pool 1 and pool 2) were mapped without (A) or with (B) mismatches to the reference
sequences of the *Solanum lycopersicum* genome (nuclear, chloroplast and mitochondrion) and
the viral genomes (IL and IS76), sorted by polarity (forward, reverse, total) and counted. The
counts of plant and viral reads mapped without mismatches were then normalized per million
of total reads (RPM) in each library (C).
(XLSX)

**S2 Dataset.** Counts of Illumina small RNA-seq reads from susceptible (S) and Ty-1 resistant (R) tomato plants mock-inoculated or infected with TYLCV-IL, its recombinant derivative TYLCV-IS76 or their combination (IL+IS76) at 10 and 30 days post inoculation (dpi). The Illumina 15-34 nt reads from each library (two biological replicates per condition: pool 1 and pool 2) were mapped without (A) or with (B) mismatches to the reference sequences of the *Solanum lycopersicum* genome (nuclear, chloroplast and mitochondrion) and the viral genomes (IL and IS76), sorted by size (15 nt through 34 nt) and polarity (forward, reverse, total) and then counted. The counts of plant and viral reads mapped without mismatches were then normalized per million of total reads (RPM) in each library (C) and were also sorted by 5'-terminal nucleotide identity (5'A, 5'C, 5'G, 5'U) and then counted in percentage of total (D).
(XLSX)

**S3 Dataset.** Single nucleotide resolution maps of Illumina mRNA-seq reads representing viral transcripts from susceptible (S) and Ty-1 resistant (R) tomato plants infected with TYLCV-IL, its recombinant derivative TYLCV-IS76 or their combination (IL+IS76) at 10 and 30 days post inoculation (dpi). For each condition, Illumina 100 nt paired-end reads of the two biological replicates (1 and 2) were mapped onto the reference sequences of IL and IS76 using BWA and the resulting BAM files were analysed by MISIS-2 (Seguin et al. 2016 [60]) to generate tables of reads mapped to each reference sequence with zero mismatches. The reference sequences were extended at the 3-end by 99 nts from the 5'-terminal sequence to allow for mapping RNAs derived from the circular viral genome including the first and last nucleotide of the linear reference. In each table, the first column gives nucleotide positions of the corresponding viral genome sequence. In the next columns, the positions of 5'-terminal nucleotide of sense RNAs and 3'-terminal nucleotide of antisense RNAs along the reference sequence are indicated, and the read counts are given for each RNA mapped with zero mismatches to the forward (rightward) strand (columns fwd1 and fwd2) and the reverse (leftward) strand (columns rev1 and rev2), along with the total counts of reads mapped at the respective positions of the forward (rightward) and reverse (leftward) strands in the two replicates divided by 2 (i.e., average counts). In each table file on the right side, histograms of the average counts of rightward and leftward reads are inserted with the rightward reads colored in blue and the leftward reads colored in red. In the case of mixed infections (IL+IS76), the number of reads derived from each virus was counted at each SNP using MISIS-2 (Seguin et al. 2006 [60]) and a percentage of reads derived from each virus (or its selected region) was calculated. The average percentage at all SNPs of the viral genome (or its selected region) was applied on all parts of the genome (or its selected region) that contain no SNPs to estimate the number of reads derived from the entire genome of each virus (or its selected region) or each strand of the viral genome (or its selected region).
(XLSX)

**S4 Dataset.** Single-nucleotide resolution maps of viral 20-25 nt small (s)RNAs in susceptible (S) and Ty-1 resistant (R) tomato plants infected with TYLCV-IL, its recombinant derivative TYLCV-IS76 or their combination (IL+IS76) at 10 and 30 days post inoculation
(dpi). For each condition, Illumina 20–25 nt reads of the two biological replicates were com-
bined and mapped onto the reference sequences of IL and IS76 using BWA and the resulting
BAM files were analysed by MISIS-2 (Seguin et al. 2016 [60]) to generate tables of reads
mapped to each reference sequence with zero mismatches and sorted by size and polarity. The
reference sequences were extended at the 3'-end by 33 nts from the 5'-terminal sequence to
allow for mapping sRNAs derived from the circular viral genome (at the junction of the first
and last nucleotide of the linear reference). The counts of reads mapped to the extended
sequence were then added to the 5'-sequence. In each table, the first column gives nucleotide
positions of the corresponding viral genome sequence. In the next columns, the positions of
5'-terminal nucleotide of sense sRNAs and 3'-terminal nucleotide of antisense siRNAs along
the reference sequence are indicated, and the read counts are given for each sRNA of 20-, 21-,
22-, 23-, 24- and 25-nt classes mapped with zero mismatches to the forward (rigthward) strand
(columns 20 rightward, 21 rightward, 22 rightward, 23 rightward, 24 rightward, 25 rightward)
and the reverse (leftward) strand (columns 20 leftward, 21 leftward, 22 leftward, 23 leftward,
24 leftward, 25 leftward), along with the total counts of 20–25 nt sRNAs mapped on the for-
ward (rightward) and reverse (leftward) strands. In each table file on the right side, histograms
of three major size-classes of siRNAs (21, 22, and 24 nt rightward and leftward reads) are
inserted with the rightward reads colored in blue and the leftward reads colored in red. In the
case of mixed infections (IL+IS76), the number of reads derived from each virus was counted
at each SNP using MISIS-2 (Seguin et al. 2006 [60]) and a percentage of reads derived from
each virus (or its selected region) was calculated. The average percentage at all SNPs of the
viral genome (or its selected region) was applied on all parts of the genome (or its selected
region) that contain no SNPs to estimate the number of reads derived from the entire genome
of each virus (or its selected region) or each strand of the viral genome (or its selected region).
(XLSX)

**S5 Dataset. Reference sequences of the viral genome IL and IS76 and their pairwise alignment.** The start and stop codons of viral ORFs are coloured in red and underlined, the CAAT and TATA-boxes of the promoters coloured in brick red, the TATA-associated composite element (TACE) and conserved late elements (CLE) highlighted in green and cyan, respectively, the iterons highlighted in grey and SNPs and indels highlighted in yellow.

