321ef60859d2180d7b218b7624817bf8 26TV28_Sci_Vicient_pub.pdf 1dd8556b1bfc7504c639a8674a45dc7946bcdf65 26TV28_Sci_Vicient_pub.pdf bc189890e5f624747711e153567a4517a5faeef82a7bb9cff692fdbf6abddfd2 26TV28_Sci_Vicient_pub.pdf Title: Predicting the Capsid Architecture of Florendoviruses: Molecular Fossils of Ancient Caulimovirid-like Viruses Subject: Endogenous viral elements derived from members of the family Caulimoviridae are widely distributed across plant genomes. Once integrated, they accumulate extensive mutations; most are no longer biologically active and can therefore be regarded as molecular fossils. Their loss of activity precludes the recovery of viral particles, thereby preventing direct experimental characterization of their capsid architecture. Here, we combined sequence-based phylogenetic analyses with artificial-intelligence-assisted protein structure prediction to investigate the coat proteins of florendoviruses, the most abundant endogenous caulimovirid lineage. Phylogenetic analysis placed florendovirus coat proteins in close proximity to those of the genus Petuvirus. The structural prediction of the coat protein is limited by the presence of an intrinsically disordered N-terminal region, whose structure cannot be reliably predicted. In contrast, the central capsid domain yields robust predictions, revealing similarity not only to caulimovirus coat proteins but also to retrotransposon Gag proteins. Structural comparisons indicate that the florendovirus coat domain is most closely related to those of Petuvirus. Because petuviruses assemble into isometric particles, our data support the hypothesis that the ancestral episomal forms of florendoviruses possessed a similar capsid organization. Our findings extend the study of ancient viruses whose morphology cannot be directly investigated using conventional phylogenetic and AI-assisted structure prediction methods. Keywords: endogenous viral element; endogenous caulimovirid; florendovirus; AlphaFold 3; AI-assisted structural biology Author: Carlos M. Vicient Creator: LaTeX with hyperref Producer: pdfTeX-1.40.25; modified using OpenPDF 1.4.2 CreationDate: Mon Sep 14 13:01:47 2026 CEST ModDate: Mon Sep 14 13:07:42 2026 CEST Custom Metadata: yes Metadata Stream: no Tagged: no UserProperties: no Suspects: no Form: none JavaScript: no Pages: 11 Encrypted: no Page size: 595.276 x 841.89 pts (A4) Page rot: 0 File size: 2516468 bytes Optimized: no PDF version: 1.7 name type encoding emb sub uni object ID ------------------------------------ ----------------- ---------------- --- --- --- --------- YKDVGV+URWPalladioL-Bold Type 1 Custom yes yes yes 75 0 QREMOG+URWPalladioL-Roma Type 1 Custom yes yes yes 76 0 XKPOZG+URWPalladioL-Ital Type 1 Custom yes yes yes 77 0 PDTLUH+CMSY10 Type 1 Builtin yes yes yes 159 0 CKBPVA+EURM10 Type 1 Builtin yes yes yes 160 0 LKJGPB+PalatinoLinotype TrueType WinAnsi yes yes no 186 0 LKJGPB+PalatinoLinotype TrueType WinAnsi yes yes no 245 0 LKJGPB+PalatinoLinotype TrueType WinAnsi yes yes no 264 0 LKJGPB+PalatinoLinotype TrueType WinAnsi yes yes no 289 0 Jhove (Rel. 1.28.0, 2023-05-18) Date: 2026-09-23 04:02:46 CEST RepresentationInformation: 26TV28_Sci_Vicient_pub.pdf ReportingModule: PDF-hul, Rel. 1.12.4 (2023-03-16) LastModified: 2026-09-22 09:41:25 CEST Size: 2516468 Format: PDF Version: 1.7 Status: Well-Formed and valid SignatureMatches: PDF-hul MIMEtype: application/pdf PDFMetadata: Objects: 382 FreeObjects: 1 IncrementalUpdates: 0 DocumentCatalog: ViewerPreferences: HideToolbar: false HideMenubar: false HideWindowUI: false FitWindow: true CenterWindow: false DisplayDocTitle: false NonFullScreenPageMode: UseNone Direction: L2R ViewArea: CropBox ViewClip: CropBox PrintArea: CropBox PageClip: CropBox PageLayout: SinglePage PageMode: UseNone Outlines: Item: Title: Introduction Item: Title: Methods Children: Item: Title: Sequence Selection Item: Title: Phylogenetic Analysis Item: Title: AI-Assisted Structural Inference Item: Title: Results and Discussion Item: Title: Conclusions Item: Title: References Info: Title: Predicting the Capsid Architecture of Florendoviruses: Molecular Fossils of Ancient Caulimovirid-like Viruses Author: Carlos M. Vicient Subject: Endogenous viral elements derived from members of the family Caulimoviridae are widely distributed across plant genomes. Once integrated, they accumulate extensive mutations; most are no longer biologically active and can therefore be regarded as molecular fossils. Their loss of activity precludes the recovery of viral particles, thereby preventing direct experimental characterization of their capsid architecture. Here, we combined sequence-based phylogenetic analyses with artificial-intelligence-assisted protein structure prediction to investigate the coat proteins of florendoviruses, the most abundant endogenous caulimovirid lineage. Phylogenetic analysis placed florendovirus coat proteins in close proximity to those of the genus Petuvirus. The structural prediction of the coat protein is limited by the presence of an intrinsically disordered N-terminal region, whose structure cannot be reliably predicted. In contrast, the central capsid domain yields robust predictions, revealing similarity not only to caulimovirus coat proteins but also to retrotransposon Gag proteins. Structural comparisons indicate that the florendovirus coat domain is most closely related to those of Petuvirus. Because petuviruses assemble into isometric particles, our data support the hypothesis that the ancestral episomal forms of florendoviruses possessed a similar capsid organization. Our findings extend the study of ancient viruses whose morphology cannot be directly investigated using conventional phylogenetic and AI-assisted structure prediction methods. 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