{"id":{"repo_id":"cambridge","oai_identifier":"oai:www.repository.cam.ac.uk:1810/384880"},"canonical_url":"https://search.dev.ndltd.org/etd/cambridge/oai:www.repository.cam.ac.uk:1810/384880","repository":{"repo_id":"cambridge","name":"Cambridge University","base_url":"https://api.repository.cam.ac.uk/server/oai/request"},"display":{"title":"Persistent viruses in Capsicum annuum plants: Understanding the mystery guests","abstract":"Most work on plant viruses focuses on their pathogenicity, but recent studies suggest viruses may benefit their hosts, at least under some conditions. Plant-infecting viruses of the Partitiviridae and Endornaviridae are transmitted only vertically, via pollen and seed, generally cause no disease symptoms, and in recent literature have been referred to as ‘persistent’ plant viruses. Previous work with legumes and pepper (Capsicum spp.) suggested persistent viruses have mutualistic properties. To test this hypothesis, I investigated the effects of these viruses on host phenotypes in a range of pepper cultivars. Using reverse transcription polymerase chain reaction (RT-PCR) assays I identified cultivars carrying single infections of the endornavirus bell pepper endornavirus (BPEV) or the partitiviruses pepper cryptic virus 1 (PCV1) or PCV2. Plants infected with these viruses harboured similar viral RNA levels in all tissues, consistent with previous studies. I investigated virus-virus interactions between persistent viruses and two pathogenic viruses. Tobacco mosaic virus (TMV) and cucumber mosaic virus (CMV) infection increased BPEV accumulation while PCV1 RNA levels were not affected by either. PCV2 RNA levels decreased in CMV-infected plants but were unaffected by TMV. Thus, pathogenic viruses can interfere with persistent viruses. Neither TMV nor CMV RNA accumulation was affected by BPEV, PCV1 or PCV2, but these studies were not straightforward to interpret since they required comparisons between pepper cultivars that either harboured, or did not harbour persistent viruses, but were not genetically identical. To overcome this, I used a tobacco rattle virus vector for virus-induced gene silencing to ‘cure’ plants of cultivars harbouring BPEV, PCV1 or PCV2. For seven cultivars I obtained pairs of isogenic lines that either carried or no longer carried BPEV, PCV1 or PCV2. PCV1 significantly increased seed mass in both Gourmet Jalapeno and Mirasol chilli cultivars while BPEV and PCV2 showed mixed results. BPEV increased seed mass in Californian Wonder but not in Red King. PCV2 had different impacts on seed mass in different cultivars: increased in Hungarian Wax, decreased in Cayenne Red, with no effect in Poupila. PCV1 increased seed size whereas BPEV decreased it. PCV2 increased seed size in Hungarian Wax but decreased seed size in Cayenne Red and Poupila. None of the persistent viruses affected seed yield significantly. Illumina-based transcriptome sequencing of isogenic cured and uncured lines showed that persistent viruses affect host gene expression differentially. BPEV upregulated >20 genes involved in plant-pathogen interactions, while PCV1 and PCV2, respectively, down- and up-regulated genes involved in photosynthesis. In conclusion, my results show that PCV1 has potentially positive effects on host reproductive fitness via increased seed mass, while BPEV and PCV2 may confer benefits to the host through effects on plant metabolism.","abstract_html":"Most work on plant viruses focuses on their pathogenicity, but recent studies suggest viruses may benefit their hosts, at least under some conditions. Plant-infecting viruses of the Partitiviridae and Endornaviridae are transmitted only vertically, via pollen and seed, generally cause no disease symptoms, and in recent literature have been referred to as ‘persistent’ plant viruses. Previous work with legumes and pepper (Capsicum spp.) suggested persistent viruses have mutualistic properties. To test this hypothesis, I investigated the effects of these viruses on host phenotypes in a range of pepper cultivars. Using reverse transcription polymerase chain reaction (RT-PCR) assays I identified cultivars carrying single infections of the endornavirus bell pepper endornavirus (BPEV) or the partitiviruses pepper cryptic virus 1 (PCV1) or PCV2. Plants infected with these viruses harboured similar viral RNA levels in all tissues, consistent with previous studies. I investigated virus-virus interactions between persistent viruses and two pathogenic viruses. Tobacco mosaic virus (TMV) and cucumber mosaic virus (CMV) infection increased BPEV accumulation while PCV1 RNA levels were not affected by either. PCV2 RNA levels decreased in CMV-infected plants but were unaffected by TMV. Thus, pathogenic viruses can interfere with persistent viruses. Neither TMV nor CMV RNA accumulation was affected by BPEV, PCV1 or PCV2, but these studies were not straightforward to interpret since they required comparisons between pepper