cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.15156/bio/sh1141881.09fu
title: SH1141881.09FU

description: UNITE provides a unified way for delimiting, identifying, communicating, and working with DNA-based Species Hypotheses (SH). All fungal ITS sequences in the international nucleotide sequence databases are clustered to approximately the species level by applying a set of dynamic distance values (<0.5 - 3.0%). All species hypotheses are given a unique, stable name in the form of a DOI, and their taxonomic and ecological annotations are verified through distributed, web-based third-party annotation efforts. SHs are connected to a taxon name and its classification as far as possible (phylum, class, order, etc.) by taking into account identifications for all sequences in the SH. An automatically or manually designated sequence is chosen to represent each such SH. These sequences are released (https://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and next-generation sequencing analysis pipelines. The system and the data are updated automatically as the number of public fungal ITS sequences grows.
DOI: 10.15156/bio/sh1141882.09fu
title: SH1141882.09FU

description: UNITE provides a unified way for delimiting, identifying, communicating, and working with DNA-based Species Hypotheses (SH). All fungal ITS sequences in the international nucleotide sequence databases are clustered to approximately the species level by applying a set of dynamic distance values (<0.5 - 3.0%). All species hypotheses are given a unique, stable name in the form of a DOI, and their taxonomic and ecological annotations are verified through distributed, web-based third-party annotation efforts. SHs are connected to a taxon name and its classification as far as possible (phylum, class, order, etc.) by taking into account identifications for all sequences in the SH. An automatically or manually designated sequence is chosen to represent each such SH. These sequences are released (https://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and next-generation sequencing analysis pipelines. The system and the data are updated automatically as the number of public fungal ITS sequences grows.
DOI: 10.15156/bio/sh1141883.09fu
title: SH1141883.09FU

description: UNITE provides a unified way for delimiting, identifying, communicating, and working with DNA-based Species Hypotheses (SH). All fungal ITS sequences in the international nucleotide sequence databases are clustered to approximately the species level by applying a set of dynamic distance values (<0.5 - 3.0%). All species hypotheses are given a unique, stable name in the form of a DOI, and their taxonomic and ecological annotations are verified through distributed, web-based third-party annotation efforts. SHs are connected to a taxon name and its classification as far as possible (phylum, class, order, etc.) by taking into account identifications for all sequences in the SH. An automatically or manually designated sequence is chosen to represent each such SH. These sequences are released (https://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and next-generation sequencing analysis pipelines. The system and the data are updated automatically as the number of public fungal ITS sequences grows.
DOI: 10.6084/m9.figshare.22615513
title: Additional file 3 of Whole-genome sequencing of cryopreserved resources from French Large White pigs at two distinct sampling times reveals strong signatures of convergent and divergent selection between the dam and sire lines

description: Additional file 3. Full list of genes included in genomic regions under recent selection in French Large White pigs. Similar to Table 1 but with the full list of genes within each candidate region.
DOI: 10.6084/m9.figshare.22615513.v1
title: Additional file 3 of Whole-genome sequencing of cryopreserved resources from French Large White pigs at two distinct sampling times reveals strong signatures of convergent and divergent selection between the dam and sire lines

description: Additional file 3. Full list of genes included in genomic regions under recent selection in French Large White pigs. Similar to Table 1 but with the full list of genes within each candidate region.
DOI: 10.15156/bio/sh1141884.09fu
title: SH1141884.09FU

description: UNITE provides a unified way for delimiting, identifying, communicating, and working with DNA-based Species Hypotheses (SH). All fungal ITS sequences in the international nucleotide sequence databases are clustered to approximately the species level by applying a set of dynamic distance values (<0.5 - 3.0%). All species hypotheses are given a unique, stable name in the form of a DOI, and their taxonomic and ecological annotations are verified through distributed, web-based third-party annotation efforts. SHs are connected to a taxon name and its classification as far as possible (phylum, class, order, etc.) by taking into account identifications for all sequences in the SH. An automatically or manually designated sequence is chosen to represent each such SH. These sequences are released (https://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and next-generation sequencing analysis pipelines. The system and the data are updated automatically as the number of public fungal ITS sequences grows.
DOI: 10.15156/bio/sh1141885.09fu
title: SH1141885.09FU

description: UNITE provides a unified way for delimiting, identifying, communicating, and working with DNA-based Species Hypotheses (SH). All fungal ITS sequences in the international nucleotide sequence databases are clustered to approximately the species level by applying a set of dynamic distance values (<0.5 - 3.0%). All species hypotheses are given a unique, stable name in the form of a DOI, and their taxonomic and ecological annotations are verified through distributed, web-based third-party annotation efforts. SHs are connected to a taxon name and its classification as far as possible (phylum, class, order, etc.) by taking into account identifications for all sequences in the SH. An automatically or manually designated sequence is chosen to represent each such SH. These sequences are released (https://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and next-generation sequencing analysis pipelines. The system and the data are updated automatically as the number of public fungal ITS sequences grows.
DOI: 10.6084/m9.figshare.22615516
title: Additional file 4 of Whole-genome sequencing of cryopreserved resources from French Large White pigs at two distinct sampling times reveals strong signatures of convergent and divergent selection between the dam and sire lines

