volume 13 Number 8 1985 Nucleic Acids Research Eleven new sequence variants of citrus exocortis viroid and the correlation of sequence with pathogenicity Jane E.Visvader and Robert H.Symons Adelaide University Centre for Gene Technology, Department of Biochemistry, University of Adelaide, Adelaide, South Australia 5000, Australia Received 4 March 1985; Accepted 22 March 1985 ABSTRACT Full-length double-stranded cDNA was prepared from p u r i f i e d c i r c u l a r RNA of two new Australian f i e l d isolates of c i t r u s exocortis v i r o i d (CEV) using two synthetic oligodeoxynucleotide primers. The cDNA was then cloned into the phage vector M13mp9 for sequence analysis. Sequencing of nine cDNA clones of isolate CEV-0E30 and eleven cDNA clones of isolate CEV-J indicated that both isolates consisted of a mixture of v i r o i d species and led to the discovery of eleven new sequence variants of CEV. These new variants, together with the six reported previously, form two classes of sequence which d i f f e r by a minimum of 26 nucleotides in a t o t a l of 370 to 375 residues. These two classes correlate with two b i o l o g i c a l l y d i s t i n c t groups when propagated on tomato plants where one produces severe symptoms and the other gives rise to mild symptoms. Two regions of the native structure of CEV, comprising 18% of the t o t a l residues, d i f f e r between the sequence variants of mild and severe i s o l a t e s . Whether or not both of these regions are essential for the variation i n pathogenicity has yet to be determined. INTRODUCTION: Viroids are an unusual group of autonomously replicating plant pathogens and consist of a low molecular weight, c i r c u l a r , single-stranded RNA molecule which exists as a highly base-paired, rod-like structure (1,2). No viroid appears to encode protein products, either in vivo (3) or in vitro (4,5). These infectious agents must therefore interact d i r e c t l y with host factors, via sequence and structural signals, in order to replicate and exert their pathogenic effects. Sequence comparisons of naturally occurring variants of the same viroid are of importance in defining the conserved and variable features of the viroid molecule and may reflect regions that have a role in viroid replication and symptom expression in the host plant. Citrus exocortis viroid (CEV) is the causative agent of the exocortis disease of citrus (6). In addition to citrus species (family Rutaceae), CEV also infects members of the Solanaceae, Compositae, Cucurbitaceae, Leguminosae and Umbelliferae families (7). An isolate of CEV is defined as the viroid RNA obtained from a single citrus tree in the f i e l d and may consist of one or more © IRL Press Limited, Oxford, England. 2907 Nucleic Acids Research sequence v a r i a n t s . CEV-A, our reference Australian i s o l a t e (8) and a Californian i s o l a t e , CEV-C ( 9 ) , were both found to be mixtures of at least two RNA species. In a d d i t i o n , we have sequenced the major, or only variant two other Australian i s o l a t e s , CEV-DE25 and CEV-OE26 (10). in A l l of the s i x sequence variants of CEV reported so far contain 371 residues. In t h i s paper we report the sequences of CEV variants found in two new Australian i s o l a t e s , CEV-J and CEV-0E30. Sequence analysis revealed that both isolates contained a complex mixture of variants and has defined 11 new sequence variants which vary i n length from 370 t o 375 residues. Thus, 17 n a t u r a l l y occurring sequence variants of CEV have now been determined. D i f f e r e n t f i e l d isolates of potato spindle tuber v i r o i d (PSTV) e x i s t which produce symptoms varying from mild t o lethal on tomato plants (1). These changes in pathogenicity have been correlated with nucleotide differences occurring i n one region of the PSTV molecule ( 1 ) . causes d i f f e r e n t pathological effects on certain hosts ( 7 ) . Like PSTV, CEV Although CEV i s usually associated with stunting of growth and scaling of bark of c i t r u s species propagated on Poncirus t r i f o l i a t a rootstock, dwarfing can sometimes occur without scaling (11,12). The symptoms of exocortis can take months to appear on sensitive indicator plants such as Etrog c i t r o n (Citrus medica) or several years for orange trees (C. sinensis) grafted on P. rootstock ( 6 ) . trifoliata A more convenient host t o study s t r u c t u r e - f u n c t i