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Additional file 2: Table S2 Retroviral-related Pol polyproteins identified in Yarrowia-like yeast genomes. We identified a total of 15 genes that are annotated as retrovirus-related Pol polyproteins within the genome of the five YLYs analyzed. The proteins belong to three different categories which are ‘Line-1’, ‘transposon 297’ and ‘opus’. While the clade II genomes of Y. strains B02, F05 and H10 do only encode for one such protein per genome, genomes of the clade I genomes of Y. strains C11 and E02 encode for several retrovirus-related Pol polyproteins. Thereby, it has to be noted that the type ‘opus’ is only present in the genome of strain E02 and that all respective genes belong to the set of singleton genes (*) of E02.

Additional file 7: Table S1. Overview of the sampling locations for the plant material. Names of the fields belonging to the Biodiversity Exploratory or greenhouse populations are shown. As well as the location, coordinates and conditions (mown/cut and not mown/uncut). Table S3. Sources and basis for description and classification of the top 20 DEG. Table S4. Number of reads for each sequenced library (transcriptome ID) before and after trimming. Table S5. General features of the transcriptome of T. pratense. Table S6. Overall alignment rate of the single transcriptomes to the references transcriptome, values above 80% are good. Table S7. Annotation of T. pratense plant-specific against different databases. Table S8. Quality of the replicates. For each library replicate the number of transcripts above TPM of 1 is shown. Further the number of transcripts shared between to related replica is shown, as well as the number of transcripts unique for a replica. The similarity of the replicas was evaluated by calculating he percentage of the shared transcripts compared to the total number of transcripts of a replica. Table S10. Main classes based on the DE contigs. 16 main classes were developed to group the DE contigs. Table S11. GO Terms specifically enriched in the individual transcriptomes. Table S12. Shared contigs with corresponding annotation. Table S13. Detailed information about transcripts described during the discussion part. Table S14. Primer sequences.

Additional file 1: Table S1 Singleton genes of Yarrowia-like yeast genomes. Singleton genes were calculated with EDGAR [31]. Singletons are defined as genes without a reasonable BLAST hit against any gene within the other genomes in the comparison. We identified eight singletons for Y. strain C11, nine singletons for Y. strain E02 and one singleton for Y. strain H10.

Additional file 6: Figure S6. Plant architectural characteristics and growth habit of gibberellin treated plants. A-E: Measured, counted or calculated plant characteristics during phenotypic monitoring experiments. Gibberellin treated plants, blue; control plants, orange. Graphs show average values and 95% confidence intervals. Time is shown in weeks. Growth habit of control plants (left side) vs. gibberellin treated plants (right side), after approximately 2 weeks of gibberellin treatment and regrowth (F), and after 4 weeks (G).

Additional file 4: Figure S4. Enrichment analysis of the DEG GO terms. A: Enriched GO terms in mown and non-mown greenhouse samples. B: Enriched GO terms in mown and non-mown field B samples. C: Enriched GO terms in mown and non-mown field A samples. Information about the respective GO number can be found in Table S11.

Additional file 5: Figure S5. Expressed transcription factor family members in mown and not mown T. pratense plants. The y-axis shows the number of upregulated transcription factors that are members of the respective transcription factor family. Names of the transcriptomes (GM, GNM, FaM, FaNM; FbM, FbNM) and transcription factor families are given on the x-axis. Expression of transcription factor members were compared in a pairwise manner (GM vs GNM, FaM vs FaNM, FbM vs FbNM). Comparisons that resulted in a difference of more than 10% of the contigs significantly upregulated in either the mown or the unmown condition were marked red, differences between 5 and 9 % were marked orange.

Rhizoctonia solani AG1-IB of the phylum Basidiomycota is known as phytopathogenic fungus affecting various economically important crops, such as bean, rice, soybean, figs, cabbage and lettuce. The isolates 1/2/21 and O8/2 of the anastomosis group AG1-IB originating from lettuce plants with bottom rot symptoms represent two less aggressive R. solani isolates, as confirmed in a pathogenicity test on lettuce. They were deeply sequenced on the Illumina MiSeq system applying the mate-pair and paired-end mode to establish their genome sequences. Assemblies of obtained sequences resulted in 2092 and 1492 scaffolds, respectively, for isolate 1/2/21 and O8/2, amounting to a size of approximately 43 Mb for each isolate. Gene prediction by applying AUGUSTUS (v. 3.2.1.) yielded 12,827 and 12,973 identified genes, respectively. Based on automatic functional annotation, genes potentially encoding cellulases and enzymes involved in secondary metabolite synthesis were identified in the AG1-IB genomes. The annotated genome sequences of the less aggressive AG1-IB isolates were compared with the isolate 7/3/14, which is highly aggressive on lettuce and other vegetable crops such as bean, cabbage and carrot. This analysis revealed the first insights into core genes of AG1-IB isolates and unique determinants of each genome that may explain the different aggressiveness levels of the strains.

