{"id":{"repo_id":"uiuc","oai_identifier":"oai:www.ideals.illinois.edu:2142/90897"},"canonical_url":"https://search.dev.ndltd.org/etd/uiuc/oai:www.ideals.illinois.edu:2142/90897","repository":{"repo_id":"uiuc","name":"University of Illinois - Urbana-Champaign","base_url":"https://www.ideals.illinois.edu/oai-pmh"},"display":{"title":"Molecular characterization of novel soybean-associated viruses identified by high-throughput sequencing","abstract":"High-throughput sequencing of mRNA from soybean leaf samples collected from North Dakota and Illinois soybean fields revealed the presence of two novel soybean-associated viruses. The first virus has a single-stranded positive-sense RNA genome consisting of 8,693 nt that contains two large open reading frames (ORFs). The predicted amino acid sequence of the first ORF showed similarity to structural proteins, of members of the invertebrate-infecting Dicistroviridae and the sequence of the second ORF which is a nonstructural proteins lack affinity to other virus sequences available in GenBank. The presence of separate ORFs for the structural and nonstructural proteins was similar to members of the family Dicistroviridae, but the order of the two ORFs in the new virus was opposite to that of the family Dicistroviridae. Because of the virus' unique genome organization and the lack of strong phylogenetic association with previously described virus families, the soybean-associated virus may represent a novel virus family. The second virus also has a single stranded positive sense RNA genome, but has two genomic segments. The larger segment (RNA1), which is 8,208 nt long, encodes the replication-related proteins while the smaller segment (RNA2), which is 5,806 nt long, encodes the structural and movement proteins. Both the segments have a very long 3' untranslated regions with lengths of more than 1,550 nt. The predicted amino acid sequences for both the segments were closely related to members of subgroup C of the genus Nepovirus.","abstract_html":"High-throughput sequencing of mRNA from soybean leaf samples collected from North Dakota and Illinois soybean fields revealed the presence of two novel soybean-associated viruses. The first virus has a single-stranded positive-sense RNA genome consisting of 8,693 nt that contains two large open reading frames (ORFs). The predicted amino acid sequence of the first ORF showed similarity to structural proteins, of members of the invertebrate-infecting Dicistroviridae and the sequence of the second ORF which is a nonstructural proteins lack affinity to other virus sequences available in GenBank. The presence of separate ORFs for the structural and nonstructural proteins was similar to members of the family Dicistroviridae, but the order of the two ORFs in the new virus was opposite to that of the family Dicistroviridae. Because of the virus' unique genome organization and the lack of strong phylogenetic association with previously described virus families, the soybean-associated virus may represent a novel virus family. The second virus also has a single stranded positive sense RNA genome, but has two genomic segments. The larger segment (RNA1), which is 8,208 nt long, encodes the replication-related proteins while the smaller segment (RNA2), which is 5,806 nt long, encodes the structural and movement proteins. Both the segments have a very long 3' untranslated regions with lengths of more than 1,550 nt. The predicted amino acid sequences for both the segments were closely related to members of subgroup C of the genus Nepovirus.","abstract_has_math":false,"creators":["Yasmin, Tuba"],"institution":"University of Illinois at Urbana-Champaign","degree_name":"M.S.","degree_level":"Thesis","degree_discipline":"Crop Sciences","degree_department":null,"school":null,"contributors":["Domier, Leslie L."],"advisors":[],"committee_chairs":[],"committee_members":[],"year":2016,"date_issued":"2016-07-07T21:14:42Z","date_published":"2016-07-07T21:14:42Z","updated_at":"2026-07-22T22:26:34Z","subjects":["Soybean","High-throughput sequencing","RNASeq","Plant Virus","Nepovirus","Picornavirales"],"languages":["en"],"rights":["Copyright 2016 Tuba Yasmin"],"rights_urls":[],"identifier_entries":[]},"links":{"outbound_url":"http://hdl.handle.net/2142/90897","outbound_label":"Handle","outbound_source":"dc:identifier"},"metadata_groups":[{"id":"people","label":"People","entries":[{"key":"dc:contributor","label":"Contributor","values":["Domier, Leslie L."]