(PDF)

**Acknowledgments**

We are thankful to Martine Granier and Sophie Le Blaye for technical assistance.

**Author Contributions**

**Conceptualization:** Michel Peterschmitt, Mikhail M. Pooggin.

**Data curation:** Margaux Jammes, Victor Golyaev, Mikhail M. Pooggin.

**Formal analysis:** Margaux Jammes, Victor Golyaev, Michel Peterschmitt, Mikhail M. Pooggin.

**Funding acquisition:** Michel Peterschmitt, Mikhail M. Pooggin.

**Investigation:** Margaux Jammes, Victor Golyaev, Alejandro Fuentes, Nathalie Laboureau, Mikhail M. Pooggin.

**Methodology:** Alejandro Fuentes, Cica Urbino, Clemence Plissonneau, Michel Peterschmitt, Mikhail M. Pooggin.
(dpi). For each condition, Illumina 20–25 nt reads of the two biological replicates were com-
bined and mapped onto the reference sequences of IL and IS76 using BWA and the resulting
BAM files were analysed by MISIS-2 (Seguin et al. 2016 [60]) to generate tables of reads
mapped to each reference sequence with zero mismatches and sorted by size and polarity. The
reference sequences were extended at the 3'-end by 33 nts from the 5'-terminal sequence to
allow for mapping sRNAs derived from the circular viral genome (at the junction of the first
and last nucleotide of the linear reference). The counts of reads mapped to the extended
sequence were then added to the 5'-sequence. In each table, the first column gives nucleotide
positions of the corresponding viral genome sequence. In the next columns, the positions of
5'-terminal nucleotide of sense sRNAs and 3'-terminal nucleotide of antisense siRNAs along
the reference sequence are indicated, and the read counts are given for each sRNA of 20-, 21-,
22-, 23-, 24- and 25-nt classes mapped with zero mismatches to the forward (rigthward) strand
(columns 20 rightward, 21 rightward, 22 rightward, 23 rightward, 24 rightward, 25 rightward)
and the reverse (leftward) strand (columns 20 leftward, 21 leftward, 22 leftward, 23 leftward,
24 leftward, 25 leftward), along with the total counts of 20–25 nt sRNAs mapped on the for-
ward (rightward) and reverse (leftward) strands. In each table file on the right side, histograms
of three major size-classes of siRNAs (21, 22, and 24 nt rightward and leftward reads) are
inserted with the rightward reads colored in blue and the leftward reads colored in red. In the
case of mixed infections (IL+IS76), the number of reads derived from each virus was counted
at each SNP using MISIS-2 (Seguin et al. 2006 [60]) and a percentage of reads derived from
each virus (or its selected region) was calculated. The average percentage at all SNPs of the
viral genome (or its selected region) was applied on all parts of the genome (or its selected
region) that contain no SNPs to estimate the number of reads derived from the entire genome
of each virus (or its selected region) or each strand of the viral genome (or its selected region).
(XLSX)

**S5 Dataset. Reference sequences of the viral genome IL and IS76 and their pairwise alignment.** The start and stop codons of viral ORFs are coloured in red and underlined, the CAAT and TATA-boxes of the promoters coloured in brick red, the TATA-associated composite element (TACE) and conserved late elements (CLE) highlighted in green and cyan, respectively, the iterons highlighted in grey and SNPs and indels highlighted in yellow.

(PDF)

**Acknowledgments**

We are thankful to Martine Granier and Sophie Le Blaye for technical assistance.

**Author Contributions**

**Conceptualization:** Michel Peterschmitt, Mikhail M. Pooggin.

**Data curation:** Margaux Jammes, Victor Golyaev, Mikhail M. Pooggin.

**Formal analysis:** Margaux Jammes, Victor Golyaev, Michel Peterschmitt, Mikhail M. Pooggin.

**Funding acquisition:** Michel Peterschmitt, Mikhail M. Pooggin.

**Investigation:** Margaux Jammes, Victor Golyaev, Alejandro Fuentes, Nathalie Laboureau, Mikhail M. Pooggin.

**Methodology:** Alejandro Fuentes, Cica Urbino, Clemence Plissonneau, Michel Peterschmitt, Mikhail M. Pooggin.
**Project administration:** Michel Peterschmitt, Mikhail M. Pooggin.

**Resources:** Cica Urbino, Clemence Plissonneau, Michel Peterschmitt.

**Supervision:** Cica Urbino, Clemence Plissonneau, Michel Peterschmitt, Mikhail M. Pooggin.

**Visualization:** Margaux Jammes, Mikhail M. Pooggin.

**Writing – original draft:** Margaux Jammes, Mikhail M. Pooggin.

**Writing – review & editing:** Cica Urbino, Michel Peterschmitt, Mikhail M. Pooggin.

## References

1. Jeske H. Geminiviruses. In: de Villiers EM, Hausen HZ. Editors. TT Viruses. Current Topics in Microbiology and Immunology, vol 331. Springer, Berlin, Heidelberg; 2009. pp. 185–226. https://doi.org/10.1007/978-3-540-70972-5_11.