Additional file 3: Figure S3. qRT-PCR analysis of selected T. pratense genes: A) tdn_146439/ENGase85A (encodes a cytosolic beta-endo-N-acetyglucosaminidase (ENGase), B) tdn_69411/LTP (Lipid transfer protein, a pathogenesis-related protein), C) tdn85889/PME44 (pectin methylesterase 44), D) K65_9861 P5CS (DELTA1-PYRROLINE-5-CARBOXYLATE SYNTHASE 1). Two additional T. pratense tissues (axial meristem (AM) and leaves (L)) were included and also the six RNA extractions also used for constructing the transcriptome libraries. Transcriptome data are marked with TPM, all samples are from mown (M) or not mown (NM) plants. Gene expression levels were normalized to the housekeeping contig k65_5754 (not annotated, but with similar expression throughout the transcriptomes). Shown are mean values of the fold change of the respective contig in relation to the expression of contig K65_5754 with error bars that represent standard deviation. On the right side of each graph, the log2 values of the respective gene in each transcriptome are shown for better comparison of expression patterns.

Background Red clover (Trifolium pratense) is globally used as a fodder plant due its high nutritional value and soil improving qualities. In response to mowing, red clover exhibits specific morphological traits to compensate the loss of biomass. The morphological reaction is well described, but the underlying molecular mechanisms and its role for plants grown in the field are unclear. Results Here, we characterize the global transcriptional response to mowing of red clover by comparing plants grown under greenhouse conditions with plants growing on agriculturally used fields. Unexpectedly, we found that biotic and abiotic stress related changes of plants grown in the field overlay their regrowth related transcriptional changes and characterized transcription related protein families involved in these processes. Further, we can show that gibberellins, among other phytohormones, also contribute to the developmental processes related to regrowth after biomass-loss. Conclusions Our findings show that massive biomass loss triggers less transcriptional changes in field grown plants than their struggle with biotic and abiotic stresses and that gibberellins also play a role in the developmental program related to regrowth after mowing in red clover. Our results provide first insights into the physiological and developmental processes of mowing on red clover and may serve as a base for red clover yield improvement. Supplementary Information The online version contains supplementary material available at 10.1186/s12870-021-02867-0.

Additional file 1: Figure S1. Uncropped images. Figure S2. CircRNAs identified in the exosome iCLIP analysis of S. solfataricus. Figure S3. Distribution of bases in RNA-tails detected in the aRrp41-iCLIP of the archaeal exosome. Figure S4. Poly(A) stretches in RNA are bound by the exosome. Figure S5. Global analysis of RNAs enriched by coimmunoprecipitation with the archaeal exosome by iCLIP. Figure S6. Antisense RNAs as preferred substrates of the archaeal exosome. Figure S7. Binding of the archaeal exosome to 5’and 3’parts of selected genes. Figure S8. Low affinity of the archaeal exosome to the abundant mRNA tmoA (SSO_RS06040 gene encoding toluene-4-monooxygenase system protein). Figure S9. Distribution of read counts in the genome of S. solfataricus was analyzed with respect to biotype RNA. Figure S10. Clustering of read counts at the 5′-and 3′-end of protein coding genes. Figure S11. Clustering of crosslink sites at the 5′ and 3′ end of predicted operons. Figure S12. Distribution of crosslink sites around the ends of annotated genes

Additional file 6: Nucleotide content of the linear non-mapped cDNA reads in the iCLIP analysis of S. solfataricus.

Red clover (Trifolium pratense) is used worldwide as a fodder plant due its high nutritional value. In response to mowing, red clover exhibits specific morphological traits to compensate the loss of biomass. The morphological reaction is well described, but knowledge of the underlying molecular mechanisms are still lacking. Here we characterize the molecular genetic response to mowing of red clover by using comparative transcriptomics in greenhouse conditions and agriculturally used field. The analysis of mown and control plants revealed candidate genes possibly regulating crucial steps of the genetic network governing the regrowth reaction. In addition, multiple identified gibberellic acid (GA) related genes suggest a major role for GA in establishing the regrowth morphology of red clover. Mown red clover plants showing this regrowth morphology were partially “rescued” by exogenous GA application, demonstrating the influence of GA during regrowth. Our findings provide insights into the physiological and genetic processes of mowing red clover, to serve as a base for red clover yield improvement.

Figure S2. Immunophenotyping of bone marrow and spleen. (A) Relative frequencies of LSK (mean ± SD. n = 6 to 16). (B) Relative frequencies of LK (mean ± SD. n = 6 to 16). (C) Relative frequencies of GMP, CMP, and MEP (mean ± SEM. n = 3 to 4). (D) Relative myeloid populations (mean ± SD. n = 6 to 16). (E) Relative frequencies of B-cells (B220+), T-cells (CD3+), erythrocytes (TER119+) and megakaryocytes (CD41+) (mean ± SEM. n = 3 to 10). (F) Relative frequencies of B-cells (B220+), T-cells (CD3+), erythrocytes (TER119+) and megakaryocytes (CD41+) (mean ± SEM. n = 3 to 10). A 1-way ANOVA or 2-way ANOVA with Tukey’s multiple comparison was used for p values. *p

Figure S5. Working model. Activation of NFATC1 by an inflammatory environment rewires the transcriptional program induced by FLT3-ITD in stem cells, which promotes leukemic transformation. The FLT3-ITD/NFATC1 synergism activates multiple oncogenic pathways such as WNT/B-Catenin, Hedgehog, and K-RAS, causing extensive proliferation and drug resistance. (PPTX 91 kb)

Figure S4. GSEA analysis from C3 H database for mutual FCN and F genes. Summary table for analysis from GSEA H database: 14 pathways enriched in both FCN and F (only values for FCN are shown). (PPTX 80 kb)