BackgroundSenescence, despite its destructive character, is a process that is precisely-regulated. The control of senescence is required to achieve remobilization of resources, a principle aspect of senescence. Remobilization allows plants to recapture valuable resources that would otherwise be lost to the environment with the senescing organ. Autophagy is one of the critical processes that is switched on during senescence. This evolutionarily conserved process plays dual, antagonistic roles. On the one hand, it counteracts instantaneous cell death and allows the process of remobilization to be set in motion, while on the other hand, it participates in the degradation of cellular components. Autophagy has been demonstrated to occur in many plant species during the senescence of leaves and flower petals. Little is known, however, about the senescence process in other ephemeral organs, such as fine roots, whose lifespan is also relatively short. We hypothesized that, like the case of seasonal leaf senescence, autophagy also plays a role in the senescence of fine roots, and that both processes are synchronized in their timing.ResultsWe evaluated which morphological and cytological symptoms are universal or unique in the senescence of fine roots and leaves. The results of our study confirmed that autophagy plays a key role in the senescence of fine roots, and is associated also with the process of cellular components degradation. In both organs, structures related to autophagy were observed, such as autophagic bodies and autophagosomes. The role of autophagy in the senescence of these plant organs was further confirmed by an analysis of ATG gene expression and protein detection.ConclusionsThe present study is the first one to examine molecular mechanisms associated with the senescence of fine roots, and provide evidence that can be used to determine whether senescence of fine roots can be treated as another example of developmentally programmed cell death (dPCD). Our results indicate that there is a strong similarity between the senescence of fine roots and other ephemeral organs, suggesting that this process occurs by the same autophagy-related mechanisms in all plant ephemeral organs.Electronic supplementary materialThe online version of this article (10.1186/s12870-018-1439-6) contains supplementary material, which is available to authorized users.

Tomato black ring virus (TBRV) is the only member of the Nepovirus genus that is known to form defective RNA particles (D RNAs) during replication. Here, de novo generation of D RNAs was observed during prolonged passages of TBRV isolates originated from Solanum lycopersicum and Lactuca sativa in Chenopodium quinoa plants. D RNAs of about 500 nt derived by a single deletion in the RNA1 molecule and contained a portion of the 5' untranslated region and viral replicase, and almost the entire 3' non-coding region. Short regions of sequence complementarity were found at the 5' and 3' junction borders, which can facilitate formation of the D RNAs. Moreover, in this study we analyzed the effects of D RNAs on TBRV replication and symptoms development of infected plants. C. quinoa, S. lycopersicum, Nicotiana tabacum, and L. sativa were infected with the original TBRV isolates (TBRV-D RNA) and those containing additional D RNA particles (TBRV + D RNA). The viral accumulation in particular hosts was measured up to 28 days post inoculation by RT-qPCR. Statistical analyses revealed that D RNAs interfere with TBRV replication and thus should be referred to as defective interfering particles. The magnitude of the interference effect depends on the interplay between TBRV isolate and host species.

Main conclusion Autophagy is involved in developmentally programmed cell death and is identified during the early development of phloem, as well as xylem with a dual role, as both an inducer and executioner of cell death.

Viruses cause epidemics on all major crops of agronomic importance, and a timely and accurate identification is essential for control. High throughput sequencing (HTS) is a technology that allows the identification of all viruses without prior knowledge on the targeted pathogens. In this paper, we used HTS technique for the detection and identification of different viral species occurring in single and mixed infections in plants in Poland. We analysed various host plants representing different families. Within the 20 tested samples, we identified a total of 13 different virus species, including those whose presence has not been reported in Poland before: clover yellow mosaic virus (ClYMV) and melandrium yellow fleck virus (MYFV). Due to this new finding, the obtained sequences were compared with others retrieved from GenBank. In addition, cucurbit aphid-borne yellows virus (CABYV) was also detected, and due to the recent occurrence of this virus in Poland, a phylogenetic analysis of these new isolates was performed. The analysis revealed that CABYV population is highly diverse and the Polish isolates of CABYV belong to two different phylogenetic groups. Our results showed that HTS-based technology is a valuable diagnostic tool for the identification of different virus species originating from variable hosts, and can provide rapid information about the spectrum of plant viruses previously not detected in a region.