o n relationships of CEV i s tomato (Lycopersicon escuientum) on which symptoms appear two to three weeks a f t e r i n o c u l a t i o n . We have propagated f i v e d i f f e r e n t isolates of CEV on tomato and have i d e n t i f i e d two d i s t i n c t b i o l o g i c a l groups, severe isolates and mild i s o l a t e s . A comparison of the sequence variants of mild and severe isolates has allowed the determination of regions of the CEV molecule which are associated with pathogenicity. MATERIALS AND METHODS Materials Avian myeloblastosis virus reverse transcriptase was obtained from Molecular Genetic Resources ( F l o r i d a ) and bacteriophage T4 DNA ligase and polynucleotide kinase from Boehringer. The Klenow fragment of E. c o l i DNA poiymerase I and a-32P-dATP and a-32P-dCTP (both 2,400 Ci/mmol) were obtained from BRESA Pty. Limited (Adelaide). CEV-specific oligodeoxynucleotides were kindly synthesized by Stephen Rogers and Derek Skingle. The phage M13- s p e c i f i c sequencing oligodeoxynucleotide primer was from New England Biolabs. 2908 Nucleic Acids Research Propagation of CEV Isolates and Purification of CEV Isolate CEV-DE30 was kindly provided by Dr. M. Schwingharaer as a leaf sample of a Bellamy navel orange on P. t r i f o l i a t a rootstock (Yanco, New South Wales; budline 033). Isolate CEV-J was a leaf sample of a Leng navel orange tree on P. t r i f o l i a t a rootstock and was kindly provided by R.H. Lloyd, Paringi, New South Wales. Both trees were dwarfed and showed marked scaling of the bark of the rootstock. Isolates CEV-A, CEV-DE25 and CEV-0E26 have been described previously (8,10). Extracts (13) of infected leaves were inoculated onto one week old tomato seedlings (L. esculentum cv. Grosse Lisse) and grown under a r t i f i c i a l l i g h t at 28°C for 14 h and in the dark about 22°C for 10 h. Partially purified nucleic acid extracts of tomato leaves harvested three to four weeks after inoculation were prepared (13) and used either for further propagation or for purification of CEV (13). The biological properties of isolates CEV-A, CEV-DE25, CEV-DE26, CEV-DE30 and CEV-J were examined on tomato. Plants were harvested four weeks after inoculation and nucleic acids extracted (14) from 15 g of infected leaves. The levels of CEV in these extracts were compared by Northern blot analysis (14). Synthesis and Cloning of Full-Length Double-Stranded cDNA of CEV The procedure used to construct full-length cDNA clones of CEV (Fig. 1) was similar to that of Fields and Winter (15) for the preparation of f u l l length cDNA clones of influenza virus RNAs. First strand cDNA was synthesized from 1 pg of circular CEV and 2.2 ug of DNA primer d(CGAAAGGAAGGAGACGAGCTCCTG) for 1.5 h at 44°C with 27 units of reverse transcriptase in a volume of 20 y l ; the concentration of KC1 was reduced from 70 mM to 35 mM. The products were denatured at 100°C for 2 minutes, incubated with 0.1 ug/ml RNase A at 37°C for 1 h and then fractionated by electrophoresis on a 3% polyacrylamide gel in 90 mM Tris base, 90 mM boric acid, 2 mM EDTA, 8 M urea, pH 8.3. Full-length cDNA was eluted, 5'-phosphorylated with ATP and polynucleotide kinase, hybridized with 0.27 ug of 5'-phosphorylated primer, d(CTGCTGGCTCCACAUCCGA), and incubated with the Klenow fragment of DNA polymerase I for 1 h at 25°C. The reaction was terminated by extraction with water-saturated phenol:chloroform (1:1), followed by ether washing, ethanol precipitation and, f i n a l l y , precipitation with 5 mM spermine (16) to remove unhybridized DNA primer and residual unincorporated deoxynucleotides. After blunt-end ligation of the doublestranded cDNA into the Smal site of the replicative form of the phage vector M13mp9 (17) using T4 DNA ligase, E. coli JM101 was transformed and singlestranded phage M13 DNA prepared from recombinant plaques. Phage DNA was 2909 Nucleic Acids Research sequenced by the dideoxy nucleotide chain termination technique (18) using an M13 specific DNA primer (17-mer). Gel compressions were resolved by the use of dITP (19) in the sequencing reactions or by electrophoresis of reaction mixtures in 6% polyaery 1 amide gels containing 40% formamide and 8 M urea. RESULTS Biological Properties of Five Isolates of CEV on Tomato Propagation of isolates CEV-A (8), CEV-OE25 (10), CEV-0E26 (10), CEV-DE30 and CEV-J on tomato has identified two groups of isolates according to t h e i r biological