cultivars that either harboured, or did not harbour persistent viruses, but were not genetically identical. To overcome this, I used a tobacco rattle virus vector for virus-induced gene silencing to ‘cure’ plants of cultivars harbouring BPEV, PCV1 or PCV2. For seven cultivars I obtained pairs of isogenic lines that either carried or no longer carried BPEV, PCV1 or PCV2. PCV1 significantly increased seed mass in both Gourmet Jalapeno and Mirasol chilli cultivars while BPEV and PCV2 showed mixed results. BPEV increased seed mass in Californian Wonder but not in Red King. PCV2 had different impacts on seed mass in different cultivars: increased in Hungarian Wax, decreased in Cayenne Red, with no effect in Poupila. PCV1 increased seed size whereas BPEV decreased it. PCV2 increased seed size in Hungarian Wax but decreased seed size in Cayenne Red and Poupila. None of the persistent viruses affected seed yield significantly. Illumina-based transcriptome sequencing of isogenic cured and uncured lines showed that persistent viruses affect host gene expression differentially. BPEV upregulated >20 genes involved in plant-pathogen interactions, while PCV1 and PCV2, respectively, down- and up-regulated genes involved in photosynthesis. In conclusion, my results show that PCV1 has potentially positive effects on host reproductive fitness via increased seed mass, while BPEV and PCV2 may confer benefits to the host through effects on plant metabolism.","abstract_has_math":false,"creators":["Viswanathan, Satish"],"institution":"University of Cambridge","degree_name":"Doctor of Philosophy (PhD)","degree_level":"Doctoral","degree_discipline":null,"degree_department":null,"school":null,"contributors":[],"advisors":["Carr, John"],"committee_chairs":[],"committee_members":[],"year":2024,"date_issued":"2024-09-30","date_published":"2024-09-30","updated_at":"2026-07-22T22:24:30Z","subjects":["Capsicum spp.","Endornavirus","Host-virus interactions","Mutualism","Partitivirus","Persistent plant viruses","Plant-pathogen interactions","Virus-induced gene silencing (VIGS)"],"languages":[],"rights":[],"rights_urls":["https://apollo8-f-pro.lib.cam.ac.uk/bitstreams/14354a54-78c6-4cbe-bb9a-0075dd29d3f8/download","http://purl.org/NET/rdflicense/allrightsreserved"],"identifier_entries":[]},"links":{"outbound_url":"https://doi.org/10.17863/CAM.118733","outbound_label":"DOI","outbound_source":"dc:identifier.doi"},"metadata_groups":[{"id":"people","label":"People","entries":[{"key":"dc:contributor.advisor","label":"Advisor","values":["Carr, John"]},{"key":"dc:creator","label":"Author","values":["Viswanathan, Satish"]}]},{"id":"academic_context","label":"Academic Context","entries":[{"key":"dc:date.issued","label":"Date","values":["2024-09-30"]},{"key":"dc:publisher.institution","label":"Dc Publisher Institution","values":["University of Cambridge"]},{"key":"dc:relation.isreferencedby.uri","label":"Dc Relation Isreferencedby URI","values":["https://www.repository.cam.ac.uk/handle/1810/384880"]},{"key":"dc:type","label":"Dc Type","values":["Thesis"]},{"key":"dc:type.qualificationlevel","label":"Dc Type Qualificationlevel","values":["Doctoral"]},{"key":"dc:type.qualificationname","label":"Dc Type Qualificationname","values":["Doctor of Philosophy (PhD)"]}]},{"id":"subjects_keywords","label":"Subjects and Keywords","entries":[{"key":"dc:subject","label":"Dc Subject","values":["Capsicum spp.","Endornavirus","Host-virus interactions","Mutualism","Partitivirus","Persistent plant viruses","Plant-pathogen interactions","Virus-induced gene silencing (VIGS)"]}]},{"id":"language_rights","label":"Language and Rights","entries":[{"key":"dc:rights","label":"Dc Rights","values":["https://apollo8-f-pro.lib.cam.ac.uk/bitstreams/14354a54-78c6-4cbe-bb9a-0075dd29d3f8/download","http://purl.org/NET/rdflicense/allrightsreserved"]},{"key":"dc:rights.embargodate","label":"Dc Rights Embargodate","values":["2026-05-30"]},{"key":"dc:rights.embargotype","label":"Dc Rights Embargotype","values":["embargo"]}]},{"id":"identifiers","label":"Identifiers","entries":[{"key":"dc:identifier.doi","label":"DOI","values":["https://doi.org/10.17863/CAM.118733"]},{"key":"dc:identifier.uri","label":"Identifier URI","values":["https://apollo8-f-pro.lib.cam.ac.uk/bitstreams/93ac22d5-fab4-4ce1-893e-bad4bf41bdb4/download"]}]},{"id":"additional","label":"Additional Metadata","entries":[{"key":"dc:description.abstract","label":"Abstract","values":["Most work on plant viruses focuses on their pathogenicity, but recent studies suggest viruses may benefit their hosts, at least under some conditions. Plant-infecting viruses of the Partitiviridae and Endornaviridae are transmitted only vertically, via pollen and seed, generally cause no disease symptoms, and in recent literature have been referred to as ‘persistent’ plant viruses. Previous work with legumes and pepper (Capsicum spp.) suggested persistent viruses have mutualistic properties. To test this hypothesis, I