Tomato black ring virus (TBRV), a member of the Nepovirus genus, is a serious plant pathogen distributed worldwide. It causes significant damage to several economically important crops, such as artichoke or strawberry. The TBRV bipartite genome consists of two polyadenylated single‐stranded positive‐sense RNA molecules, which may be accompanied by subviral particles such as defective interfering RNAs (DI RNAs) and satellite RNAs (satRNAs). In this study, we obtained the complete genome sequence of six TBRV isolates originating from different hosts and determined the presence of eight TBRV satRNAs. Subsequently, genetic variability, recombination, phylogenetic and selection pressure analyses were performed. The results revealed that the TBRV population is genetically diverse. The occurrence of potential recombination events, evidence of positive selection pressure acting on particular codons and the diversification of satRNAs within the TBRV population indicated that the virus mutates and can rapidly adapt to new environmental conditions or hosts. The presented data shed some light on TBRV evolutionary dynamics and epidemiology.

Environmental waters, e.g. rivers, lakes and irrigation water, are a good source of many plant viruses. The pathogens can infect plants getting through damaged root hairs or small wounds that appear during plant growth. First results demonstrated common incidence of Tobacco mosaic virus (TMV) and Tomato mosaic virus (ToMV) in water samples collected from irrigation ditches and drainage canals surrounding fields in Southern Greater Poland. Principal objective of this work was to examine if environmental water might be the source of viruses infective to cereals. The investigation was focused on mechanically transmitted pathogens. Virus identification was performed by biological, electron microscopic, serological and molecular methods. Preliminary assays demonstrated Brome mosaic virus (BMV) infections in symptomatic plants inoculated with 9 out of the 17 tested concentrated water samples. The final identification was confirmed by molecular methods for selected isolates named: BMV-Ch1, -DBS, -N, -R and -S. Partial coding sequences of polymerase 1a (RNA1) and 2a (RNA2) and complete nucleotide sequence of coat protein (CP) gene (RNA3) of each BMV isolate were determined and compared with corresponding sequences of other known BMV isolates.Results confirmed the highest amino acid sequence homology in the fragment of polymerase 2a (99.2% -100%) and the most divergence in CP (96.2% -100%). This is the first report on the detection of an infective cereal virus in aqueous environment.

Here we describe two Brome mosaic virus (BMV) isolates from the Wielkopolska region of Poland. The BMV-Sr and BMV-Sz isolates were collected from maize [Zea mays L. ssp. Indentata] and triticale [× Triticosecale Wittm. ex A. Camus] plants respectively. Newly emerged BMV isolates, similarly to the BMV-M2 strain derived from an Arkansas isolate, have a wide host range that includes species in the Poaceae and Fabaceae families. Furthermore, immunological reactions of icosahedral virions from non-inoculated cowpea [Vigna unguiculata L.] leaves with a specific immunoglobulin confirmed that each of these isolates can systemically infect cowpea. We characterized the BMV-Sr and BMV-Sz genomic sequences encoding the replication protein (1a), polymerase (2a), complete movement protein (3a) and coat protein (CP) genes. The 1a, 2a, 3a and CP gene sequences showed 98.9, 97.6, 98.4 and 97.7 % nucleotide sequence identity between the Polish isolates respectively. Phylogenetic analysis based on these four genes confirmed the species identity of the isolates. A phylogenetic tree based on RNA3 (3a and CP genes) showed independent clustering of the Polish isolates. Amino acid sequence analysis of the 3a protein revealed that both Polish isolates are characterized by a single amino acid mutation at the 81st position, when compared with the Russian isolate. It had been previously reported that four amino acid mutations in this region determined BMV systemic infection in cowpea. Our results indicate that a single non-synonymous substitution in the cell-to-cell movement protein may be crucial for the nature of cowpea infection.

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