BUSCADOR RECOLECTA

Additional file 6: Fig. S4. XBP1 knockdown. (A) mRNA levels of XBP1 in H929 determined by qRT-PCR 48 h after transfection with XBP1 siRNA. (B) Western blot of XBP1 in H929. (C) mRNA levels of the indicated genes in XBP1 knockdown cells determined by qRT-PCR. H929 cells were treated in the presence or absence of thapsigargin. All results are presented as the means ± SD of three experiments. (*p < 0.05, **p < 0.01, ***p < 0.001). “NS” indicates not significant (p > 0.05)., Instituto de Salud Carlos III Gerencia Regional de Salud, Junta de Castilla y León Asociación Española Contra el Cancer (AECC) Consejería de Educación, Junta de Castilla y León, Peer reviewed

1 table., Endogenous viral elements (EVEs) are viral sequences that have been integrated into the nuclear chromosomes. Endogenous pararetrovirus (EPRV) are a class of EVEs derived from DNA viruses of the family Caulimoviridae. Previous works based on a limited number of genome assemblies demonstrated that EPRVs are abundant in plants and are present in several species. The availability of genome sequences has been immensely increased in the recent years and we took advantage of these resources to have a more extensive view of the presence of EPRVs in plant genomes. We analyzed 278 genome assemblies corresponding to 267 species (254 from Viridiplantae) using tBLASTn against a collection of conserved domains of the Reverse Transcriptases (RT) of Caulimoviridae. We concentrated our search on complete and well-conserved RT domains with an uninterrupted ORF comprising the genetic information for at least 300 amino acids. We obtained 11.527 sequences from the genomes of 202 species spanning the whole Tracheophyta clade. These elements were grouped in 57 clusters and classified in 13 genera, including a newly proposed genus we called Wendovirus. Wendoviruses are characterized by the presence of four open reading frames and two of them encode for aspartic proteinases. Comparing plant genomes, we observed important differences between the plant families and genera in the number and type of EPRVs found. In general, florendoviruses are the most abundant and widely distributed EPRVs. The presence of multiple identical RT domain sequences in some of the genomes suggests their recent amplification., Peer reviewed

1 table., Endogenous viral elements (EVEs) are viral sequences that have been integrated into the nuclear chromosomes. Endogenous pararetrovirus (EPRV) are a class of EVEs derived from DNA viruses of the family Caulimoviridae. Previous works based on a limited number of genome assemblies demonstrated that EPRVs are abundant in plants and are present in several species. The availability of genome sequences has been immensely increased in the recent years and we took advantage of these resources to have a more extensive view of the presence of EPRVs in plant genomes. We analyzed 278 genome assemblies corresponding to 267 species (254 from Viridiplantae) using tBLASTn against a collection of conserved domains of the Reverse Transcriptases (RT) of Caulimoviridae. We concentrated our search on complete and well-conserved RT domains with an uninterrupted ORF comprising the genetic information for at least 300 amino acids. We obtained 11.527 sequences from the genomes of 202 species spanning the whole Tracheophyta clade. These elements were grouped in 57 clusters and classified in 13 genera, including a newly proposed genus we called Wendovirus. Wendoviruses are characterized by the presence of four open reading frames and two of them encode for aspartic proteinases. Comparing plant genomes, we observed important differences between the plant families and genera in the number and type of EPRVs found. In general, florendoviruses are the most abundant and widely distributed EPRVs. The presence of multiple identical RT domain sequences in some of the genomes suggests their recent amplification., Peer reviewed

1 table., Endogenous viral elements (EVEs) are viral sequences that have been integrated into the nuclear chromosomes. Endogenous pararetrovirus (EPRV) are a class of EVEs derived from DNA viruses of the family Caulimoviridae. Previous works based on a limited number of genome assemblies demonstrated that EPRVs are abundant in plants and are present in several species. The availability of genome sequences has been immensely increased in the recent years and we took advantage of these resources to have a more extensive view of the presence of EPRVs in plant genomes. We analyzed 278 genome assemblies corresponding to 267 species (254 from Viridiplantae) using tBLASTn against a collection of conserved domains of the Reverse Transcriptases (RT) of Caulimoviridae. We concentrated our search on complete and well-conserved RT domains with an uninterrupted ORF comprising the genetic information for at least 300 amino acids. We obtained 11.527 sequences from the genomes of 202 species spanning the whole Tracheophyta clade. These elements were grouped in 57 clusters and classified in 13 genera, including a newly proposed genus we called Wendovirus. Wendoviruses are characterized by the presence of four open reading frames and two of them encode for aspartic proteinases. Comparing plant genomes, we observed important differences between the plant families and genera in the number and type of EPRVs found. In general, florendoviruses are the most abundant and widely distributed EPRVs. The presence of multiple identical RT domain sequences in some of the genomes suggests their recent amplification., Peer reviewed

