Discovery and Analyses of Caulimovirid-like Sequences in Upland Cotton (<i>Gossypium hirsutum</i>)
Analyses of Illumina-based high-throughput sequencing data generated during characterization of the cotton leafroll dwarf virus population in Mississippi (2020–2022) consistently yielded contigs varying in size (most frequently from 4 to 7 kb) with identical nucleotide content and sharing similariti...
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MDPI AG
2023-07-01
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| Series: | Viruses |
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| Online Access: | https://www.mdpi.com/1999-4915/15/8/1643 |
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| author | Nina Aboughanem-Sabanadzovic Thomas W. Allen James Frelichowski Jodi Scheffler Sead Sabanadzovic |
| author_facet | Nina Aboughanem-Sabanadzovic Thomas W. Allen James Frelichowski Jodi Scheffler Sead Sabanadzovic |
| author_sort | Nina Aboughanem-Sabanadzovic |
| collection | DOAJ |
| description | Analyses of Illumina-based high-throughput sequencing data generated during characterization of the cotton leafroll dwarf virus population in Mississippi (2020–2022) consistently yielded contigs varying in size (most frequently from 4 to 7 kb) with identical nucleotide content and sharing similarities with reverse transcriptases (RTases) encoded by extant plant pararetroviruses (family <i>Caulimoviridiae</i>). Initial data prompted an in-depth study involving molecular and bioinformatic approaches to characterize the nature and origins of these caulimovirid-like sequences. As a result, here, we report on endogenous viral elements (EVEs) related to extant members of the family <i>Caulimoviridae,</i> integrated into a genome of upland cotton (<i>Gossypium hirsutum</i>), for which we propose the provisional name “endogenous cotton pararetroviral elements” (eCPRVE). Our investigations pinpointed a ~15 kbp-long locus on the A04 chromosome consisting of head-to-head orientated tandem copies located on positive- and negative-sense DNA strands (eCPRVE+ and eCPRVE-). Sequences of the eCPRVE+ comprised nearly complete and slightly decayed genome information, including ORFs coding for the viral movement protein (MP), coat protein (CP), RTase, and transactivator/viroplasm protein (TA). Phylogenetic analyses of major viral proteins suggest that the eCPRVE+ may have been initially derived from a genome of a cognate virus belonging to a putative new genus within the family. Unexpectedly, an identical 15 kb-long locus composed of two eCPRVE copies was also detected in a newly recognized species <i>G. ekmanianum</i>, shedding some light on the relatively recent evolution within the cotton family. |
| first_indexed | 2024-03-10T23:30:35Z |
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| id | doaj.art-5042b0b1192245eaa1fab29f2ff5af48 |
| institution | Directory Open Access Journal |
| issn | 1999-4915 |
| language | English |
| last_indexed | 2024-03-10T23:30:35Z |
| publishDate | 2023-07-01 |
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| series | Viruses |
| spelling | doaj.art-5042b0b1192245eaa1fab29f2ff5af482023-11-19T03:19:38ZengMDPI AGViruses1999-49152023-07-01158164310.3390/v15081643Discovery and Analyses of Caulimovirid-like Sequences in Upland Cotton (<i>Gossypium hirsutum</i>)Nina Aboughanem-Sabanadzovic0Thomas W. Allen1James Frelichowski2Jodi Scheffler3Sead Sabanadzovic4Institute for Genomics, Biocomputing and Biotechnology, Mississippi State University, 2 Research Park, Mailstop 9627, Mississippi, MS 39762, USADelta Research and Extension Center, Mississippi State University, 82 Stoneville Road, P.O. Box 197, Stoneville, MS 38776, USAUSDA-ARS Plains Area, 2881 F&B Road, College Station, TX 77845, USAUSDA-ARS Mid-South Area, 141 Experiment Station Road, Stoneville, MS 38776, USADepartment of Biochemistry, Molecular Biology, Entomology and Plant Pathology, Mississippi State University, 100 Twelve Lane, Mail Stop 9775, Mississippi, MS 39762, USAAnalyses of Illumina-based high-throughput sequencing data generated during characterization of the cotton leafroll dwarf virus population in Mississippi (2020–2022) consistently yielded contigs varying in size (most frequently from 4 to 7 kb) with identical nucleotide content and sharing similarities with reverse transcriptases (RTases) encoded by extant plant pararetroviruses (family <i>Caulimoviridiae</i>). Initial data prompted an in-depth study involving molecular and bioinformatic approaches to characterize the nature and origins of these caulimovirid-like sequences. As a result, here, we report on endogenous viral elements (EVEs) related to extant members of the family <i>Caulimoviridae,</i> integrated into a genome of upland cotton (<i>Gossypium hirsutum</i>), for which we propose the provisional name “endogenous cotton pararetroviral elements” (eCPRVE). Our investigations pinpointed a ~15 kbp-long locus on the A04 chromosome consisting of head-to-head orientated tandem copies located on positive- and negative-sense DNA strands (eCPRVE+ and eCPRVE-). Sequences of the eCPRVE+ comprised nearly complete and slightly decayed genome information, including ORFs coding for the viral movement protein (MP), coat protein (CP), RTase, and transactivator/viroplasm protein (TA). Phylogenetic analyses of major viral proteins suggest that the eCPRVE+ may have been initially derived from a genome of a cognate virus belonging to a putative new genus within the family. Unexpectedly, an identical 15 kb-long locus composed of two eCPRVE copies was also detected in a newly recognized species <i>G. ekmanianum</i>, shedding some light on the relatively recent evolution within the cotton family.https://www.mdpi.com/1999-4915/15/8/1643viruspararetroviruscotton<i>Caulimoviridae</i>genome integrationepisomal form |
| spellingShingle | Nina Aboughanem-Sabanadzovic Thomas W. Allen James Frelichowski Jodi Scheffler Sead Sabanadzovic Discovery and Analyses of Caulimovirid-like Sequences in Upland Cotton (<i>Gossypium hirsutum</i>) Viruses virus pararetrovirus cotton <i>Caulimoviridae</i> genome integration episomal form |
| title | Discovery and Analyses of Caulimovirid-like Sequences in Upland Cotton (<i>Gossypium hirsutum</i>) |
| title_full | Discovery and Analyses of Caulimovirid-like Sequences in Upland Cotton (<i>Gossypium hirsutum</i>) |
| title_fullStr | Discovery and Analyses of Caulimovirid-like Sequences in Upland Cotton (<i>Gossypium hirsutum</i>) |
| title_full_unstemmed | Discovery and Analyses of Caulimovirid-like Sequences in Upland Cotton (<i>Gossypium hirsutum</i>) |
| title_short | Discovery and Analyses of Caulimovirid-like Sequences in Upland Cotton (<i>Gossypium hirsutum</i>) |
| title_sort | discovery and analyses of caulimovirid like sequences in upland cotton i gossypium hirsutum i |
| topic | virus pararetrovirus cotton <i>Caulimoviridae</i> genome integration episomal form |
| url | https://www.mdpi.com/1999-4915/15/8/1643 |
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