cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.26685966.v1
title: Additional file 1 of Genomic insight into the origin, domestication, dispersal, diversification and human selection of Tartary buckwheat

description: Additional file 1: Table S1. Summary of the 567 Tartary buckwheat accessions and 7 outgroup accessions used in this study with the mapping rate, depth and coverage. Table S2. Distribution of SNPs into various genomic regions in Tartary buckwheat. Table S3. Statistical differences between pairwise FST values between the different populations. Table S4. Genomic fragments with evidence for introgression based on Fd and FdM.Table S5. Interpopulation introgression based on D- statistics. Table S6. Putative selective sweeps between HW and SL based on XP-CLR analysis. Table S7. Putative selective sweeps between HW and NL based on XP-CLR analysis.Table S8. Genes in selective sweeps in both between HW and SL and between HW and NL based on XP-CLR analysis. Table S9. Putative selective sweeps between HW and SL based on DCMS analysis. Table S10. Putative selective sweeps between HW and NL based on DCMS analysis. Table S11. Genes in selective sweeps in both between HW and SL and between HW and NL based on DCMS analysis. Table S12. Candidate genes associated with disease index identified by GWAS with MAF &gt;= 0.01. Table S13. Putative selective sweeps between SL and NL based on XP-CLR. Table S14. Putative selective sweeps between SL and NL based on DCMS. Table S15. Salt tolerance of Tartary buckwheat accessions. Table S16. Candidate genes associated with salt tolerance identified by GWAS. Table S17. Sequencing reads used for assembly of EDT. Table S18. Assembly statistics of the EDT genome. Table S19. BUSCO analysis of the EDT genome. Table S20. Genetic differences between EDT and DDT. Table S21. The expression of genes with insertions and deletions within the QTL inverval. Table S22. Summary of FtXIP insertion promoter cis-acting elements prediction in 1,400 bp region. Table S23. Primers used in this study.
DOI: 10.6084/m9.figshare.26685966
title: Additional file 1 of Genomic insight into the origin, domestication, dispersal, diversification and human selection of Tartary buckwheat

description: Additional file 1: Table S1. Summary of the 567 Tartary buckwheat accessions and 7 outgroup accessions used in this study with the mapping rate, depth and coverage. Table S2. Distribution of SNPs into various genomic regions in Tartary buckwheat. Table S3. Statistical differences between pairwise FST values between the different populations. Table S4. Genomic fragments with evidence for introgression based on Fd and FdM.Table S5. Interpopulation introgression based on D- statistics. Table S6. Putative selective sweeps between HW and SL based on XP-CLR analysis. Table S7. Putative selective sweeps between HW and NL based on XP-CLR analysis.Table S8. Genes in selective sweeps in both between HW and SL and between HW and NL based on XP-CLR analysis. Table S9. Putative selective sweeps between HW and SL based on DCMS analysis. Table S10. Putative selective sweeps between HW and NL based on DCMS analysis. Table S11. Genes in selective sweeps in both between HW and SL and between HW and NL based on DCMS analysis. Table S12. Candidate genes associated with disease index identified by GWAS with MAF &gt;= 0.01. Table S13. Putative selective sweeps between SL and NL based on XP-CLR. Table S14. Putative selective sweeps between SL and NL based on DCMS. Table S15. Salt tolerance of Tartary buckwheat accessions. Table S16. Candidate genes associated with salt tolerance identified by GWAS. Table S17. Sequencing reads used for assembly of EDT. Table S18. Assembly statistics of the EDT genome. Table S19. BUSCO analysis of the EDT genome. Table S20. Genetic differences between EDT and DDT. Table S21. The expression of genes with insertions and deletions within the QTL inverval. Table S22. Summary of FtXIP insertion promoter cis-acting elements prediction in 1,400 bp region. Table S23. Primers used in this study.
DOI: 10.25824/redu/pmso8w
title: res_lit_000132.txt

