Genomic Analysis Unveils the Pervasiveness and Diversity of Prophages Infecting Erwinia Species.

Prophages are abundant elements integrated into bacterial genomes and contribute to inter-strain genetic variability and, in some cases, modulate the environmental behavior of bacteria, such as pathogen virulence. Here, we described prophage occurrence and diversity in publicly available Erwinia genome assemblies, a genus containing plant pathogens. Prophage-like sequences were identified and taxonomically classified. Sequence diversity was analyzed through intergenomic similarities. Furthermore, we searched for anti-phage defense systems in Erwinia spp., such as DISARM, BREX, and CRISPR-Cas systems, and identified the putative targets of CRISPR spacers. We identified 939 prophage-like sequences in 221 Erwinia spp. genome assemblies. Only 243 prophage-like sequences were classified, all belonging to the Caudoviricetes class. The set of putative Erwinia prophages was mostly unique since only three sequences showed more than 70% intergenomic similarities to known Erwinia phages. Overall, the number and type of CRISPR-Cas systems were conserved within Erwinia species, with many spacers directed to the putative prophages identified. This study increased the knowledge of the diversity and distribution of Erwinia prophages, contributing to the characterization of genetic and ecological factors influencing Erwinia spp. environmental fitness.

Widespread distribution of prophages signaling the potential for adaptability and pathogenicity evolution of Ralstonia solanacearum species complex.

Integrated bacteriophages (prophages) can impact host cells, affecting their lifestyle, genomic diversity, and fitness. However, many basic aspects of how these organisms affect the host cell remain poorly understood. Ralstonia solanacearum is a gram-negative plant pathogenic bacterium that encompasses a great diversity of ecotypes regarded as a species complex (R. solanacearum Species Complex - RSSC). RSSC genomes have a mosaic structure containing numerous elements, signaling the potential for its evolution through horizontal gene transfer. Here, we analyzed 120 Ralstonia spp. genomes from the public database to identify prophage sequences. In total, 379 prophage-like elements were found in the chromosome and megaplasmid of Ralstonia spp. These elements encode genes related to host fitness, virulence factors, antibiotic resistance, and niche adaptation, which might contribute to RSSC adaptability. Prophage-like elements are widespread into the complex in different species and geographic origins, suggesting that the RSSC phages are ancestrally acquired. Complete prophages belonging to the families Inoviridae, Myoviridae, and Siphoviridae were found, being the members of Inoviridae the most abundant. Analysis of CRISPR-Cas spacer sequences demonstrated the presence of prophages sequences that indicate successive infection events during bacterial evolution. Besides complete prophages, we also demonstrated 14 novel putative prophages integrated into Ralstonia spp. genomes. Altogether, our results provide insights into the diversity of prophages in RSSC genomes and suggest that these elements may deeply affect the virulence and host adaptation and shaping the genomes among the strains of this important pathogen.

A novel mycovirus associated to Alternaria alternata comprises a distinct lineage in Partitiviridae.

In the present work, we report a novel mycovirus that infects Alternaria alternata. The mycovirus has isometric particles of approximately 30nm and the genome consists of two molecules of dsRNA, dsRNA1 with 1833bp, encoding a putative RNA-dependent RNA polymerase (RdRp) and dsRNA2, with 1680bp in length, encoding the putative capsid protein (CP). RdRp analysis revealed low amino acid identity with RdRps with species in the genus Gammapartitivirus, and the alignment of the RdRp revealed all the six conserved motifs present in members of Partitiviridae. The putative coat protein (CP) analysis revealed similarity with the putative CP of Botryosphaeria dothidea partitivirus 1 (BdPV1), a divergent partitivirus. We propose that Alternaria alternata partitivirus 1 (AtPV1) is a novel species and comprises a distinct lineage related to genus Gammapartitivirus in the family Partitiviridae, apparently on the threshold of radiation of a new genus, together with BdPV1. Vertical transmission tests showed that AtPV1 was transmitted to 100% conidial progeny and standard curing was unable to eliminate it from the host, characterizing it as a persistent virus. The absence of a virus-free isogenic lineage prevented us from accessing the details of the interaction between AtPV1 and A. alternata. Therefore, it remains unclear whether the morphological plasticity observed or the inability of the A. alternata isolate AVi1 to cause disease in plants is associated with AtPV1 infection.