2. Hanley-Bowdoin L, Bejarano ER, Robertson D, Mansoor S. Geminiviruses: masters at redirecting and reprogramming plant processes. Nat Rev Microbiol. 2013; 11:777–88. https://doi.org/10.1038/nrmicro3117 PMID: 24100361

3. Palanichelvam K, Kunik T, Citovsky V, Gafni Y. The capsid protein of tomato yellow leaf curl virus binds cooperatively to single-stranded DNA. J Gen Virol. 1998; 79:2829–2833. https://doi.org/10.1099/0022-1317-79-11-2829 PMID: 9820160

4. Hallan V, Gafni Y. Tomato yellow leaf curl virus (TYLCV) capsid protein (CP) subunit interactions: implications for viral assembly. Arch Virol. 2001; 146:1765–73. https://doi.org/10.1007/s007050170062 PMID: 11699961

5. Rojas MR, Jiang H, Salati R, Xoconostle-Cázares B, Sudarshana MR, Lucas WJ, et al. Functional analysis of proteins involved in movement of the monopartite begomovirus, Tomato yellow leaf curl virus. Virology. 2001; 291:110–25. https://doi.org/10.1006/viro.2001.1194 PMID: 11878881

6. Luna AP, Morilla G, Voinnet O, Bejarano ER. Functional analysis of gene-silencing suppressors from tomato yellow leaf curl disease viruses. Mol Plant Microbe Interact. 2012; 25:1294–306. https://doi.org/10.1094/MPMI-04-12-0094-R PMID: 22712505

7. Zrachya A, Glick E, Levy Y, Arazi T, Citovsky V, Gafni Y. Suppressor of RNA silencing encoded by Tomato yellow leaf curl virus-Israel. Virology. 2007; 358:159–65. https://doi.org/10.1016/j.virol.2006.08.016 PMID: 16979684

8. Glick E, Zrachya A, Levy Y, Mett A, Gidoni D, Belausov E, et al. Interaction with host SGS3 is required for suppression of RNA silencing by tomato yellow leaf curl virus V2 protein. Proc Natl Acad Sci U S A. 2008; 105:157–61. https://doi.org/10.1073/pnas.0709036105 PMID: 18165314

9. Wang B, Li F, Huang C, Yang X, Qian Y, Xie Y, et al. V2 of tomato yellow leaf curl virus can suppress methylation-mediated transcriptional gene silencing in plants. J Gen Virol. 2014; 95: 225–230. https://doi.org/10.1099/vir.0.055798-0 PMID: 24187017

10. Wang B, Yang X, Wang Y, Xie Y, Zhou X. Tomato Yellow Leaf Curl Virus V2 Interacts with Host Histone Deacetylase 6 To Suppress Methylation-Mediated Transcriptional Gene Silencing in Plants. J Virol. 2018; 92:e00036–18. https://doi.org/10.1128/JVI.00036-18 PMID: 29950418

11. Wang L, Ding Y, He L, Zhang G, Zhu JK, Lozano-Duran R. A virus-encoded protein suppresses methylation of the viral genome through its interaction with AGO4 in the Cajal body. Elife. 2020; 9:e55542. https://doi.org/10.7554/eLife.55542 PMID: 33064077

12. Desbiez C, David C, Mettouchi A, Laufs J, Gronenborn B. Rep protein of tomato yellow leaf curl geminivirus has an ATPase activity required for viral DNA replication. Proc Natl Acad Sci U S A. 1995; 92:5640–4. https://doi.org/10.1073/pnas.92.12.5640 PMID: 7777563

13. Noris E, Jupin I, Accotto GP, Gronenborn B. DNA-binding activity of the C2 protein of tomato yellow leaf curl geminivirus. Virology. 1996; 217:607–12. https://doi.org/10.1006/viro.1996.0157 PMID: 8610454

14. Dong X, van Wezel R, Stanley J, Hong Y. Functional characterization of the nuclear localization signal for a suppressor of posttranscriptional gene silencing. J Virol. 2003; 77:7026–33. https://doi.org/10.1128/jvi.77.12.7026-7033.2003 PMID: 12768021

15. Settlage SB, See RG, Hanley-Bowdoin L. Geminivirus C3 protein: replication enhancement and protein interactions. J Virol. 2005; 79(15):9885–95. https://doi.org/10.1128/JVI.79.15.9885-9895.2005 PMID: 16014949

16. Jupin I, De Kouchkovsky F, Jouanneau F, Gronenborn B. Movement of tomato yellow leaf curl geminivirus (TYLCV): involvement of the protein encoded by ORF C4. Virology. 1994; 204:82–90. https://doi.org/10.1006/viro.1994.1512 PMID: 8091687
**Project administration:** Michel Peterschmitt, Mikhail M. Pooggin.

**Resources:** Cica Urbino, Clemence Plissonneau, Michel Peterschmitt.

**Supervision:** Cica Urbino, Clemence Plissonneau, Michel Peterschmitt, Mikhail M. Pooggin.

**Visualization:** Margaux Jammes, Mikhail M. Pooggin.

**Writing – original draft:** Margaux Jammes, Mikhail M. Pooggin.

**Writing – review & editing:** Cica Urbino, Michel Peterschmitt, Mikhail M. Pooggin.

## References

1. Jeske H. Geminiviruses. In: de Villiers EM, Hausen HZ. Editors. TT Viruses. Current Topics in Microbiology and Immunology, vol 331. Springer, Berlin, Heidelberg; 2009. pp. 185–226. https://doi.org/10.1007/978-3-540-70972-5_11

2. Hanley-Bowdoin L, Bejarano ER, Robertson D, Mansoor S. Geminiviruses: masters at redirecting and reprogramming plant processes. Nat Rev Microbiol. 2013; 11:777–88. https://doi.org/10.1038/nrmicro3117 PMID: 24100361

