), whereas no such amplification was obtained from

103 asymptomatic plants, thus, indicating the association of a

104 begomovirus with symptomatic samples. To detect the pres-

105 ence of betasatellite, amplification was carried out with uni-

106 versal betasatellite primers b01/b02 [1], however, the reaction

107did not showed any positive result even with repetitive

108attempts.

109Full length genomeof the begomoviruswas isolated through

110rolling circle amplification (RCA) using/29DNApolymerase

111(ThermoScientific, USA) following the standard protocol [15].

112The RCA products digested with BglI, EcoRV and XbaI pro-

113duced c.a. 2.7 kb fragments corresponding to the unit genome-

114length of begomovirus, while PstI enzyme produced a c.a.

1152.7 kb fragment along with one c.a. 1.5 kb and one c.a. 1.2 kb

116fragments (Fig. 1c). The 2.7 kb fragments generated separately

117byPstI (PstAG) andXbaI (XbaAG)were purified usingWizard

118SV Gel and PCR Clean-up System (Promega Corporation,

119Madison, WI, USA) and ligated to PstI and XbaI—linearized

120pUC18 vector, respectively. The ligation mixture was used to

121transform Escherichia coli strain DH5a. Vectors containing

122inserts of the expected size were identified in miniprep

123screening by size estimation. The sequences of PstAG (2,738

124nucleotides) and XbaAG (2,694 nucleotides) were obtained in

125forward and reverse directions from commercial facility

126(ChromousBiotech, India) and the sequenceswere deposited in

127the nucleotide sequences database with the accession numbers

128JN208136 and JN208137, respectively. The sequences of

129PstAG and XbaAG were initially searched for similarity using

130BLASTnProgram (http://www.ncbi.nlm.nih.gov/BLAST) and

131the sequences which showed high scores were selected for

132further analysis. The genome organization was deter-

133mined by analyzing those sequences using ORF Finder

134(www.ncbi.nlm.nih.gov/gorf/gorf.html). Sequence identity

135matrix was generated using Bioedit Sequence Alignment Edi-

136tor (version 5.0.9) [4]. After multiple alignment, phylogenetic

137analysis was done inMEGA4.0 software [19] using the default

138parameters of Maximum Parsimony, and the Bootstrapped

139consensus dendrogram was generated with 1,000 replication

140(Fig. 2).

141Sequences of PstAG and XbaAG showed[90 and[86 %

142sequence identities with DNA-A and DNA-B sequences of

143different isolates of ToLCNDV, respectively. Among the

Fig. 1 a Symptom of yellowing, puckering and vein thickening in ash

gourd leaf. b Detection of begomovirus through PCR. Lane 1–7:

symptomatic sample yielded a 1.2 kb amplicon which was not present

in asymptomatic samples. c RCA product digested with BglI (lane 1),

EcoRV (lane 2), PstI (lane 3) and XbaI. M 1 kb molecular weight

marker, AS asymptomatic sample

A. Roy et al.

123Journal : Large 13337 Dispatch : 15-9-2012 Pages : 4

Article No. : 115h LE h TYPESET

MS Code : INJV-D-12-00126 h CP h DISK4 4

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144 different isolates of ToLCNDV, the DNA-A (PstAG) and

145 DNA-B (XbaAG) of the present isolate showed highest 99.6

146 and 96.8 % sequence identity with that of pumpkin isolate

147 (DNA-A: AM286433, DNA-B: AM286435) reported from

148 New Delhi. A total of 33 begomovirus isolates were taken for

149 phylogenetic relationship study which revealed that the present

150 isolate formed cluster with different isolates of ToLCNDV

151 with respect to both DNA-A and DNA-B sequences. Based on

152 sequence analysis, it is evident that the present isolate of be-

153 gomovirus, associated with yellow stunt disease of ash gourd,

154 is an isolate of ToLCNDV and hence, the descriptor for this

155 isolate is proposed as ToLCNDV-[India:New Delhi:Ash

156 gourd:2011] (ToLCNDV-[IN:ND:Ash:11]).