},{"key":"dc:creator","label":"Author","values":["Yasmin, Tuba"]}]},{"id":"academic_context","label":"Academic Context","entries":[{"key":"dc:date","label":"Dc Date","values":["2016-07-07T21:14:42Z","2018-07-08T09:15:36Z","2016-04-21","2016-05"]},{"key":"dc:type","label":"Dc Type","values":["text"]},{"key":"thesis:degree_discipline","label":"Discipline","values":["Crop Sciences"]},{"key":"thesis:degree_level","label":"Degree Level","values":["Thesis"]},{"key":"thesis:degree_name","label":"Degree Name","values":["M.S."]},{"key":"thesis:institution_name","label":"Thesis Institution Name","values":["University of Illinois at Urbana-Champaign"]}]},{"id":"subjects_keywords","label":"Subjects and Keywords","entries":[{"key":"dc:subject","label":"Dc Subject","values":["Soybean","High-throughput sequencing","RNASeq","Plant Virus","Nepovirus","Picornavirales"]}]},{"id":"language_rights","label":"Language and Rights","entries":[{"key":"dc:language","label":"Dc Language","values":["en"]},{"key":"dc:rights","label":"Dc Rights","values":["Copyright 2016 Tuba Yasmin"]}]},{"id":"identifiers","label":"Identifiers","entries":[{"key":"dc:identifier","label":"Identifier","values":["http://hdl.handle.net/2142/90897"]}]},{"id":"additional","label":"Additional Metadata","entries":[{"key":"dc:description","label":"Description","values":["High-throughput sequencing of mRNA from soybean leaf samples collected from North Dakota and Illinois soybean fields revealed the presence of two novel soybean-associated viruses. The first virus has a single-stranded positive-sense RNA genome consisting of 8,693 nt that contains two large open reading frames (ORFs). The predicted amino acid sequence of the first ORF showed similarity to structural proteins, of members of the invertebrate-infecting Dicistroviridae and the sequence of the second ORF which is a nonstructural proteins lack affinity to other virus sequences available in GenBank. The presence of separate ORFs for the structural and nonstructural proteins was similar to members of the family Dicistroviridae, but the order of the two ORFs in the new virus was opposite to that of the family Dicistroviridae. Because of the virus' unique genome organization and the lack of strong phylogenetic association with previously described virus families, the soybean-associated virus may represent a novel virus family. The second virus also has a single stranded positive sense RNA genome, but has two genomic segments. The larger segment (RNA1), which is 8,208 nt long, encodes the replication-related proteins while the smaller segment (RNA2), which is 5,806 nt long, encodes the structural and movement proteins. Both the segments have a very long 3' untranslated regions with lengths of more than 1,550 nt. The predicted amino acid sequences for both the segments were closely related to members of subgroup C of the genus Nepovirus.","Submission published under a 24 month embargo labeled 'Closed Access', the embargo will last until 2018-05-01","The student, Tuba Yasmin, accepted the attached license on 2016-04-13 at 22:10.","The student, Tuba Yasmin, submitted this Thesis for approval on 2016-04-13 at 22:26.","This Thesis was approved for publication on 2016-04-21 at 16:03.","DSpace SAF Submission Ingestion Package generated from Vireo submission #9217 on 2016-07-07 at 14:16:42","Made available in DSpace on 2016-07-07T21:14:42Z (GMT). No. of bitstreams: 2 YASMIN-THESIS-2016.pdf: 1092733 bytes, checksum: d4dd96277fe41fe9d14e86eab4226bfe (MD5) LICENSE.txt: 4208 bytes, checksum: a7c6333ea88aae304c7e200c383f37db (MD5) Previous issue date: 2016-04-21","Embargo set by: Seth Robbins for item 93251 Lift date: 2018-07-07T21:14:52Z Reason: Author requested closed access (OA after 2yrs) in Vireo ETD system","Embargo set by: Seth Robbins for item 93251 Lift date: 2018-07-07T21:18:16Z Reason: Author requested closed access (OA after 2yrs) in Vireo ETD system","Limited Restriction Lifted for Item 93251 on 2018-07-08T09:15:36Z."]