3. Palanichelvam K, Kunik T, Citovsky V, Gafni Y. The capsid protein of tomato yellow leaf curl virus binds cooperatively to single-stranded DNA. J Gen Virol. 1998; 79:2829–2833. https://doi.org/10.1099/0022-1317-79-11-2829 PMID: 9820160

4. Hallan V, Gafni Y. Tomato yellow leaf curl virus (TYLCV) capsid protein (CP) subunit interactions: implications for viral assembly. Arch Virol. 2001; 146:1765–73. https://doi.org/10.1007/s007050170062 PMID: 11699961

5. Rojas MR, Jiang H, Salati R, Xoconostle-Cázares B, Sudarshana MR, Lucas WJ, et al. Functional analysis of proteins involved in movement of the monopartite begomovirus, Tomato yellow leaf curl virus. Virology. 2001; 291:110–25. https://doi.org/10.1006/viro.2001.1194 PMID: 11878881

6. Luna AP, Morilla G, Voinnet O, Bejarano ER. Functional analysis of gene-silencing suppressors from tomato yellow leaf curl disease viruses. Mol Plant Microbe Interact. 2012; 25:1294–306. https://doi.org/10.1094/MPMI-04-12-0094-R PMID: 22712505

7. Zrachya A, Glick E, Levy Y, Arazi T, Citovsky V, Gafni Y. Suppressor of RNA silencing encoded by Tomato yellow leaf curl virus-Israel. Virology. 2007; 358:159–65. https://doi.org/10.1016/j.virol.2006.08.016 PMID: 16979684

8. Glick E, Zrachya A, Levy Y, Mett A, Gidoni D, Belausov E, et al. Interaction with host SGS3 is required for suppression of RNA silencing by tomato yellow leaf curl virus V2 protein. Proc Natl Acad Sci U S A. 2008; 105:157–61. https://doi.org/10.1073/pnas.0709036105 PMID: 18165314

9. Wang B, Li F, Huang C, Yang X, Qian Y, Xie Y, et al. V2 of tomato yellow leaf curl virus can suppress methylation-mediated transcriptional gene silencing in plants. J Gen Virol. 2014; 95: 225–230. https://doi.org/10.1099/vir.0.055798-0 PMID: 24187017

10. Wang B, Yang X, Wang Y, Xie Y, Zhou X. Tomato Yellow Leaf Curl Virus V2 Interacts with Host Histone Deacetylase 6 To Suppress Methylation-Mediated Transcriptional Gene Silencing in Plants. J Virol. 2018; 92:e00036–18. https://doi.org/10.1128/JVI.00036-18 PMID: 29950418

11. Wang L, Ding Y, He L, Zhang G, Zhu JK, Lozano-Duran R. A virus-encoded protein suppresses methylation of the viral genome through its interaction with AGO4 in the Cajal body. Elife. 2020; 9:e55542. https://doi.org/10.7554/eLife.55542 PMID: 33064077

12. Desbiez C, David C, Mettouchi A, Laufs J, Gronenborn B. Rep protein of tomato yellow leaf curl geminivirus has an ATPase activity required for viral DNA replication. Proc Natl Acad Sci U S A. 1995; 92:5640–4. https://doi.org/10.1073/pnas.92.12.5640 PMID: 7777563

13. Noris E, Jupin I, Accotto GP, Gronenborn B. DNA-binding activity of the C2 protein of tomato yellow leaf curl geminivirus. Virology. 1996; 217:607–12. https://doi.org/10.1006/viro.1996.0157 PMID: 8610454

14. Dong X, van Wezel R, Stanley J, Hong Y. Functional characterization of the nuclear localization signal for a suppressor of posttranscriptional gene silencing. J Virol. 2003; 77:7026–33. https://doi.org/10.1128/jvi.77.12.7026-7033.2003 PMID: 12768021

15. Settlage SB, See RG, Hanley-Bowdoin L. Geminivirus C3 protein: replication enhancement and protein interactions. J Virol. 2005; 79(15):9885–95. https://doi.org/10.1128/JVI.79.15.9885-9895.2005 PMID: 16014949

16. Jupin I, De Kouchkovsky F, Jouanneau F, Gronenborn B. Movement of tomato yellow leaf curl geminivirus (TYLCV): involvement of the protein encoded by ORF C4. Virology. 1994; 204:82–90. https://doi.org/10.1006/viro.1994.1512 PMID: 8091687
17. Xie Y, Zhao L, Jiao X, Jiang T, Gong H, Wang B, Briddon RW, Zhou X. A recombinant begomovirus resulting from exchange of the C4 gene. J Gen Virol. 2013; 94(Pt 8):1896-1907. https://doi.org/10.1099/vir.0.053181-0 PMID: 23720217

18. Padmanabhan C, Zheng Y, Shamimuzzaman M, Wilson JR, Gilliard A, Fei Z, et al. The tomato yellow leaf curl virus C4 protein alters the expression of plant developmental genes correlating to leaf upward cupping phenotype in tomato. PLoS One. 2022; 17:e0257936. https://doi.org/10.1371/journal.pone.0257936 PMID: 35551312

19. Mullineaux PM, Rigden JE, Dry IB, Krake LR, Rezaian MA. Mapping of the polycistronic RNAs of tomato leaf curl geminivirus. Virology, 1993; 193:414-23. https://doi.org/10.1006/viro.1993.1138 PMID: 8438578

20. Frischmuth S, Frischmuth T, Jeske H. Transcript mapping of Abutilon mosaic virus, a geminivirus. Virol-ogy. 1991; 185:596-604. https://doi.org/10.1016/0042-6822(91)90530-o PMID: 1962440

