Significance: Mycoviruses generally contain dsRNA genomes but ssRNA and ssDNA examples are known. Mycovirus diversity is increasing, and here we describe a unique example that contains four dsRNA elements nominated Aspergillus fumigatus tetramycovirus-1 (AfuTmV-1). We show for the first time (to our knowledge) that both purified AfuTmV-1 and its dsRNA are infectious for protoplasts and that the virus genome is not conventionally encapsidated and has a unique organization. Separation of the genes encoding the RNA-dependent RNA polymerase enzyme responsible for copying the viral genome and an S -adenosyl methionine-dependent methyltransferase capping enzyme on different dsRNAs is also previously unreported for a mycovirus. AfuTmV-1 appears to be intermediate between dsRNA and positive-strand ssRNA viruses, as well as between encapsidated and capsidless RNA viruses.

The present study explored culturable halophilic and halotolerant fungi from man-made solar salterns in Pattani Province, Thailand. A total of 24 fungal isolates were discovered and characterized using morphological and molecular identification. Production of extracellular enzymes, secondary metabolites and mycoviruses was examined. Growth was observed in salinity and temperature ranges between 0%-20% and 28–40°C, respectively. Growth in different environmental conditions confirmed the halophilic or halotolerant nature of some strains. Fungal isolates were phylogenetically classified into seven different genera belonging to Aspergillus, Cladosporium, Curvularia, Diaporthe, Ectophoma, Fusarium and Penicillium. An enzymatic production test revealed that thirteen isolates could produce proteases and amylases at different levels. The presence of mycoviruses was detected in three isolates. Seventeen of the 24 isolates produced antimicrobial metabolites. The majority of these active isolates were identified as Aspergillus and Penicillium species. Crude extracts of the fungal mycelia and culture broths from these isolates had an inhibitory effect on both Gram-positive and Gram-negative bacteria and human pathogenic fungi. Research into fungi from saline environments could reveal fungal strains of biotechnological and industrial interest.

Novel families of short interspersed nuclear element (SINE) sequences in the human pathogenic fungus Aspergillus fumigatus, clinical isolate Af293, were identified and categorised into tRNA-related and 5S rRNA-related SINEs. Eight predicted tRNA-related SINE families originating from different tRNAs, and nominated as AfuSINE2 sequences, contained target site duplications of short direct repeat sequences (4–14 bp) flanking the elements, an extended tRNA-unrelated region and typical features of RNA polymerase III promoter sequences. The elements ranged in size from 140–493 bp and were present in low copy number in the genome and five out of eight were actively transcribed. One putative tRNA^Arg-derived sequence, AfuSINE2-1a possessed a unique feature of repeated trinucleotide ACT residues at its 3’-terminus. This element was similar in sequence to the I-4_AO element found in A. oryzae and an I-1_AF long nuclear interspersed element-like sequence identified in A. fumigatus Af293. Families of 5S rRNA-related SINE sequences, nominated as AfuSINE3, were also identified and their 5'-5S rRNA-related regions show 50–65% and 60–75% similarity to respectively A. fumigatus 5S rRNAs and SINE3-1_AO found in A. oryzae. A. fumigatus Af293 contains five copies of AfuSINE3 sequences ranging in size from 259–343 bp and two out of five AfuSINE3 sequences were actively transcribed. Investigations on AfuSINE distribution in the fungal genome revealed that the elements are enriched in pericentromeric and subtelomeric regions and inserted within gene-rich regions. We also demonstrated that some, but not all, AfuSINE sequences are targeted by host RNA silencing mechanisms. Finally, we demonstrated that infection of the fungus with mycoviruses had no apparent effects on SINE activity.