RESUMEN
Fusarium wilt pathogens represent an ongoing threat to pepper production worldwide. This is the first report providing data on the molecular identification of Fusarium fungi that cause wilt in pepper in the southern regions of Russia. Monitoring of the Fusarium infection on pepper was carried out in 2019-2022 in two economically important regions of this culture production: the Krasnodar Krai and Crimea. Based on a phylogenetic analysis of the translation elongation factor (EF1a) and the internal transcribed spacer (ITS), as well as the macro- and micromorphological characteristics of the fungi, the causative agents of Fusarium wilt have been identified. The causative agents identified as representatives of the Fusarium species composition included: F. clavus, F. solani, F. oxysporum, F. verticillioides, F. commune, F. torulosum, and F. sporotrichioides. Depending on the region, the specifics of biodiversity and the ratio of these species in pathocomplexes were noted. In Crimea, wilting could be attributed to all of the identified species; in the Krasnodar Krai, F. verticillioides and F. clavus were found to contribute to wilting. The pathogenicity test showed that the pathogens of pepper wilting in Russia, in addition to the already known F. oxysporum and F. solani, are the species F. clavus and F. verticillioides. This is the first report on the ability of these species to cause Fusarium wilt in pepper cultures. The obtained data will be of practical value for the development of biological control measures for fungi of the genus Fusarium, which cause pepper wilt in areas of industrial production and seed production. In addition, data on species composition and aggressive isolates will be used in a pepper breeding program for resistance to Fusarium wilt.
RESUMEN
The intergenic space of plant genomes encodes many functionally important yet unexplored RNAs. The genomic loci encoding these RNAs are often considered "junk", DNA as they are frequently associated with repeat-rich regions of the genome. The latter makes the annotations of these loci and the assembly of the corresponding transcripts using short RNAseq reads particularly challenging. Here, using long-read Nanopore direct RNA sequencing, we aimed to identify these "junk" RNA molecules, including long non-coding RNAs (lncRNAs) and transposon-derived transcripts expressed during early stages (10 days post anthesis) of seed development of triticale (AABBRR, 2n = 6x = 42), an interspecific hybrid between wheat and rye. Altogether, we found 796 lncRNAs and 20 LTR retrotransposon-related transcripts (RTE-RNAs) expressed at this stage, with most of them being previously unannotated and located in the intergenic as well as intronic regions. Sequence analysis of the lncRNAs provide evidence for the frequent exonization of Class I (retrotransposons) and class II (DNA transposons) transposon sequences and suggest direct influence of "junk" DNA on the structure and origin of lncRNAs. We show that the expression patterns of lncRNAs and RTE-related transcripts have high stage specificity. In turn, almost half of the lncRNAs located in Genomes A and B have the highest expression levels at 10-30 days post anthesis in wheat. Detailed analysis of the protein-coding potential of the RTE-RNAs showed that 75% of them carry open reading frames (ORFs) for a diverse set of GAG proteins, the main component of virus-like particles of LTR retrotransposons. We further experimentally demonstrated that some RTE-RNAs originate from autonomous LTR retrotransposons with ongoing transposition activity during early stages of triticale seed development. Overall, our results provide a framework for further exploration of the newly discovered lncRNAs and RTE-RNAs in functional and genome-wide association studies in triticale and wheat. Our study also demonstrates that Nanopore direct RNA sequencing is an indispensable tool for the elucidation of lncRNA and retrotransposon transcripts.