21. Shivaprasad PV, Akbergenov R, Trinks D, Rajeswaran R, Veluthambi K, Hohn T, et al. Promoters, transcripts, and regulatory proteins of Mungbean yellow mosaic geminivirus. J Virol. 2005; 79:8149-63. https://doi.org/10.1128/JVI.79.13.8149-8163.2005 PMID: 15956560

22. Eagle PA, Orozco BM, Hanley-Bowdoin L. 1994. A DNA sequence required for geminivirus replication also mediates transcriptional regulation. Plant Cell 6: 1157-70. https://doi.org/10.1105/tpc.6.8.1157 PMID: 7919985

23. Sunter G, Bisaro DM. Transactivation of geminivirus AR1 and BR1 gene expression by the viral AL2 gene product occurs at the level of transcription. Plant Cell. 1992; 4:1321-31. https://doi.org/10.1105/tpc.4.10.1321 PMID: 1446172

24. Zakay Y, Navot N, Zeidan M, Kedar N, Rabinowitch H, Czosnek H, et al. Screening Lycopersicon accessions for resistance to tomato yellow leaf curl virus: Presence of viral DNA and symptom development. Plant Disease. 1991; 75:279-281. https://www.apsnet.org/publications/plantdisease/backissues/Documents/1991Abstracts/PD_75_279.htm.

25. Zamir D, Ekstein-Michelson I, Zakay Y, Navot N, Zeidan M, Sarfatti M, et al. Mapping and introgression of a tomato yellow leaf curl virus tolerance gene, TY-1. Theoretical and Applied Genetics. 1994; 88:141-146. https://doi.org/10.1007/BF00225889 PMID: 24185918

26. El-Sappah AH, Qi S, Soaud SA, Huang Q, Saleh AM, Abourehab MAS, et al. Natural resistance of tomato plants to Tomato yellow leaf curl virus. Front Plant Sci. 2022; 13:1081549. https://doi.org/10.3389/fpls.2022.1081549 PMID: 36600922

27. Verlaan MG, Hutton SF, Ibrahem RM, Kormelink R, Visser RG, Scott JW, et al. The Tomato Yellow Leaf Curl Virus resistance genes Ty-1 and Ty-3 are allelic and code for DFDGD-class RNA-dependent RNA polymerases. PLoS Genet. 2013; 9:e1003399. https://doi.org/10.1371/journal.pgen.1003399 PMID: 23555305

28. Borges F, Martienssen RA. The expanding world of small RNAs in plants. Nat Rev Mol Cell Biol. 2015; 16:727-41. https://doi.org/10.1038/nrm4085 PMID: 26530390

29. Fang X, Qi Y. RNAi in Plants: An Argonaute-Centered View. Plant Cell. 2016; 28:272-85. https://doi.org/10.1105/tpc.15.00920 PMID: 26869699

30. Blevins T, Rajeswaran R, Shivaprasad PV, Beknazariants D, Si-Ammour A, Park HS, et al. Four plant Dicers mediate viral small RNA biogenesis and DNA virus induced silencing. Nucleic Acids Res. 2006; 34:6233-46. https://doi.org/10.1093/nar/gkl886 PMID: 17090584

31. Aregger M, Borah BK, Seguin J, Rajeswaran R, Gubaeva EG, Zvereva AS, et al. Primary and secondary siRNAs in geminivirus-induced gene silencing. PLoS Pathog. 2012; 8:e1002941. https://doi.org/10.1371/journal.ppat.1002941 PMID: 23028332

32. Pooggin MM. How can plant DNA viruses evade siRNA-directed DNA methylation and silencing? Int J Mol Sci. 2013; 14:15233-59. https://doi.org/10.3390/ijms140815233 PMID: 23887650

33. Wassenegger M, Krczal G. Nomenclature and functions of RNA-directed RNA polymerases. Trends Plant Sci. 2006; 11:142-51. https://doi.org/10.1016/j.tplants.2006.01.003 PMID: 16473542

34. Jha V, Narjala A, Basu D, Sujith TN, Pachamuthu K, Chenna S, et al. Essential role of γ-clade RNA-dependent RNA polymerases in rice development and yield-related traits is linked to their atypical polymerase activities regulating specific genomic regions. New Phytol. 2021; 232(4):1674-1691. https://doi.org/10.1111/nph.17700 PMID: 34449900

35. Schiebel W, Haas B, Marinković S, Klanner A, Sänger HL. RNA-directed RNA polymerase from tomato leaves. II. Catalytic in vitro properties. J Biol Chem. 1993; 268: 11858-67. https://doi.org/10.1016/S0021-9258(19)50279-4. PMID: 7685023

36. Fuentes A, Carlos N, Ruiz Y, Callard D, Sánchez Y, Ochagavía ME, et al. Field Trial and Molecular Characterization of RNAi-Transgenic Tomato Plants That Exhibit Resistance to Tomato Yellow Leaf
17. Xie Y, Zhao L, Jiao X, Jiang T, Gong H, Wang B, Briddon RW, Zhou X. A recombinant begomovirus resulting from exchange of the C4 gene. J Gen Virol. 2013; 94(Pt 8):1896-1907. https://doi.org/10.1099/vir.0.053181-0 PMID: 23720217

18. Padmanabhan C, Zheng Y, Shamimuzzaman M, Wilson JR, Gilliard A, Fei Z, et al. The tomato yellow leaf curl virus C4 protein alters the expression of plant developmental genes correlating to leaf upward cupping phenotype in tomato. PLoS One. 2022; 17:e0257936. https://doi.org/10.1371/journal.pone.0257936 PMID: 35551312

19. Mullineaux PM, Rigden JE, Dry IB, Krake LR, Rezaian MA. Mapping of the polycistronic RNAs of tomato leaf curl geminivirus. Virology, 1993; 193:414-23. https://doi.org/10.1006/viro.1993.1138 PMID: 8438578

