RESUMO
Viroids and viroid-like covalently closed circular (ccc) RNAs are minimal replicators that typically encode no proteins and hijack cellular enzymes for replication. The extent and diversity of viroid-like agents are poorly understood. We developed a computational pipeline to identify viroid-like cccRNAs and applied it to 5,131 metatranscriptomes and 1,344 plant transcriptomes. The search yielded 11,378 viroid-like cccRNAs spanning 4,409 species-level clusters, a 5-fold increase compared to the previously identified viroid-like elements. Within this diverse collection, we discovered numerous putative viroids, satellite RNAs, retrozymes, and ribozy-like viruses. Diverse ribozyme combinations and unusual ribozymes within the cccRNAs were identified. Self-cleaving ribozymes were identified in ambiviruses, some mito-like viruses and capsid-encoding satellite virus-like cccRNAs. The broad presence of viroid-like cccRNAs in diverse transcriptomes and ecosystems implies that their host range is far broader than currently known, and matches to CRISPR spacers suggest that some cccRNAs replicate in prokaryotes.
Assuntos
RNA Catalítico , Viroides , RNA Circular/metabolismo , Viroides/genética , Viroides/metabolismo , RNA Catalítico/genética , RNA Viral/genética , RNA Viral/metabolismo , Ecossistema , Doenças das PlantasRESUMO
Viroids are a unique class of plant pathogens that consist of small circular RNA molecules, between 220 and 450 nucleotides in size. Viroids encode no proteins and are the smallest known infectious agents. Viroids replicate via the rolling circle mechanism, producing multimeric intermediates which are cleaved to unit length either by ribozymes formed from both polarities of the viroid genomic RNA or by coopted host RNAses. Many viroid-like small circular RNAs are satellites of plant RNA viruses. Ribozyviruses, represented by human hepatitis delta virus, are larger viroid-like circular RNAs that additionally encode the viral nucleocapsid protein. It has been proposed that viroids are direct descendants of primordial RNA replicons that were present in the hypothetical RNA world. We argue, however, that much later origin of viroids, possibly, from recently discovered mobile genetic elements known as retrozymes, is a far more parsimonious evolutionary scenario. Nevertheless, viroids and viroid-like circular RNAs are minimal replicators that are likely to be close to the theoretical lower limit of replicator size and arguably comprise the paradigm for replicator emergence. Thus, although viroid-like replicators are unlikely to be direct descendants of primordial RNA replicators, the study of the diversity and evolution of these ultimate genetic parasites can yield insights into the earliest stages of the evolution of life.
RESUMO
We introduce ViroidDB, a value-added database that attempts to collect all known viroid and viroid-like circular RNA sequences into a single resource. Spanning about 10 000 unique sequences, ViroidDB includes viroids, retroviroid-like elements, small circular satellite RNAs, ribozyviruses, and retrozymes. Each sequence's secondary structure, ribozyme content, and cluster membership are predicted via a custom pipeline optimized for handling circular RNAs. The data can be explored via a purpose-built user interface that features visualizations, multiple sequence alignments, and a portal for downloading bulk data. Users can browse the data by sequence type, taxon, or typo-tolerant search of metadata fields. The database is freely accessible at https://viroids.org.
Assuntos
Bases de Dados de Ácidos Nucleicos , RNA Catalítico/genética , RNA Circular/genética , RNA Viral/genética , Software , Viroides/genética , Sequência de Bases , Internet , Metadados , Conformação de Ácido Nucleico , Doenças das Plantas/virologia , Plantas/virologia , RNA Catalítico/química , RNA Catalítico/classificação , RNA Catalítico/metabolismo , RNA Circular/química , RNA Circular/classificação , RNA Circular/metabolismo , RNA Viral/química , RNA Viral/classificação , RNA Viral/metabolismo , Alinhamento de Sequência , Viroides/classificação , Viroides/metabolismoRESUMO
Raw DNA sequences contain an immense amount of meaningful biological information. However, these sequences are hard for humans to intuitively interpret. To solve this problem, a number of methods have been proposed to transform DNA sequences into two-dimensional visualizations. DNAvisualization.org implements several of these methods in a cost effective and performant manner via a novel, entirely serverless architecture. By taking advantage of recent developments in serverless parallel computing and selective data retrieval, the website is able to offer users the ability to visualize up to thirty 4.5 Mb DNA sequences simultaneously using one of five supported methods and to export these visualizations in a variety of publication-ready formats.
Assuntos
Sequência de Bases/genética , DNA/genética , Análise de Sequência de DNA/métodos , Software , Humanos , Armazenamento e Recuperação da Informação , Internet , Interface Usuário-ComputadorRESUMO
SUMMARY: Squiggle is a software tool that automatically generates interactive web-based two-dimensional graphical representations of raw DNA sequences. Built with ease of use in mind, Squiggle implements several prior sequence visualization algorithms and introduces novel visualization methods designed to maximize human usability. AVAILABILITY AND IMPLEMENTATION: Squiggle is written in Python 3 and freely available under the permissive MIT license. The open-source code can be downloaded from github.com/Lab41/squiggle as well as the Python Package Index. The installation instructions and user guide are available at squiggle.readthedocs.org.
Assuntos
Algoritmos , Software , DNA , Humanos , Análise de Sequência de DNARESUMO
Treatment of full-thickness rotator cuff tears vary in surgical technique dependent on the amount of retraction of the rotator cuff and/or delamination of the soft tissue. The described technique addresses both of those concerns. We present a modification of the SpeedBridge technique used to address retracted or delaminated repairs and effectively expand the indications for use of the double-row knotless technique. In this modification, the reduction is performed by an initial anchor with several stay sutures providing provisional reduction of the tissue in a controlled fashion. This is followed by compression through a standard double-row technique.