description: :unav
DOI: 10.25824/redu/ivjaap
title: res_lit_000294.txt

description: :unav
DOI: 10.25824/redu/yj8qjv
title: res_lit_000085.txt

description: :unav
DOI: 10.25824/redu/9tkawk
title: res_lit_000352.txt

description: :unav
DOI: 10.25824/redu/gyyj5i
title: res_lit_000289.txt

description: :unav
DOI: 10.25824/redu/ep8td5
title: res_lit_000313.txt

description: :unav
DOI: 10.25824/redu/xo0twb
title: res_lit_000315.txt

description: :unav
DOI: 10.25824/redu/8v2nij
title: res_lit_000029.txt

description: :unav
DOI: 10.25824/redu/ui1ua4
title: res_lit_000329.txt

description: :unav
DOI: 10.25824/redu/hh09iv
title: res_lit_000077.txt

description: :unav
DOI: 10.25824/redu/gfkxnp
title: res_lit_000088.txt

description: :unav
DOI: 10.25824/redu/yuuamx
title: res_lit_000064.txt

description: :unav
DOI: 10.25824/redu/xreuac
title: res_lit_000246.txt

description: :unav
DOI: 10.25824/redu/ybxkxg
title: res_lit_000027.txt

description: :unav
DOI: 10.25824/redu/earnlg
title: res_lit_000091.txt

description: :unav
DOI: 10.6084/m9.figshare.26685996.v1
title: Additional file 1 of Combining full-length gene assay and SpliceAI to interpret the splicing impact of all possible SPINK1 coding variants

description: Additional file 1: Table S1. SpliceAI predictions for all possible SPINK1 coding SNVs.
DOI: 10.25824/redu/rwd6kj
title: res_lit_000044.txt

description: :unav
DOI: 10.6084/m9.figshare.26685996
title: Additional file 1 of Combining full-length gene assay and SpliceAI to interpret the splicing impact of all possible SPINK1 coding variants

description: Additional file 1: Table S1. SpliceAI predictions for all possible SPINK1 coding SNVs.
DOI: 10.15468/dl.ew4fkz
title: Occurrence Download

description: A dataset containing 265 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Nassella trichotoma (Nees) Hack. & Arechav.)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "Year is greater than or equal to 1900",
 "BasisOfRecord is one of (Specimen)",
 "Country is one of (Australia)",
 {
 "or" : [
 "CoordinateUncertaintyInMeters is less than or equal to 20000",
 "CoordinateUncertaintyInMeters is null"
 ]
 }
 ]
}

 The dataset includes 265 records from 21 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0067459-240626123714530/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.25824/redu/zcxcn1
title: res_lit_000177.txt

description: :unav
DOI: 10.25824/redu/iwn8dp
title: res_lit_000269.txt

description: :unav
DOI: 10.25824/redu/cn9noa
title: res_lit_000330.txt

description: :unav
DOI: 10.25824/redu/0hvvcc
title: res_lit_000381.txt

description: :unav
DOI: 10.25824/redu/jkexra
title: res_lit_000128.txt

description: :unav
DOI: 10.6084/m9.figshare.26572195.v1
title: Additional file 2 of Oligonucleotide usage in coronavirus genomes mimics that in exon regions in host genomes

description: Additional file 2. Table S1: The list of strains of human- and bat-CoV. Table S2: Comparison of the frequency of di-, tri-, and tetra-nucleotides between human- and bat-CoV. Table S3: Comparison of the frequency of di-, tri-, and tetra-nucleotides between human and bat genomes. Table S4: The list of oligonucleotides with significant differences in frequency between human and bat introns. Table S5: The list of oligonucleotides with significant differences in frequency between human and bat genomes. Table S6: Comparisons of the frequency of oligonucleotides between human exons and those of additional five bat species. Table S7: Level of adaptation of each oligonucleotide. Table S8: The number of isolates per month of each SARS-CoV-2 variant. Table S9: Changes in the oligonucleotide locus number of SARS-CoV-2.
DOI: 10.25824/redu/c64q25
title: res_lit_000342.txt

description: :unav
DOI: 10.15468/dl.5s7xg9
title: Occurrence Download

description: A dataset containing 32 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Colombia",
 "DatasetKey is one of (Herbarium GB, University of Gothenburg, Herbario Amazónico Colombiano, Herbario Nacional Colombiano (COL))",
 "OccurrenceStatus is Present",
 "TaxonKey is Rhizophora mangle L."
 ]
}

 The dataset includes 32 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0067461-240626123714530/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.ahrpzq
title: Occurrence Download

description: A dataset containing 49 species occurrences available in GBIF matching the query:
{
 "Geometry" : [
 "MULTIPOLYGON (((147.623897 -32.721823, 147.626142 -32.721823, 147.626142 -32.726315, 147.63288 -32.726315, 147.63288 -32.728561, 147.630634 -32.728561, 147.630634 -32.733052, 147.637371 -32.733052, 147.637371 -32.735298, 147.644109 -32.735298, 147.644109 -32.726315, 147.637371 -32.726315, 147.637371 -32.721823, 147.644109 -32.721823, 147.644109 -32.719578, 147.639617 -32.719578, 147.639617 -32.71284, 147.630634 -32.71284, 147.630634 -32.710594, 147.626142 -32.710594, 147.626142 -32.719578, 147.623897 -32.719578, 147.623897 -32.721823)), ((147.623897 -32.721823, 147.621651 -32.721823, 147.621651 -32.726315, 147.623897 -32.726315, 147.623897 -32.721823)), ((147.644109 -32.719578, 147.646355 -32.719578, 147.646355 -32.715086, 147.644109 -32.715086, 147.644109 -32.719578)))"
 ]
}