Peer reviewed

Endogenous viral elements (EVEs) are viral sequences that have been integrated into the nuclear chromosomes. Endogenous pararetrovirus (EPRV) are a class of EVEs derived from DNA viruses of the family Caulimoviridae. Previous works based on a limited number of genome assemblies demonstrated that EPRVs are abundant in plants and are present in several species. The availability of genome sequences has been immensely increased in the recent years and we took advantage of these resources to have a more extensive view of the presence of EPRVs in plant genomes. We analyzed 278 genome assemblies corresponding to 267 species (254 from Viridiplantae) using tBLASTn against a collection of conserved domains of the Reverse Transcriptases (RT) of Caulimoviridae. We concentrated our search on complete and well-conserved RT domains with an uninterrupted ORF comprising the genetic information for at least 300 amino acids. We obtained 11.527 sequences from the genomes of 202 species spanning the whole Tracheophyta clade. These elements were grouped in 57 clusters and classified in 13 genera, including a newly proposed genus we called Wendovirus. Wendoviruses are characterized by the presence of four open reading frames and two of them encode for aspartic proteinases. Comparing plant genomes, we observed important differences between the plant families and genera in the number and type of EPRVs found. In general, florendoviruses are the most abundant and widely distributed EPRVs. The presence of multiple identical RT domain sequences in some of the genomes suggests their recent amplification., Peer reviewed

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Peer reviewed

Supplemental Figure 1: U. maydis Rip1 gene structure and transcription in planta. (Supports Figure 1.). -- Supplemental Figure 2: Rip1 secretion and expression in planta. (Supports Figure 1.). -- Supplemental Figure 3: Virus-mediated expression of Rip1-HA in maize. (Supports Figure 1.). -- Supplemental Figure 4: Rip1 suppresses the flg22-triggered ROS burst in N. benthamiana (Supports Figure 1.). -- Supplemental Figure 5: Rip1 acts as a PTI-suppressor in different subcellular compartments. (Supports Figure 1.). -- Supplemental Figure 6: Rip1 orthologs from different smut fungi. (Supports Figure 2.). -- Supplemental Figure 7: Rip1 truncation study. (Supports Figure 2.). -- Supplemental Figure 8: Localization of Rip1 and MpRip1 with and without the RIFL motif. (Supports Figure 2.) Localization of mCherry, Rip1, Rip1 with the RIFL motif deleted, MpRip1, MpRip1 fused with the RIFL motif and mCherry fused with the RIFL motif were assessed via confocal microscopy. Bars = 40 μm. -- Supplemental Figure 9: Nblox6 co-immunoprecipitates with Rip1. (Supports Figure 3.). -- Supplemental Figure 10: Nblox6 shows homology to Zmlox3. (Supports Figure 3.) Sequence alignment of NbLox6 and ZmLox3 created in CLC Main Workbench. -- Supplemental Figure 11: Anti-lox antibody and silencing construct for Nblox6 (Supports Figure 3.). -- Supplemental Figure 12: Nblox6 is a negative regulator of PAMP-triggered ROS accumulation. (Supports Figure 3). -- Supplemental Figure 13: Rip1 relocates Lox3 to the nucleus in N. benthamiana cells. (Supports Figure 4.). -- Supplemental Figure 14: Nuclear localization of Rip1 is a prerequisite for Lox3 relocalization to the nucleus.(Supports Figure 4.). -- Supplemental Figure 15: ZmLox3 mislocalization in planta. (Supports Figure 4.). -- Supplemental Figure 16: ZmLox3 fusion proteins and their activity in vitro. (Supports Figure 4.). -- Supplemental File 1. Sequence alignment used to produce the phylogenetic tree in Supplemental Figure 6B. -- Supplemental Table 4: Statistical analysis tables., Peer reviewed

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