20. Frischmuth S, Frischmuth T, Jeske H. Transcript mapping of Abutilon mosaic virus, a geminivirus. Virol-ogy. 1991; 185:596-604. https://doi.org/10.1016/0042-6822(91)90530-o PMID: 1962440

21. Shivaprasad PV, Akbergenov R, Trinks D, Rajeswaran R, Veluthambi K, Hohn T, et al. Promoters, transcripts, and regulatory proteins of Mungbean yellow mosaic geminivirus. J Virol. 2005; 79:8149-63. https://doi.org/10.1128/JVI.79.13.8149-8163.2005 PMID: 15956560

22. Eagle PA, Orozco BM, Hanley-Bowdoin L. 1994. A DNA sequence required for geminivirus replication also mediates transcriptional regulation. Plant Cell 6: 1157-70. https://doi.org/10.1105/tpc.6.8.1157 PMID: 7919985

23. Sunter G, Bisaro DM. Transactivation of geminivirus AR1 and BR1 gene expression by the viral AL2 gene product occurs at the level of transcription. Plant Cell. 1992; 4:1321-31. https://doi.org/10.1105/tpc.4.10.1321 PMID: 1446172

24. Zakay Y, Navot N, Zeidan M, Kedar N, Rabinowitch H, Czosnek H, et al. Screening Lycopersicon accessions for resistance to tomato yellow leaf curl virus: Presence of viral DNA and symptom development. Plant Disease. 1991; 75:279-281. https://www.apsnet.org/publications/plantdisease/backissues/Documents/1991Abstracts/PD_75_279.htm.

25. Zamir D, Ekstein-Michelson I, Zakay Y, Navot N, Zeidan M, Sarfatti M, et al. Mapping and introgression of a tomato yellow leaf curl virus tolerance gene, TY-1. Theoretical and Applied Genetics. 1994; 88:141-146. https://doi.org/10.1007/BF00225889 PMID: 24185918

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43. Jammes M, Urbino C, Diouf MB, Peterschmitt M. Refining the emergence scenario of the invasive recombinant Tomato yellow leaf curl virus -IS76. Virology. 2023; 578:71-80. https://doi.org/10.1016/j.virol.2022.11.006 PMID: 36473279

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45. Cantú-Iris M, Pastor-Palacios G, Mauricio-Castillo JA, Bañuelos-Hernández B, Avalos-Calleros JA, Juárez-Reyes A, et al. Analysis of a new begomovirus unveils a composite element conserved in the CP gene promoters of several Geminiviridae genera: Clues to comprehend the complex regulation of late genes. PLoS One. 2019; 14:e0210485. https://doi.org/10.1371/journal.pone.0210485 PMID: 30673741

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48. Cao M, Du P, Wang X, Yu YQ, Qiu YH, Li W, Gal-On A, et al. Virus infection triggers widespread silencing of host genes by a distinct class of endogenous siRNAs in Arabidopsis. Proc Natl Acad Sci U S A. 2014; 111:14613-8. https://doi.org/10.1073/pnas.1407131111 PMID: 25201959

49. Wang T, Deng Z, Zhang X, Wang H, Wang Y, Liu X, et al. Tomato DCL2b is required for the biosynthesis of 22-nt small RNAs, the resulting secondary siRNAs, and the host defense against ToMV. Hortic Res. 2018; 5:62. https://doi.org/10.1038/s41438-018-0073-7 PMID: 30181890

50. Yifhar T, Pekker I, Peled D, Friedlander G, Pistunov A, Sabban M, et al. Failure of the tomato trans-acting short interfering RNA program to regulate AUXIN RESPONSE FACTOR3 and ARF4 underlies the wiry leaf syndrome. Plant Cell. 2012; 24:3575-89. https://doi.org/10.1105/tpc.112.100222 PMID: 23001036

51. Kravchik M, Damodharan S, Stav R, Arazi T. Generation and characterization of a tomato DCL3-silencing mutant. Plant Sci. 2014;221-222:81-9. https://doi.org/10.1016/j.plantsci.2014.02.007 PMID: 24656338

52. Alcaide C, Donaire L, Aranda MA. Transcriptome analyses unveiled differential regulation of AGO and DCL genes by pepino mosaic virus strains. Mol Plant Pathol. 2022; 23:1592-1607. https://doi.org/10.1111/mpp.13249 PMID: 35852033
Curl Geminivirus. Mol Plant Microbe Interact. 2016; 29:197-209. https://doi.org/10.1094/MPMI-08-15-0181-R PMID: 26713353

37. Piedra-Aguilera Á, Jiao C, Luna AP, Villanueva F, Dabad M, Esteve-Codina A, et al. Integrated single-base resolution maps of transcriptome, sRNAome and methylome of Tomato yellow leaf curl virus (TYLCV) in tomato. Sci Rep. 2019; 9:2863. https://doi.org/10.1038/s41598-019-39239-6 PMID: 30814535

38. Voorburg CM, Bai Y, Kormelink R. Small RNA Profiling of Susceptible and Resistant Ty-1 Encoding Tomato Plants Upon Tomato Yellow Leaf Curl Virus Infection. Front Plant Sci. 2021; 12:757165. https://doi.org/10.3389/fpls.2021.757165 PMID: 34868151

39. Butterbach P, Verlaan MG, Dullemans A, Lohuis D, Visser RG, Bai Y, et al. Tomato yellow leaf curl virus resistance by Ty-1 involves increased cytosine methylation of viral genomes and is compromised by cucumber mosaic virus infection. Proc Natl Acad Sci U S A. 2014; 111:12942-7. https://doi.org/10.1073/pnas.1400894111 PMID: 25136118