description: Additional file 4. Summary plots of the scan for selection for all candidate regions of Table 1. Each file of this archive corresponds to a different candidate region, whose genomic position can be read in the file name. The top panel shows the results of the four tests for selection applied in the region. Values of the time-LWD (in blue), time-LWS (in green), hapFLK (in red) and FLK (in purple) tests are plotted (y axis) according to genomic position (x axis). Opposite signs are used for time-LWD and time-LWS on the one hand and hapFLK and FLK on the other hand, i.e. high test statistic values correspond to highly negative points for time-LWD and time-LWS and to highly positive points for hapFLK and FLK. All variants (AV set) were considered for these analyses. The bottom panel shows the position and name of genes located in the region.
DOI: 10.6084/m9.figshare.22615516.v1
title: Additional file 4 of Whole-genome sequencing of cryopreserved resources from French Large White pigs at two distinct sampling times reveals strong signatures of convergent and divergent selection between the dam and sire lines

description: Additional file 4. Summary plots of the scan for selection for all candidate regions of Table 1. Each file of this archive corresponds to a different candidate region, whose genomic position can be read in the file name. The top panel shows the results of the four tests for selection applied in the region. Values of the time-LWD (in blue), time-LWS (in green), hapFLK (in red) and FLK (in purple) tests are plotted (y axis) according to genomic position (x axis). Opposite signs are used for time-LWD and time-LWS on the one hand and hapFLK and FLK on the other hand, i.e. high test statistic values correspond to highly negative points for time-LWD and time-LWS and to highly positive points for hapFLK and FLK. All variants (AV set) were considered for these analyses. The bottom panel shows the position and name of genes located in the region.
DOI: 10.6084/m9.figshare.22615519
title: Additional file 5 of Whole-genome sequencing of cryopreserved resources from French Large White pigs at two distinct sampling times reveals strong signatures of convergent and divergent selection between the dam and sire lines

description: Additional file 5. Haplotype frequency plots for all candidate regions of Table 1. Each file of this archive corresponds to a different candidate region, whose genomic position can be read in the file name. It shows the haplotype diversity in this region, estimated using hapFLK with 10 haplotype clusters (for one single EM run). For a given genomic position, each color corresponds to a different haplotype cluster and the height of the color band in a given population (represented by one of the panels) gives the frequency of the cluster in this population. All variants (AV set) were considered for these analyses.
DOI: 10.6084/m9.figshare.22615519.v1
title: Additional file 5 of Whole-genome sequencing of cryopreserved resources from French Large White pigs at two distinct sampling times reveals strong signatures of convergent and divergent selection between the dam and sire lines

description: Additional file 5. Haplotype frequency plots for all candidate regions of Table 1. Each file of this archive corresponds to a different candidate region, whose genomic position can be read in the file name. It shows the haplotype diversity in this region, estimated using hapFLK with 10 haplotype clusters (for one single EM run). For a given genomic position, each color corresponds to a different haplotype cluster and the height of the color band in a given population (represented by one of the panels) gives the frequency of the cluster in this population. All variants (AV set) were considered for these analyses.
DOI: 10.6084/m9.figshare.22615522.v1
title: Additional file 6 of Whole-genome sequencing of cryopreserved resources from French Large White pigs at two distinct sampling times reveals strong signatures of convergent and divergent selection between the dam and sire lines

description: Additional file 6. Functional enrichment for lists of genes within (or flanking) candidate regions under selection. Sheet 1. List of genes within or flanking candidate regions; region name and category are reported for each gene. Sheets 2–4. Enriched functions among genes from all selection categories, based on GOBP (sheet 2), KEGG (sheet 3) or MGI (sheet 4) databases. Sheet 5. Co-annotation enrichment among genes from the LWD, conv(LWD) and div categories. Sheet 6. Co-annotation enrichment among genes from the LWS, conv(LWS) and conv categories. P values were adjusted for multiple tests using the Benjamini–Hochberg correction (BH &lt; 0.05). Co-annotation enrichment (sheets 5–6) was performed with Genecodi4 using the human genome as reference, merging annotations from GOBP, KEGG and MGI databases. The minimal number of genes used to find enrichment is given in brackets; this parameter is 2 or 3 according to the total number of genes per condition tested.
DOI: 10.6084/m9.figshare.22615522
title: Additional file 6 of Whole-genome sequencing of cryopreserved resources from French Large White pigs at two distinct sampling times reveals strong signatures of convergent and divergent selection between the dam and sire lines