properties: (1) severe isolates which produce severe stunting and leaf epinasty, and (2) mild isolates which are essentially symptomless. The results are summarized in Table 1 . When equivalent amounts of extract from plants infected with each isolate of CEV were examined by Northern blot analysis after denaturation of the nucleic acids by glyoxalation (20), no significant differences were found in the concentration of CEV (data not shown). This finding indicated that variation in symptom expression from mild to severe was independent of the level of CEV in the host plant. Differences in pathogenicity could therefore be d i r e c t l y correlated with changes in nucleotide sequence of the variants. Construction of Full-Length cDNA Clones Preliminary sequencing of the viroid p u r i f i e d from tomatoes infected with the CEV-0E30 and CEV-J isolates using partial enzymatic cleavage methods (21) revealed that the viroids were mixtures of RNA species and thus could not be sequenced by direct methods. In order to determine the sequences of the variants in each i s o l a t e , i t was necessary to construct f u l l - l e n g t h cONA clones ( F i g . 1 ) . F i r s t strand cDNA synthesis was i n i t i a t e d on circular CEV with a synthetic oligonucleotide (24-mer) which hybridized to residues 175-198 (8) at the right-hand end of the proposed native structure of CEV. For second strand synthesis, a synthetic oligonucleotide (19-mer) corresponding to residues 199-217 was used as primer. The double-stranded cDNA was then bluntend ligated into the Smal site of the phage vector M13mp9 to produce f u l l length clones. The length of the oligonucleotide and/or the site of priming were found to be important c r i t e r i a for e f f i c i e n t synthesis of f i r s t strand cDNA. I n i t i a l l y , a short DNA primer (15-mer), complementary to part of the highly conserved central region of viroids (22), was used but i t was found to prime poorly. In contrast, the 24-mer DNA primed very e f f i c i e n t l y at the right-hand end of CEV where there i s less secondary structure and few G-C base 2910 Nucleic Acids Research TABLE 1 : Biological P r o p e r t i e s on Tomato S e e d l i n g s o f F i v e I s o l a t e s o f CEV REFERENCE ISOLATE PATHOGENICITY ON TOMATO ( c v . Gross pairs. Lisse) CEV-A 8 Severe CEV-DE25 10 Severe CEV-DE26 10 Mild CEV-DE30 T h i s work CEV-J T h i s work Mild Severe The complete sequences of 20 cDNA clones were determined by the dideoxy chain termination procedure (18). Sequences of Variants in Isolates CEV-DE30 and CEV-J Four variants were found in the nine cDNA clones of CEV-DE30 that were sequenced, while nine variants were found in 11 cDNA clones of CEV-J sequenced. These variants f a l l into two classes on the basis of their sequence: Class A sequences are very similar to that of CEV-A (8) while Class B sequences can be closely aligned with that of CEV-DE26 (10) which differs from CEV-A by 27 nucleotide changes (Fig. 2 ) . The nucleotide changes occurring in the sequence variants of the CEV-DE30 and CEV-J isolates relative to either of the CEV-A or CEV-0E26 isolates are shown in Fig. 3. Sequence changes are indicated with respect to CEV-A i f the variant belongs to the so 0 /r Cool to RT \ s—x ( \ dNTPs Reverse Transcriptase B A 24 ntier primer electrophoresis 3 T4 ONA l l g u e Sma I M13 mp»3 ' 5 ' 1. 19mer primer c 2. dNTPs * Klenow 3' RF Figure 1: Outline of the procedure used in the construction of full-length cONA clones of CEV. See Materials and Methods for d e t a i l s . The site of priming of the 24-mer DNA primer at the right-hand end of the predicted native structure of CEV is indicated by an arrow. 2911 Nucleic Acids Research 2% is B :a « 1:8 :s Us W III si! 3:3 Sil S.'S :::= jii Is :s H—8 iii S| S.'S 3:s -O in -a o t- sit o o 1- 01 a.