157 The genome organization of the DNA-A and DNA-B of

158 ToLCNDV-[IN:ND:Ash:11] was similar to that of all other

159 Old World bipartite begomoviruses. DNA-A has four open

160 reading frames (ORFs) on the complementary strand (AC1;

161 1,499–2,584, AC2; 1,177–1,596, AC3; 1,047–1,457, and

162 AC4; 2,251–2,427) and two ORFs on the viral sense strand

163 (AV1; 280–1,053 and AV2; 120–458). The AV1 (CP) ORF

164 was 774 nt long encoding 28.6 kDa coat protein. AV2 was

165 339 nt long encoding 12.5 kDa protein. The AC1 was

166 1,086 nt long encoding 40.2 kDa replication associated

167 protein (Rep). AC2 was 420 nt long encoding (15.5 kDa)

168 transcription activator protein. The AC3 was 411 nt long

169 encoding 15.2 kDa replication enhancer protein. The AC4

170was 177 nt long encoding 6.5 kDa protein. DNA-B con-

171tains two ORFs, one on the complementary strand (BC1;

1721,306–2,151) and the other on sense strand (BV1; 442–

1731,248) coding for a movement protein (31.3 kDa) and a

174nuclear shuttle protein (29.8 kDa), respectively.

175ToLCNDV is an emerging problem in various agricul-

176tural crops in India, Pakistan, Bangladesh and Thailand [8].

177It was reported for the first time in India from tomato and

178further its infectivity study demonstrated that both DNA-A

179and DNA-B are essential for symptom development [10].

180ToLCNDV is known to infect tomato in India since nearly

181two decades, but during the last one decade, its host range

182has increased enormously to various crops such as potato

183[21], papaya [12], eggplant [11] okra [23] and several

184cucurbitaceous vegetables like bottle gourd, bitter gourd,

185cucumber, ivy gourd, long melon, pumpkin, ridge gourd

186and watermelon in northern India and chayote in north-

187western India [7, 16, 17, 20]. In Pakistan, besides tomato,

188ToLCNDV was also reported on crops like chilli [5], bitter

189gourd [18], and on weed Eclipta prostrata [3]. In Thailand,

190ToLCNDV has been reported to infect bottle gourd,

191cucumber and muskmelon [6]. The frequency of new strains

192of ToLCNDV emerging in several agricultural crops and

193non-crop species indicated that the virus species has diverse

194virulent strains in the field and thus pose a serious threat to

195vegetable cultivation particularly in Indian sub-continent.

Fig. 2 Phylogenetic analysis of the DNA-A (a), and DNA-B (b) of

ToLCNDV associated with yellow stunt disease of ash gourd,

showing distinct relationships to isolates of ToLCNDV. ToLCBV

tomato leaf curl bangalore virus, ToLCKeV tomato leaf curl kerala

virus, ToLCPNV tomato leaf curl pune virus, ToLCJoV tomato leaf

curl joydebpur virus, ToLCRV tomato leaf curl rajasthan virus,

ToLCGV tomato leaf curl gujarat virus, ToLCKV tomato leaf curl

karnataka virus. The maximum parsimonious tree was constructed

using MEGA 4.0 software. Percent bootstrap values are indicated in

the node

Molecular Evidence for Occurrence of Tomato Leaf Curl New Delhi Virus

123Journal : Large 13337 Dispatch : 15-9-2012 Pages : 4

Article No. : 115h LE h TYPESET

MS Code : INJV-D-12-00126 h CP h DISK4 4

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196 In the present study, we report the occurrence of a

197 severe yellow stunt disease in ash gourd germplasm from

198 India and documented complete sequence of an isolate of

199 ToLCNDV associated with such disease of ash gourd for

200 the first time. The use of such susceptible germplasm

201 accessions in breeding programme is a serious matter of

202 concern as it may lead to introduction of susceptible genes

203 into cultivated varieties and such event has already been

204 reported in many other crops [22]. Occurrence of ToL-

205 CNDV in cucurbitaceous crops was not recorded before

206 1980s. Presently ToLCNDV is a serious concern for most

207 of the cucurbitaceous vegetable crops. These crops are

208 mainly grown during Kharif season and their harvesting

209 time often coincides with the sowing time of tomato in

210 northern India. Thus on the epidemiological point of view

211 the natural occurrence of ToLCNDV in newer cucurbita-

212 ceous host strongly supports its perpetuation in absence of

213 main host and its subsequent spread to tomato.

214 Acknowledgments The authors wish to thank Director, National215 Bureau of Plant Genetic Resources, New Delhi, India for providing216 necessary facilities to carry out the study.

217 References

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