description: Additional file 6. Functional enrichment for lists of genes within (or flanking) candidate regions under selection. Sheet 1. List of genes within or flanking candidate regions; region name and category are reported for each gene. Sheets 2–4. Enriched functions among genes from all selection categories, based on GOBP (sheet 2), KEGG (sheet 3) or MGI (sheet 4) databases. Sheet 5. Co-annotation enrichment among genes from the LWD, conv(LWD) and div categories. Sheet 6. Co-annotation enrichment among genes from the LWS, conv(LWS) and conv categories. P values were adjusted for multiple tests using the Benjamini–Hochberg correction (BH &lt; 0.05). Co-annotation enrichment (sheets 5–6) was performed with Genecodi4 using the human genome as reference, merging annotations from GOBP, KEGG and MGI databases. The minimal number of genes used to find enrichment is given in brackets; this parameter is 2 or 3 according to the total number of genes per condition tested.
DOI: 10.6084/m9.figshare.22615525
title: Additional file 7 of Whole-genome sequencing of cryopreserved resources from French Large White pigs at two distinct sampling times reveals strong signatures of convergent and divergent selection between the dam and sire lines

description: Additional file 7. Candidate causal variants in each candidate region under selection. This archive contains three types of results. (i) Each file with suffix .annot corresponds to a different candidate region, whose genomic position can be read in the file name. It provides a list of candidate variants detected by the statistical approach in this region, together with their SnpEff annotation. (ii) The all strong.func file provides a list of candidate variants with a functional effect (according to SnpEff) selected by this approach for all regions, together with their annotation. The all weak.func file provides the same, but for variants that could only be detected by the functional approach. (iii) Each file with the suffix .png corresponds to a different candidate region, whose genomic position can be read in the file name. It provides a plot showing the values of the relevant statistic(s) in this region with additional details concerning the status of each variant: ‘invalid’ (i.e. with low call rate or allele frequency patterns inconsistent with the type of selection in the region), ‘valid’ (high call rate and consistent allele frequency patterns) or ‘candidate’ (those ‘valid’ variants with the highest value of the statistic, also listed in the .annot file). When functional candidate variants exist in a region, these are plotted in black, while all other variants are plotted in a color depending on the test represented. Finally, the rate of missing genotypes in sliding windows of 2 kb are represented by the black points on the negative part of the y axis, from 0 (no missing data) to − 1 (only missing data). Horizontal dashed lines at − 0.5 and − 1 help visualize the missing rates achieved at a given position.
DOI: 10.15156/bio/sh1141886.09fu
title: SH1141886.09FU

description: UNITE provides a unified way for delimiting, identifying, communicating, and working with DNA-based Species Hypotheses (SH). All fungal ITS sequences in the international nucleotide sequence databases are clustered to approximately the species level by applying a set of dynamic distance values (<0.5 - 3.0%). All species hypotheses are given a unique, stable name in the form of a DOI, and their taxonomic and ecological annotations are verified through distributed, web-based third-party annotation efforts. SHs are connected to a taxon name and its classification as far as possible (phylum, class, order, etc.) by taking into account identifications for all sequences in the SH. An automatically or manually designated sequence is chosen to represent each such SH. These sequences are released (https://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and next-generation sequencing analysis pipelines. The system and the data are updated automatically as the number of public fungal ITS sequences grows.
DOI: 10.15156/bio/sh1141887.09fu
title: SH1141887.09FU

description: UNITE provides a unified way for delimiting, identifying, communicating, and working with DNA-based Species Hypotheses (SH). All fungal ITS sequences in the international nucleotide sequence databases are clustered to approximately the species level by applying a set of dynamic distance values (<0.5 - 3.0%). All species hypotheses are given a unique, stable name in the form of a DOI, and their taxonomic and ecological annotations are verified through distributed, web-based third-party annotation efforts. SHs are connected to a taxon name and its classification as far as possible (phylum, class, order, etc.) by taking into account identifications for all sequences in the SH. An automatically or manually designated sequence is chosen to represent each such SH. These sequences are released (https://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and next-generation sequencing analysis pipelines. The system and the data are updated automatically as the number of public fungal ITS sequences grows.
DOI: 10.6084/m9.figshare.22612646.v1
title: Additional file 12 of The Weimberg pathway: an alternative for Myceliophthora thermophila to utilize d-xylose

description: Additional file 12: The profiles of transcriptional data.
DOI: 10.6084/m9.figshare.22615525.v1
title: Additional file 7 of Whole-genome sequencing of cryopreserved resources from French Large White pigs at two distinct sampling times reveals strong signatures of convergent and divergent selection between the dam and sire lines