— o 3 c c •a 0.0 a> —. W (0 < o 2912 SIS, CO lis CO CO < s d 3:5 I- O • Z3 US CT T3 O J •r CU1 Nucleic Acids Research Class A of sequence or relative to CEV-OE26 if the variant belongs to Class B. The nucleotide differences occurring in each sequence variant are summarized in Table 2 where variants (V) of CEV-DE30 are designated V-a to V-d, and those of CEV-J are designated V-a to V-h. The four sequence variants of isolate CEV-0E30 belong to Class B and differ in only one to three residues. Isolate CEV-J exhibited greater complexity and consisted of seven sequence variants of Class A (CEV-J, V-a to V-g) and two of Class B (CEV-J, V-h and V-i). Only one variant was identical between the CEV-0E30 and CEV-J isolates. The variant RNAs of CEV-0E30 and CEV-J range in size from 370 to 375 residues (Table 2 ) . In contrast to the five sequence variants of PSTV which are all 359 residues long (1), it would appear that strict conservation of the size of the CEV molecule is not an essential feature for replication. Only one of the sequence variants of isolates CEV-DE30 and CEV-J which have been determined so far has been found previously. Thus, these two isolates have defined 11 new sequence variants of CEV. The complexity of CEVDE30 and CEV-J suggests that the sequencing of further full-length cDNA clones will define even more new variants. Apart from the sequence heterogeneity occurring at six residues (residues 250, 251, 260, 263, 264 and 278) in the central region of the native structures of CEV-0E30 and CEV-J (Fig. 3 ) , the nucleotide differences are restricted to two regions on either side of the centre of the molecule. The majority of the nucleotide changes occurring in the variants of each sequence class alter the predicted secondary structure relative to that of the reference sequence of each class (Fig. 2 ) . Although the nucleotide changes at residues 260, 263, 264 and 278 are present in the centre of the native structure, they do not occur among the residues that constitute the highly conserved central region found in CEV, PSTV, chrysanthemum stunt viroid (CSV), coconut cadang cadang viroid (CCCV), tomato apical stunt viroid (TASV) and tomato planto macho viroid'(TPMV) (22,23). Seventeen Sequence Variants of CEV and their Correlation with Pathogenicity Sequence analysis of six different isolates of CEV has defined 17 variants which appear to form two classes of sequence, Class A and Class B (Figs. 2, 3 ) . The two classes correlate with differences in pathogenicity on tomato plants: Class A sequences are found in severe isolates of CEV (CEV-A, CEV-DE25 and CEV-J) while Class B sequences are found in mild isolates (CEVDE26 and CEV-0E30) as well as in CEV-J. CEV-J, a mixture of both Class A and B sequences, is associated with severe symptoms since the Class A sequence is 2913 UCUU *G6U0CC U %eu aC Ue»CCI) 8 g f if. I ' ' SO 371 39 50 /ii ^jt-300 .y. 300 A Au ^ C C Jf ^300 CEV-DE3O SEQUENCE VARIANTS .L.-.-W 1 2. c*iuiKtf *ASAGSC«S CS 66S8**MAS t ' i r /i eeu8C*6«C*CS***»M* CEV-J SEQUENCE VARIANTS C KCIT *Mtracei^»Miew«cii"ecg«cj.M a t * i»« \cc»u^uUt9tccM»t ccctu*iatsah e*McctfCv^EBC| e B / \ 1 1. CLASS B SEQUENCES I U JSO 80*i)CU \ t 37i c CEV-J SEQUENCE VARIANTS CLASS A SEQUENCES 6 c, * 8 C(KG C * « £ CC6«86 WO COGS««« *««ir e ^B'GUCUCUCUUCB, if. * -k fc e ^250 S MSU C k6BnCGBB6SS * S ^.250 6c \ if. if. if. 1. . "' A C if.jf.if.wa WO * 150 C U66 C U I 200 C C C 200 aC6UC(Clltlac 200 CC*GC68*6*»» iC C 8 C60AH C tWBBC 150 150 tC *«6°CSSfiMSfi* e « C a«C«Kfi6l) e M C 6 eGMtl C "ii\ I * « e CCBBB 6 jtActgUctc, K s s *0CC CCGS6fi 100 «SBAB C U U IG6ABCU D «ccuc g a Nucleic Acids Research present. Although the biological properties of the Californian isolate of CEV (CEV-C) sequenced by Gross et al. (9) are unknown, we predict that it would cause severe symptoms on tomato, on the basis of its Class A sequence. Monomeric full-length cDNA clones of the sequence variants CEV-A and CEVAM (10) in the BamHI site of the vector pSP6-4 (24) are infectious on tomato where they produce severe symptoms (unpublished results). Both these variants are Class A sequences and thus confirm the correlation between Class A sequence and the severe phenotype. Unfortunately, the monomeric full-length cDNA clones of isolates CEV-J and CEV-DE30 described in this paper are not infectious on tomato. This is presumably a consequence of the site in the CEV molecule (right-hand end) used in the construction of these clones. This lack of infectivity precluded the definitive confirmation of the correlation between Class B sequences and the mild phenotype. Sequence heterogeneity within the 17 sequence variants of CEV occurs in the central region and in two regions on either side of this. The nucleotide changes located in the central area occur in both severe and mild isolates (Fig. 3) and are thus independent of changes in pathogenicity. Severe and mild isolates differ in two regions, designated P L and PR (P = pathogenicity), of the native structure (Figs. 3,4). It is concluded that either one or both of these