},{"key":"dc:format","label":"Dc Format","values":["application/pdf"]},{"key":"dc:title","label":"Title","values":["Molecular characterization of novel soybean-associated viruses identified by high-throughput sequencing"]}]}],"canonical_facts":{"dc:contributor":["Domier, Leslie L."],"dc:creator":["Yasmin, Tuba"],"dc:date":["2016-07-07T21:14:42Z","2018-07-08T09:15:36Z","2016-04-21","2016-05"],"dc:description":["High-throughput sequencing of mRNA from soybean leaf samples collected from North Dakota and Illinois soybean fields revealed the presence of two novel soybean-associated viruses. The first virus has a single-stranded positive-sense RNA genome consisting of 8,693 nt that contains two large open reading frames (ORFs). The predicted amino acid sequence of the first ORF showed similarity to structural proteins, of members of the invertebrate-infecting Dicistroviridae and the sequence of the second ORF which is a nonstructural proteins lack affinity to other virus sequences available in GenBank. The presence of separate ORFs for the structural and nonstructural proteins was similar to members of the family Dicistroviridae, but the order of the two ORFs in the new virus was opposite to that of the family Dicistroviridae. Because of the virus' unique genome organization and the lack of strong phylogenetic association with previously described virus families, the soybean-associated virus may represent a novel virus family. The second virus also has a single stranded positive sense RNA genome, but has two genomic segments. The larger segment (RNA1), which is 8,208 nt long, encodes the replication-related proteins while the smaller segment (RNA2), which is 5,806 nt long, encodes the structural and movement proteins. Both the segments have a very long 3' untranslated regions with lengths of more than 1,550 nt. The predicted amino acid sequences for both the segments were closely related to members of subgroup C of the genus Nepovirus.","Submission published under a 24 month embargo labeled 'Closed Access', the embargo will last until 2018-05-01","The student, Tuba Yasmin, accepted the attached license on 2016-04-13 at 22:10.","The student, Tuba Yasmin, submitted this Thesis for approval on 2016-04-13 at 22:26.","This Thesis was approved for publication on 2016-04-21 at 16:03.","DSpace SAF Submission Ingestion Package generated from Vireo submission #9217 on 2016-07-07 at 14:16:42","Made available in DSpace on 2016-07-07T21:14:42Z (GMT). No. of bitstreams: 2 YASMIN-THESIS-2016.pdf: 1092733 bytes, checksum: d4dd96277fe41fe9d14e86eab4226bfe (MD5) LICENSE.txt: 4208 bytes, checksum: a7c6333ea88aae304c7e200c383f37db (MD5) Previous issue date: 2016-04-21","Embargo set by: Seth Robbins for item 93251 Lift date: 2018-07-07T21:14:52Z Reason: Author requested closed access (OA after 2yrs) in Vireo ETD system","Embargo set by: Seth Robbins for item 93251 Lift date: 2018-07-07T21:18:16Z Reason: Author requested closed access (OA after 2yrs) in Vireo ETD system","Limited Restriction Lifted for Item 93251 on 2018-07-08T09:15:36Z."],"dc:format":["application/pdf"],"dc:identifier":["http://hdl.handle.net/2142/90897"],"dc:language":["en"],"dc:rights":["Copyright 2016 Tuba Yasmin"],"dc:subject":["Soybean","High-throughput sequencing","RNASeq","Plant Virus","Nepovirus","Picornavirales"],"dc:title":["Molecular characterization of novel soybean-associated viruses identified by high-throughput sequencing"],"dc:type":["text"],"thesis:degree_discipline":["Crop Sciences"],"thesis:degree_level":["Thesis"],"thesis:degree_name":["M.S."],"thesis:institution_name":["University of Illinois at Urbana-Champaign"]},"updated_at":"2026-07-22T22:26:34Z"}