description: Additional file 7. Candidate causal variants in each candidate region under selection. This archive contains three types of results. (i) Each file with suffix .annot corresponds to a different candidate region, whose genomic position can be read in the file name. It provides a list of candidate variants detected by the statistical approach in this region, together with their SnpEff annotation. (ii) The all strong.func file provides a list of candidate variants with a functional effect (according to SnpEff) selected by this approach for all regions, together with their annotation. The all weak.func file provides the same, but for variants that could only be detected by the functional approach. (iii) Each file with the suffix .png corresponds to a different candidate region, whose genomic position can be read in the file name. It provides a plot showing the values of the relevant statistic(s) in this region with additional details concerning the status of each variant: ‘invalid’ (i.e. with low call rate or allele frequency patterns inconsistent with the type of selection in the region), ‘valid’ (high call rate and consistent allele frequency patterns) or ‘candidate’ (those ‘valid’ variants with the highest value of the statistic, also listed in the .annot file). When functional candidate variants exist in a region, these are plotted in black, while all other variants are plotted in a color depending on the test represented. Finally, the rate of missing genotypes in sliding windows of 2 kb are represented by the black points on the negative part of the y axis, from 0 (no missing data) to − 1 (only missing data). Horizontal dashed lines at − 0.5 and − 1 help visualize the missing rates achieved at a given position.
DOI: 10.6084/m9.figshare.22615528
title: Additional file 8 of Whole-genome sequencing of cryopreserved resources from French Large White pigs at two distinct sampling times reveals strong signatures of convergent and divergent selection between the dam and sire lines

description: Additional file 8. Annotation of genes included in candidate regions under selection. Each line of the table (grouped by candidate region) corresponds to a gene and reports several types of information concerning this gene. Gene description and gene name were extracted from the Ensembl Sscrofa11.1 (GCA 000003025.6) annotation. The position of each gene on the genome is specified in bp (gene start and end). Annotations for RNA genes were retrieved from the Rfam database. Corresponding probes from the GSE56011 expression dataset are given for 48 genes together with the Wilcoxon test result (p value and BH adjusted p value) comparing gene expression between LWS (n = 10) and LWD (n = 41), see Additional file 1 for more details.
DOI: 10.6084/m9.figshare.22615528.v1
title: Additional file 8 of Whole-genome sequencing of cryopreserved resources from French Large White pigs at two distinct sampling times reveals strong signatures of convergent and divergent selection between the dam and sire lines

description: Additional file 8. Annotation of genes included in candidate regions under selection. Each line of the table (grouped by candidate region) corresponds to a gene and reports several types of information concerning this gene. Gene description and gene name were extracted from the Ensembl Sscrofa11.1 (GCA 000003025.6) annotation. The position of each gene on the genome is specified in bp (gene start and end). Annotations for RNA genes were retrieved from the Rfam database. Corresponding probes from the GSE56011 expression dataset are given for 48 genes together with the Wilcoxon test result (p value and BH adjusted p value) comparing gene expression between LWS (n = 10) and LWD (n = 41), see Additional file 1 for more details.
DOI: 10.15156/bio/sh1141888.09fu
title: SH1141888.09FU

description: UNITE provides a unified way for delimiting, identifying, communicating, and working with DNA-based Species Hypotheses (SH). All fungal ITS sequences in the international nucleotide sequence databases are clustered to approximately the species level by applying a set of dynamic distance values (<0.5 - 3.0%). All species hypotheses are given a unique, stable name in the form of a DOI, and their taxonomic and ecological annotations are verified through distributed, web-based third-party annotation efforts. SHs are connected to a taxon name and its classification as far as possible (phylum, class, order, etc.) by taking into account identifications for all sequences in the SH. An automatically or manually designated sequence is chosen to represent each such SH. These sequences are released (https://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and next-generation sequencing analysis pipelines. The system and the data are updated automatically as the number of public fungal ITS sequences grows.
DOI: 10.15156/bio/sh1141889.09fu
title: SH1141889.09FU

description: UNITE provides a unified way for delimiting, identifying, communicating, and working with DNA-based Species Hypotheses (SH). All fungal ITS sequences in the international nucleotide sequence databases are clustered to approximately the species level by applying a set of dynamic distance values (<0.5 - 3.0%). All species hypotheses are given a unique, stable name in the form of a DOI, and their taxonomic and ecological annotations are verified through distributed, web-based third-party annotation efforts. SHs are connected to a taxon name and its classification as far as possible (phylum, class, order, etc.) by taking into account identifications for all sequences in the SH. An automatically or manually designated sequence is chosen to represent each such SH. These sequences are released (https://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and next-generation sequencing analysis pipelines. The system and the data are updated automatically as the number of public fungal ITS sequences grows.