40. Voorburg CM, Yan Z, Bergua-Vidal M, Wolters AA, Bai Y, Kormelink R. Ty-1, a universal resistance gene against geminiviruses that is compromised by co-replication of a betasatellite. Mol Plant Pathol. 2020 Feb; 21(2):160-172. https://doi.org/10.1111/mpp.12885 Epub 2019 Nov 22. PMID: 31756021

41. Belabess Z, Dallot S, El-Montaser S, Granier M, Majde M, Tahiri A, et al. Monitoring the dynamics of emergence of a non-canonical recombinant of Tomato yellow leaf curl virus and displacement of its parental viruses in tomato. Virology. 2015; 486:291-306. https://doi.org/10.1016/j.virol.2015.09.011 PMID: 26519598

42. Belabess Z, Peterschmitt M, Granier M, Tahiri A, Blenzar A, Urbino C. The non-canonical tomato yellow leaf curl virus recombinant that displaced its parental viruses in southern Morocco exhibits a high selective advantage in experimental conditions. J Gen Virol. 2016; 97:3433-3445. https://doi.org/10.1099/jgv.0.000633 PMID: 27902403

43. Jammes M, Urbino C, Diouf MB, Peterschmitt M. Refining the emergence scenario of the invasive recombinant Tomato yellow leaf curl virus -IS76. Virology. 2023; 578:71-80. https://doi.org/10.1016/j.virol.2022.11.006 PMID: 36473279

44. Sunter G, Bisaro DM. Identification of a minimal sequence required for activation of the tomato golden mosaic virus coat protein promoter in protoplasts. Virology. 2003; 305:452-62. https://doi.org/10.1006/viro.2002.1757 PMID: 12573590

45. Cantú-Iris M, Pastor-Palacios G, Mauricio-Castillo JA, Bañuelos-Hernández B, Avalos-Calleros JA, Juárez-Reyes A, et al. Analysis of a new begomovirus unveils a composite element conserved in the CP gene promoters of several Geminiviridae genera: Clues to comprehend the complex regulation of late genes. PLoS One. 2019; 14:e0210485. https://doi.org/10.1371/journal.pone.0210485 PMID: 30673741

46. Garcia-Ruiz H, Takeda A, Chapman EJ, Sullivan CM, Fahlgren N, Brempelis KJ, et al. Arabidopsis RNA-dependent RNA polymerases and dicer-like proteins in antiviral defense and small interfering RNA biogenesis during Turnip Mosaic Virus infection. Plant Cell. 2010; 22:481-96. https://doi.org/10.1105/tpc.109.073056 PMID: 20190077

47. Wang XB, Wu Q, Ito T, Cillo F, Li WX, Chen X, et al. RNAi-mediated viral immunity requires amplification of virus-derived siRNAs in Arabidopsis thaliana. Proc Natl Acad Sci U S A. 2010; 107:484-9. https://doi.org/10.1073/pnas.0904086107 PMID: 19966292

48. Cao M, Du P, Wang X, Yu YQ, Qiu YH, Li W, Gal-On A, et al. Virus infection triggers widespread silencing of host genes by a distinct class of endogenous siRNAs in Arabidopsis. Proc Natl Acad Sci U S A. 2014; 111:14613-8. https://doi.org/10.1073/pnas.1407131111 PMID: 25201959

49. Wang T, Deng Z, Zhang X, Wang H, Wang Y, Liu X, et al. Tomato DCL2b is required for the biosynthesis of 22-nt small RNAs, the resulting secondary siRNAs, and the host defense against ToMV. Hortic Res. 2018; 5:62. https://doi.org/10.1038/s41438-018-0073-7 PMID: 30181890

50. Yifhar T, Pekker I, Peled D, Friedlander G, Pistunov A, Sabban M, et al. Failure of the tomato trans-acting short interfering RNA program to regulate AUXIN RESPONSE FACTOR3 and ARF4 underlies the wiry leaf syndrome. Plant Cell. 2012; 24:3575-89. https://doi.org/10.1105/tpc.112.100222 PMID: 23001036

51. Kravchik M, Damodharan S, Stav R, Arazi T. Generation and characterization of a tomato DCL3-silencing mutant. Plant Sci. 2014;221-222:81-9. https://doi.org/10.1016/j.plantsci.2014.02.007 PMID: 24656338

52. Alcaide C, Donaire L, Aranda MA. Transcriptome analyses unveiled differential regulation of AGO and DCL genes by pepino mosaic virus strains. Mol Plant Pathol. 2022; 23:1592-1607. https://doi.org/10.1111/mpp.13249 PMID: 35852033
53. Ludman M, Burgyán J, Fátyol K. Crispr/Cas9 Mediated Inactivation of Argonaute 2 Reveals its Differen-
tial Involvement in Antiviral Responses. Sci Rep. 2017; 7:1010. https://doi.org/10.1038/s41598-017-
01050-6 PMID: 28432338

54. Dellaporta SL, Wood J, Hicks JB. A plant DNA minipreparation: Version II. Plant Mol Biol Rep. 1983; 1:19-21. https://doi.org/10.1007/BF02712670

55. Ruijter JM, Ramakers C, Hoogaars WM, Karlen Y, Bakker O, van den Hoff MJ, et al. Amplification effi-
ciency: linking baseline and bias in the analysis of quantitative PCR data. Nucleic Acids Res. 2009; 37:
e45. https://doi.org/10.1093/nar/gkp045 PMID: 19237396