 The dataset includes 49 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0067460-240626123714530/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.6084/m9.figshare.26572195
title: Additional file 2 of Oligonucleotide usage in coronavirus genomes mimics that in exon regions in host genomes

description: Additional file 2. Table S1: The list of strains of human- and bat-CoV. Table S2: Comparison of the frequency of di-, tri-, and tetra-nucleotides between human- and bat-CoV. Table S3: Comparison of the frequency of di-, tri-, and tetra-nucleotides between human and bat genomes. Table S4: The list of oligonucleotides with significant differences in frequency between human and bat introns. Table S5: The list of oligonucleotides with significant differences in frequency between human and bat genomes. Table S6: Comparisons of the frequency of oligonucleotides between human exons and those of additional five bat species. Table S7: Level of adaptation of each oligonucleotide. Table S8: The number of isolates per month of each SARS-CoV-2 variant. Table S9: Changes in the oligonucleotide locus number of SARS-CoV-2.
DOI: 10.25824/redu/5bqgqf
title: res_lit_000283.txt

description: :unav
DOI: 10.25824/redu/cb9hsa
title: res_lit_000388.txt

description: :unav
DOI: 10.25824/redu/rvi2rb
title: res_lit_000231.txt

description: :unav
DOI: 10.25824/redu/kqmgly
title: res_lit_000063.txt

description: :unav
DOI: 10.25824/redu/y7c0oy
title: res_lit_000030.txt

description: :unav
DOI: 10.25824/redu/ts5ioe
title: res_lit_000239.txt

description: :unav
DOI: 10.6084/m9.figshare.26609868.v1
title: Additional file 2 of Wide-scale identification of novel/eliminated genes responsible for evolutionary transformations

description: Additional file 2: Table S2. The list-2 of differentially expressed (DE) genes of Xenopus tropicalis frog (2007 pcs) identified by the RNA-seq analysis based on two models at FDR&lt;0.01. Columns: Protein ID, Gene ID, Symbol (gene symbol), Name (gene description), Δt (two time points), logFC (Log-Fold-Change, logarithm of the gene expression ratio at two time points in “exact test” model), FDR (False Discovery Rate, probability of the type I error in “exact test” model).
DOI: 10.25824/redu/5rghzr
title: res_lit_000080.txt

description: :unav
DOI: 10.25824/redu/9exflo
title: res_lit_000117.txt

description: :unav
DOI: 10.6084/m9.figshare.26609874.v1
title: Additional file 4 of Wide-scale identification of novel/eliminated genes responsible for evolutionary transformations

description: Additional file 4: Table S4. The list-4 of Xenopus tropicalis frog genes (109 pcs.) that are simultaneously: present in fish; absent from reptilians, birds, and mammals; significantly change their expression level after the amputation of tail, at the standard parameters with r1 = 1 Mbp, r2 = 2 Mbp, r3 = 5 Mbp. For the column descriptions ref. to Table S1 and Table S2. In columns R, S, and T, the value 1 appears if the gene corresponding to this row meets the three-species condition for corresponding neighborhood size ri, otherwise the value is zero.
DOI: 10.6084/m9.figshare.26609871
title: Additional file 3 of Wide-scale identification of novel/eliminated genes responsible for evolutionary transformations

description: Additional file 3: Table S3. The list-3 of Xenopus tropicalis frog genes (268 pcs) that are simultaneously: present in fish; absent in placental mammals; significantly change their expression level after the amputation of tail, at the standard parameters. For each gene, the characteristics m. n, p, q are shown, see details in the description of Additional file 4: Table S1. For the column descriptions ref. to Additional file 4 Table S1 and Additional file 5 Table S2.
DOI: 10.6084/m9.figshare.26609865.v1
title: Additional file 1 of Wide-scale identification of novel/eliminated genes responsible for evolutionary transformations