regions are responsible for the variation in pathogenicity. Potential Translation Products of CEV Variants Potential polypeptide products of the plus and minus strands of each sequence variant were analysed since any conserved polypeptide sequence may indicate a possible functional role in vivo. We have previously reported the putative translation products of CEV-A (8) where both AUG and GUG were used as possible initiation codons. Four out of the 17 variants considered here contain one AUG in the plus strand while all 17 variants contain one AUG in the minus strand. There are no fully conserved or even partially conserved AUG-initiated polypeptides in the minus strand. Only one potential polypeptide product of 15 amino acids is conserved between the CEV variants; this initiates with a GUG at residue 339 and terminates at residue 13 (UGA) of the plus strand. Since a 5'-proximal AUG initiation codon appears essential for the initiation of translation of eukaryotic RNA (25,26), it seems highly Figure 3: Classification of the sequence variants of isolates CEV-DE30 and CEV-J into Class A and Class B sequences. The sites of the nucleotide differences occurring in the sequence variants of each isolate, relative to either CEV-A (Class A) or CEV-DE26 (Class B) are indicated by a star. Isolate CEV-J contains both Class A and Class B sequences whereas isolate CEV-DE3O contains Class B sequences only. 2915 Nucleic Acids Research TABLE 2: SEQUENCE HETEROGENEITY OF VAR IANTS IN ISOLATES CEV-DE30 AND CEV-J CEV ISOLATE SEQUENCE VARIANTS (V) DETERMINED FOR EACH ISOLATE SIZE (RESIDUES) CEV-0E30 (Class B) V-a V-b V-c V-d 371 370 371 372 CEV-J (Class A) V-a 371 V-b 371 V-c 371 V-d 372 V-e 372 V-f 374 V-g 375 V-h V-i 371 371 CEV-J (Class B) NUCLEOTIDE CHANGES RELATIVE TO EITHER CEV-A (CLASS A) OR CEV-DE26 (CLASS B ) * 301 U + A 250 -A, 301 U + A 263 A -• C 46 G * A, 70-71 + G, 263 A * C, 301 U + A 234 U + A, 264 G + U, 278 A + U, 301 A * G 50 G + A, 234 U + A, 264 G + U, 278 A + U, 301 A + G 70 -G, 129-130 +U, 234 U + A, 263-264 AG • CU, 278 A • U, 313 G + A 129-130 +U, 234 U • A, 263-264 AG •>• CU, 278 A + U 129-130 +U, 234 U + A, 251 G + C, 263-264 AG -> CU, 278 A + U, 313 G • A, 321 A + U, 129-130 +U, 132-133 +C, 134-135 +G, 234 U * A, 260 U + C, 263-264 AG + CU, 278 A • U, 313 G + A 129-130 +U, 132-133 +C, 134-135 +G, 231 G + C, 234 U + A, 235-236 +C, 263-264 AG + CU, 278 A • U, 313 G + A 301 U + A 251 G + C, 301 U • A * Residue numbers at the sites of change in either CEV-A (Class A) or CEV-0E26 (Class B). Nucleotide changes in CEV-J (Class A) are indicated relative to CEV-A while nucleotide changes in CEV-J (Class 8) and CEV-DE30 (Class B) are indicated relative to CEV-DE26. Nucleotide exchanges are represented by X •»• Y where X occurs in CEV-A or CEV-DE26 and Y occurs in variants of isolates CEV-J or CEV-DE30. An insertion i n a sequence variant is represented by + Y and a deletion by - X. 2916 Nucleic Acids Research 72 c /A 324 287 P, 128 139 n o 238 227 PD Figure 4: Diagram showing the two regions, P L and P R (boxed), of the native structure of CEV that differ between severe and mild isolates (Table 1 ) . Severe symptoms on tomato correlate with Class A sequences and mild symptoms with Class B sequences. The residue numbers on the outside of the boundaries of the two regions are indicated and are the same for both Class A and Class B sequences (Fig. 2 ) . unlikely that CEV encodes any functional polypeptide products. These findings are consistent with the lack of conservation between possible translation products of both the plus and minus strands of the closely related viroids, CEV, PSTV and CSV (8,21). These data, therefore, provide further evidence that viroids rely entirely on host-encoded components for their replication. DISCUSSION Sequence analysis of full-length cDNA clones of the CEV-A, CEV-DE30 and CEV-J isolates has indicated that each isolate is a mixture of RNA species. It is feasible that all naturally-occurring viroid infections contain a mixture of two or more sequence variants. If this is a general feature of viroid infection then i t has important implications in the correlation of viroid sequence with a particular biological property. Fortunately, the ability to prepare infectious full-length cDNA clones of viroids (27-30, unpublished results) allows experiments requiring infection by a single sequence variant to be carried out. The large number of sequence