investigated the effects of these viruses on host phenotypes in a range of pepper cultivars. Using reverse transcription polymerase chain reaction (RT-PCR) assays I identified cultivars carrying single infections of the endornavirus bell pepper endornavirus (BPEV) or the partitiviruses pepper cryptic virus 1 (PCV1) or PCV2. Plants infected with these viruses harboured similar viral RNA levels in all tissues, consistent with previous studies. I investigated virus-virus interactions between persistent viruses and two pathogenic viruses. Tobacco mosaic virus (TMV) and cucumber mosaic virus (CMV) infection increased BPEV accumulation while PCV1 RNA levels were not affected by either. PCV2 RNA levels decreased in CMV-infected plants but were unaffected by TMV. Thus, pathogenic viruses can interfere with persistent viruses. Neither TMV nor CMV RNA accumulation was affected by BPEV, PCV1 or PCV2, but these studies were not straightforward to interpret since they required comparisons between pepper cultivars that either harboured, or did not harbour persistent viruses, but were not genetically identical. To overcome this, I used a tobacco rattle virus vector for virus-induced gene silencing to ‘cure’ plants of cultivars harbouring BPEV, PCV1 or PCV2. For seven cultivars I obtained pairs of isogenic lines that either carried or no longer carried BPEV, PCV1 or PCV2. PCV1 significantly increased seed mass in both Gourmet Jalapeno and Mirasol chilli cultivars while BPEV and PCV2 showed mixed results. BPEV increased seed mass in Californian Wonder but not in Red King. PCV2 had different impacts on seed mass in different cultivars: increased in Hungarian Wax, decreased in Cayenne Red, with no effect in Poupila. PCV1 increased seed size whereas BPEV decreased it. PCV2 increased seed size in Hungarian Wax but decreased seed size in Cayenne Red and Poupila. None of the persistent viruses affected seed yield significantly. Illumina-based transcriptome sequencing of isogenic cured and uncured lines showed that persistent viruses affect host gene expression differentially. BPEV upregulated >20 genes involved in plant-pathogen interactions, while PCV1 and PCV2, respectively, down- and up-regulated genes involved in photosynthesis. 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Plant-infecting viruses of the Partitiviridae and Endornaviridae are transmitted only vertically, via pollen and seed, generally cause no disease symptoms, and in recent literature have been referred to as ‘persistent’ plant viruses. Previous work with legumes and pepper (Capsicum spp.) suggested persistent viruses have mutualistic properties. To test this hypothesis, I investigated the effects of these viruses on host phenotypes in a range of pepper cultivars. Using reverse transcription polymerase chain reaction (RT-PCR) assays I identified cultivars carrying single infections of the endornavirus bell pepper endornavirus (BPEV) or the partitiviruses pepper cryptic virus 1 (PCV1) or PCV2. Plants infected with these viruses harboured similar viral RNA levels in all tissues, consistent with previous studies. I investigated virus-virus interactions between persistent viruses and two pathogenic viruses. Tobacco mosaic virus (TMV) and cucumber mosaic virus (CMV) infection increased BPEV accumulation while PCV1 RNA levels were not affected by either. PCV2 RNA levels decreased in CMV-infected plants but were unaffected by TMV. Thus, pathogenic viruses can interfere with persistent viruses. Neither TMV nor CMV RNA accumulation was affected by BPEV, PCV1 or PCV2, but these studies were not straightforward to interpret since they required comparisons between pepper cultivars that either harboured, or did not harbour persistent viruses, but were not genetically identical. To overcome this, I used a tobacco rattle virus vector for virus-induced gene silencing to ‘cure’ plants of cultivars harbouring BPEV, PCV1 or PCV2. For seven cultivars I obtained pairs of isogenic lines that either carried or no longer carried BPEV, PCV1 or PCV2. PCV1 significantly increased seed mass in both Gourmet Jalapeno and Mirasol chilli cultivars while BPEV and PCV2 showed mixed results. BPEV increased seed mass in Californian Wonder but not in Red King. PCV2 had different impacts on seed mass in different cultivars: increased in Hungarian Wax, decreased in Cayenne Red, with no effect in Poupila. PCV1 increased seed size whereas BPEV decreased it. PCV2 increased seed size in Hungarian Wax but decreased seed size in Cayenne Red and Poupila. None of the persistent viruses affected seed yield significantly. Illumina-based transcriptome sequencing of isogenic cured and uncured lines showed that persistent viruses affect host gene expression differentially. BPEV upregulated >20 genes involved in plant-pathogen interactions, while PCV1 and PCV2, respectively, down- and up-regulated genes involved in photosynthesis. 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