description: Additional file 1: Table S1. The list-1 of Xenopus tropicalis frog genes (2392 pcs) that are present in fish and absent from all placental mammals considered, at the standard parameters. For each frog gene, the characteristics m (number of primitive mammals that have this gene), n (number of birds that have this gene), p (number of reptiles that have this gene), and q (number of fish that have this gene) are specified. Columns: Protein (protein ID), Gene ID (frog gene ID), Chr, Start, End, +/- (gene coordinates), Symbol (gene symbol), Name (gene description), m, n, p, q, Monodelphis,…, Takifugu (19 columns with a gene ID in the respective species, if the gene is present in it, in the following order: primitive mammals, birds, reptilians, fish).
DOI: 10.25824/redu/ew26j8
title: res_lit_000401.txt

description: :unav
DOI: 10.25824/redu/1pir5g
title: res_lit_000355.txt

description: :unav
DOI: 10.6084/m9.figshare.26609874
title: Additional file 4 of Wide-scale identification of novel/eliminated genes responsible for evolutionary transformations

description: Additional file 4: Table S4. The list-4 of Xenopus tropicalis frog genes (109 pcs.) that are simultaneously: present in fish; absent from reptilians, birds, and mammals; significantly change their expression level after the amputation of tail, at the standard parameters with r1 = 1 Mbp, r2 = 2 Mbp, r3 = 5 Mbp. For the column descriptions ref. to Table S1 and Table S2. In columns R, S, and T, the value 1 appears if the gene corresponding to this row meets the three-species condition for corresponding neighborhood size ri, otherwise the value is zero.
DOI: 10.6084/m9.figshare.26609877
title: Additional file 5 of Wide-scale identification of novel/eliminated genes responsible for evolutionary transformations

description: Additional file 5: Table S5. The final list of Xenopus tropicalis frog genes (57 pcs) that are simultaneously: present in fish; absent from reptilians, birds, and mammals; significantly change their expression level after the amputation of tail; meets the three-species condition for at least one size ri of neighborhood, at the standard parameters with r1 = 1 Mbp, r2 = 2 Mbp, r3 = 5 Mbp. For the column descriptions ref. to dditional file 4 Table S1 and Additional file 5 Table S2.
DOI: 10.6084/m9.figshare.26609877.v1
title: Additional file 5 of Wide-scale identification of novel/eliminated genes responsible for evolutionary transformations

description: Additional file 5: Table S5. The final list of Xenopus tropicalis frog genes (57 pcs) that are simultaneously: present in fish; absent from reptilians, birds, and mammals; significantly change their expression level after the amputation of tail; meets the three-species condition for at least one size ri of neighborhood, at the standard parameters with r1 = 1 Mbp, r2 = 2 Mbp, r3 = 5 Mbp. For the column descriptions ref. to dditional file 4 Table S1 and Additional file 5 Table S2.
DOI: 10.6084/m9.figshare.26686059
title: Additional file 2 of Evolution of ancient satellite DNAs in extant alligators and caimans (Crocodylia, Reptilia)

description: Additional file 2: Tables S1-S10. Table S1—Within-group pairwise similarity of satDNAs. Table S2—Summary of the results obtained from the read clustering analysis with multiple species analyzed simultaneously. Table S3—We have compared hundreds of repetitive units from each satellite and compared the mean divergence that exists between them (inter-repeat divergence) with the mean divergence that exists between the subunits that compose each repetitive unit (intra-repeat divergence). For the case of the sequences of the Group 1 constituted by repetitive units of 41 bp, we have considered each of its subunits (alpha and beta) of 21 and 20 bp, respectively, obtaining that the intra-repeat divergence was always greater than the inter-repeat divergence. Table S4—As for the Group 1 satellites, we have analyzed the 60 bp long satellites of Group 2. Here we verified that their repetitive units were made up of subunits of 20 bp each, which we have named alpha, beta, and gamma. The table shows the analysis of intra-repeats versus inter-repeats divergences, and it can also be seen here that the former is greater than the latter. Table S5—While Groups 1 and 2 were more homogeneous, Group 3 sequences are characterized as heterogeneous ones, as their sequences were derived from a repetition of two subunits of 29 bp and 11 bp. This table demonstrates that the divergence between alpha (29 bp) and beta (11 bp) subrepeats is greater than the divergence between complete repeats of these satellites. Thus, looking at their structure, we can affirm that the Group 3 satellites are not formed by repetitive units of 20 bp. In any case, it is possible that the ancestral satellite that gave rise to the group 3 satellites had a length of 29 bp and that later rearrangements, possibly mediated by unequal crossing over (see, for example, Navajas-Pérez et al. 2005 for RAYSI satDNA), generated a 40 bp repetitive unit formed by one unit plus one third of another, being now the unit of homogenization of these satellites. Table S6—Summary of the BLAST searches against Alligator sinensis genome. Table S7—Main features of the analyzed genomic libraries. Table S8—Results of RepeatMasking against the Repbase database. Table S9—Read mapping against single-copy genes for normalization of satDNA abundance. Table S10—log10 of normalized abundances of each satDNA, considering RepeatMasker counts from 0 to 20% of divergence.
DOI: 10.6084/m9.figshare.26686059.v1
title: Additional file 2 of Evolution of ancient satellite DNAs in extant alligators and caimans (Crocodylia, Reptilia)

