BUSCADOR RECOLECTA

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

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

Characterization of temperature during the FJH of SWCNT; Raman analyses; TEM images; SEM images; UV–vis characterization; and resistivity of composites made with additives., Peer reviewed

Dataset includes: RawMicrosatelliteData.txt: Genotyped microsatellite data for 9 markers for 1926 sampled individual ramets from the plant species Galium verum, collected across 35 landscapes in Sweden, Germany and Belgium. The dataset is formatted along the Spagedi-software requirements which was used to calculate the genetic diversity metrics. -- IndividualDescriptor.xlsx: Environmental descriptors of 1926 individual ramets of the plant species Galium verum sampled across 35 landscapes in Sweden, Germany and Belgium. Via their unique ID (Ind), they can be linked to their associated genotype and their geographic position as available in RawMicrosatelliteData.txt. The environmental desciptors describe in which country, landscape or element (focal patch [1], stepping stone [4] or linear feature [2 and 3]) the individual was sampled. -- Landscape_Composition.csv: Environmental descriptors including landscape and focal genetic diversity metrics for 35 landscapes across Sweden, Germany and Belgium in which the grassland perennial plant species Galium verum was sampled. Besides the descriptor "Landscape" making it possible to link these descriptors to the individual ramets in RawMicrosatelliteData.txt and IndividualDescriptor.xlsx, environmental descriptors include structural and inferred functional connectivity and various components which make up the green infrastructure, i.e. amount of semi-natural grassland habitat [ha], amount of road infrastructure [m] and the amount of forest or arable cover [ha]. Further landscape information is provided by the descriptors on "Landscape occupancy of Galium verum" and "Restored", informing on the abundance of Galium verum in the landscape surrounding each focal semi-natural grassland patch [0-1] and whether the focal semi-natural grassland patch has been restored [0/1], respectively. Genetic diversity metrics for sampled Galium verum populations include allelic richness, rarified allelic richness and gametic heterozygosity (calculated using Spagedi-software), both for the focal semi-natural grassland central in each landscape as well as for the entire landscape, i.e. the focal patch + its surrounding landscape (r = 1600 m)., This Figshare data-file contains three files which are linked via unique identifiers to reconstruct all the data needed to investigate the impact of green infrastructure on the functional connectivity in the grassland perennial Galium verum in fragmented semi-natural grassland landscapes in 35 landscapes spread across Sweden, Germany and Belgium., 2015-2016 BiodivERsA COFUND UKCEH National Capability project 06895, RawMicrosatelliteData.txt, IndividualDescriptor.xlsx, Landscape_Composition.csv, Peer reviewed

Peer reviewed

Peer reviewed

Resources available on the publisher's site: http://doi.org/10.1039/d1nr06210g, Peer reviewed

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