variants occurring in some isolates of CEV, in particular CEV-J, could be accounted for by either, (1) a high copy error rate (31) by an RNA polymerase replicating a single RNA species, or (2) infection of one plant by several sequence variants during propagation of citrus varieties by grafting or during regular practices such as pruning (6). The long potential l i f e of citrus trees in the field (over 60 years) would allow the accumulation of sequence variants in each tree by either route. It is not known i f each of the sequence variants of CEV replicate with a similar efficiency or i f a mixture is required for complementation of function to enable infection. The second possibility appears unlikely since 2917 Nucleic Acids Research certain full-length cDNA clones (i.e. unique species) of PSTV (27,30), hop stunt viroid (28,29) and CEV (unpublished results) are infectious. Two regions of the native structure of CEV, P L and P R (Fig. 4 ) , were found to differ in sequence between the two biological groups defined by Class A and Class B sequences (Fig. 2 ) . These two regions fall within the P (pathogenicity) and V (variable) domains of viroids described by Keese and Symons (32). The P|_ region is characterised by an oligo(A) sequence conserved in all viroids and has been found to correlate with variation in pathogenicity of PSTV on tomato (1). This suggests that at least the P L region of CEV is associated with symptom expression. The PR region of CEV is the most variable domain between all viroids (32). Although variation occurs at two bases in the Ppj region of the five PSTV variants sequenced so far (1), there is no correlation with pathogenicity. However, it remains to be determined whether or not the PR region is associated with pathogenicity in the host plant. One approach to resolving this problem would be to construct full-length chimeric cDNA clones of CEV with the two possible arrangements of the P L and P R regions derived from mild and severe sequence variants. Sanger (1) has recently proposed a mechanism for the involvement of the left-hand variable region of PSTV in pathogenicity, whereby this region becomes increasingly unstable, and hence is more accessible to interaction with host factors, as pathogenicity increases. Since CEV and PSTV share approximately 60% sequence homology (8,9) and possess similar host ranges and biological properties (6,7), the free energies (AG) of the predicted secondary structures of the corresponding Pj_ regions of sequence variants within severe and mild isolates of CEV were calculated (33; D. Riesner, personal communication) In direct contrast to PSTV, it was found that the stability of the P L region (residues 48-72, 297-324) of severe variants (AG -51 to -69 KJ/mol) was considerably greater than that of the mild variants (AG +7 to -5 KJ/mol). Furthermore, there does not appear to be any consensus sequence in the Pj_ regions of the mild and severe forms of PSTV and CEV. It is therefore possible that pathogenicity is influenced by a number of different sites in the P L region and/or the PR of CEV rather than a single site. In vitro mutagenesis of the P L and PR regions of full-length cDNA clones of CEV, in conjunction with infectivity studies, should define the site(s) that play a role in determining viroid pathogenicity. The correlation between two classes of CEV sequence variants and differences in pathogenicity on tomato, may not apply to citrus. Isolates CEV-0E30 and CEV-0E26 both produce mild symptoms on tomato but differ on 2918 Nucleic Acids Research citrus where CEV-0E30 is associated with scaling of the bark of the rootstock and dwarfing of the orange tree and CEV-DE26 is associated with dwarfing only (M. Schwinghamer, personal communication). Furthermore, CEV-OE25, which d i f f e r s in both sequence and symptom expression on tomato relative to CEV-DE3O and CEV-DE26, is associated with identical symptoms to CEV-DE26 on orange trees on P. t r i f o i i a t a rootstock (M. Schwinghamer, personal communication). CEV presumably interacts with homologous cellular components in c i t r u s and tomato, but the pathological effects d i f f e r according to the host. ACKNOWLEDGEMENTS We thank D r . M. Schwinghamer and R.H. Lloyd f o r s u p p l y i n g CEV-infected c i t r u s samples, D r . D. Riesner f o r unpublished thermodynamc d a t a , Stephen Rogers and D r . 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