56. Doyle JJ, Doyle JL. Isolation of plant DNA from fresh tissue. Focus 1990; 12:13-15.

57. Golyaev V, Candresse T, Rabenstein F, Pooggin MM. Plant virome reconstruction and antiviral RNAi characterization by deep sequencing of small RNAs from dried leaves. Sci Rep. 2019; 9:19268. https://doi.org/10.1038/s41598-019-55547-3 PMID: 31848375

58. Malpica-López N, Rajeswaran R. Beknazariants D, Seguin J, Golyaev V, Farinelli L, et al. Revisiting the Roles of Tobamovirus Replicase Complex Proteins in Viral Replication and Silencing Suppression. Mol Plant Microbe Interact. 2018; 31:125-144. https://doi.org/10.1094/MPMI-07-17-0164-R PMID: 29140168

59. Li H, Durbin R. Fast and accurate long-read alignment with Burrows-Wheeler transform. Bioinformatics. 2010; 26:589-95. https://doi.org/10.1093/bioinformatics/btp698 PMID: 20080505

60. Seguin J, Otten P, Baerlocher L, Farinelli L, Pooggin MM. MISIS-2: A bioinformatics tool for in-depth analysis of small RNAs and representation of consensus master genome in viral quasispecies. J Virol Methods. 2016; 233:37-40. https://doi.org/10.1016/j.jviromet.2016.03.005 PMID: 26994965

61. Anders S, Pyl PT, Huber W. HTSeq—a Python framework to work with high-throughput sequencing data. Bioinformatics. 2015; 31:166-9. https://doi.org/10.1093/bioinformatics/btu638 PMID: 25260700

62. Lambert I, Paysant-Le Roux C, Colella S, Martin-Magniette ML. DiCoExpress: a tool to process multi-factorial RNAseq experiments from quality controls to co-expression analysis through differential analysis based on contrasts inside GLM models. Plant Methods. 2020; 16:68. https://doi.org/10.1186/s13007-020-00611-7 PMID: 32426025

63. Robinson MD, McCarthy DJ, Smyth GK. edgeR: a Bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics. 2010; 26:139-140. https://doi.org/10.1093/bioinformatics/btp616 PMID: 19910308

64. Akbergenov R, Si-Ammour A, Blevins T, Amin I, Kutter C, Vanderschuren H, et al. Molecular characterization of geminivirus-derived small RNAs in different plant species. Nucleic Acids Res. 2006; 34 (2):462-71. https://doi.org/10.1093/nar/gkj447 PMID: 16421273
53. Ludman M, Burgyán J, Fátyol K. Crispr/Cas9 Mediated Inactivation of Argonaute 2 Reveals its Differen-
tial Involvement in Antiviral Responses. Sci Rep. 2017; 7:1010. https://doi.org/10.1038/s41598-017-
01050-6 PMID: 28432338

54. Dellaporta SL, Wood J, Hicks JB. A plant DNA minipreparation: Version II. Plant Mol Biol Rep. 1983; 1:19-21. https://doi.org/10.1007/BF02712670

55. Ruijter JM, Ramakers C, Hoogaars WM, Karlen Y, Bakker O, van den Hoff MJ, et al. Amplification effi-
ciency: linking baseline and bias in the analysis of quantitative PCR data. Nucleic Acids Res. 2009; 37:
e45. https://doi.org/10.1093/nar/gkp045 PMID: 19237396

56. Doyle JJ, Doyle JL. Isolation of plant DNA from fresh tissue. Focus 1990; 12:13-15.

57. Golyaev V, Candresse T, Rabenstein F, Pooggin MM. Plant virome reconstruction and antiviral RNAi characterization by deep sequencing of small RNAs from dried leaves. Sci Rep. 2019; 9:19268. https://doi.org/10.1038/s41598-019-55547-3 PMID: 31848375

58. Malpica-López N, Rajeswaran R. Beknazariants D, Seguin J, Golyaev V, Farinelli L, et al. Revisiting the Roles of Tobamovirus Replicase Complex Proteins in Viral Replication and Silencing Suppression. Mol Plant Microbe Interact. 2018; 31:125-144. https://doi.org/10.1094/MPMI-07-17-0164-R PMID: 29140168

59. Li H, Durbin R. Fast and accurate long-read alignment with Burrows-Wheeler transform. Bioinformatics. 2010; 26:589-95. https://doi.org/10.1093/bioinformatics/btp698 PMID: 20080505

60. Seguin J, Otten P, Baerlocher L, Farinelli L, Pooggin MM. MISIS-2: A bioinformatics tool for in-depth analysis of small RNAs and representation of consensus master genome in viral quasispecies. J Virol Methods. 2016; 233:37-40. https://doi.org/10.1016/j.jviromet.2016.03.005 PMID: 26994965

61. Anders S, Pyl PT, Huber W. HTSeq—a Python framework to work with high-throughput sequencing data. Bioinformatics. 2015; 31:166–9. https://doi.org/10.1093/bioinformatics/btu638 PMID: 25260700

62. Lambert I, Paysant-Le Roux C, Colella S, Martin-Magniette ML. DiCoExpress: a tool to process multi-factorial RNAseq experiments from quality controls to co-expression analysis through differential analysis based on contrasts inside GLM models. Plant Methods. 2020; 16:68. https://doi.org/10.1186/s13007-020-00611-7 PMID: 32426025

63. Robinson MD, McCarthy DJ, Smyth GK. edgeR: a Bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics. 2010; 26:139-140. https://doi.org/10.1093/bioinformatics/btp616 PMID: 19910308

64. Akbergenov R, Si-Ammour A, Blevins T, Amin I, Kutter C, Vanderschuren H, et al. Molecular characterization of geminivirus-derived small RNAs in different plant species. Nucleic Acids Res. 2006; 34 (2):462-71. https://doi.org/10.1093/nar/gkj447 PMID: 16421273