description: Additional file 2: Tables S1-S10. Table S1—Within-group pairwise similarity of satDNAs. Table S2—Summary of the results obtained from the read clustering analysis with multiple species analyzed simultaneously. Table S3—We have compared hundreds of repetitive units from each satellite and compared the mean divergence that exists between them (inter-repeat divergence) with the mean divergence that exists between the subunits that compose each repetitive unit (intra-repeat divergence). For the case of the sequences of the Group 1 constituted by repetitive units of 41 bp, we have considered each of its subunits (alpha and beta) of 21 and 20 bp, respectively, obtaining that the intra-repeat divergence was always greater than the inter-repeat divergence. Table S4—As for the Group 1 satellites, we have analyzed the 60 bp long satellites of Group 2. Here we verified that their repetitive units were made up of subunits of 20 bp each, which we have named alpha, beta, and gamma. The table shows the analysis of intra-repeats versus inter-repeats divergences, and it can also be seen here that the former is greater than the latter. Table S5—While Groups 1 and 2 were more homogeneous, Group 3 sequences are characterized as heterogeneous ones, as their sequences were derived from a repetition of two subunits of 29 bp and 11 bp. This table demonstrates that the divergence between alpha (29 bp) and beta (11 bp) subrepeats is greater than the divergence between complete repeats of these satellites. Thus, looking at their structure, we can affirm that the Group 3 satellites are not formed by repetitive units of 20 bp. In any case, it is possible that the ancestral satellite that gave rise to the group 3 satellites had a length of 29 bp and that later rearrangements, possibly mediated by unequal crossing over (see, for example, Navajas-Pérez et al. 2005 for RAYSI satDNA), generated a 40 bp repetitive unit formed by one unit plus one third of another, being now the unit of homogenization of these satellites. Table S6—Summary of the BLAST searches against Alligator sinensis genome. Table S7—Main features of the analyzed genomic libraries. Table S8—Results of RepeatMasking against the Repbase database. Table S9—Read mapping against single-copy genes for normalization of satDNA abundance. Table S10—log10 of normalized abundances of each satDNA, considering RepeatMasker counts from 0 to 20% of divergence.
DOI: 10.25824/redu/eulkza
title: res_lit_000317.txt

description: :unav
DOI: 10.6084/m9.figshare.26609871.v1
title: Additional file 3 of Wide-scale identification of novel/eliminated genes responsible for evolutionary transformations

description: Additional file 3: Table S3. The list-3 of Xenopus tropicalis frog genes (268 pcs) that are simultaneously: present in fish; absent in placental mammals; significantly change their expression level after the amputation of tail, at the standard parameters. For each gene, the characteristics m. n, p, q are shown, see details in the description of Additional file 4: Table S1. For the column descriptions ref. to Additional file 4 Table S1 and Additional file 5 Table S2.
DOI: 10.25824/redu/sah11r
title: res_lit_000195.txt

description: :unav
DOI: 10.25824/redu/abs2nq
title: res_lit_000125.txt

description: :unav
DOI: 10.25824/redu/ou96k8
title: res_lit_000014.txt

description: :unav
DOI: 10.25824/redu/g7fi5q
title: res_lit_000338.txt

description: :unav
DOI: 10.25824/redu/8crmgo
title: res_lit_000007.txt

description: :unav
DOI: 10.25824/redu/dphfd3
title: res_lit_000272.txt

description: :unav
DOI: 10.25824/redu/kbkuhf
title: res_lit_000407.txt

description: :unav
DOI: 10.25824/redu/oftz7u
title: res_lit_000137.txt

description: :unav
DOI: 10.25824/redu/y4ygnn
title: res_lit_000405.txt

description: :unav
DOI: 10.25824/redu/dyuje7
title: res_lit_000062.txt

description: :unav
DOI: 10.25824/redu/wxkuhc
title: res_lit_000249.txt

description: :unav
DOI: 10.25824/redu/tpal5y
title: res_lit_000314.txt

description: :unav
DOI: 10.15468/dl.crxr7n
title: Occurrence Download

description: A dataset containing 292434 species occurrences available in GBIF matching the query:
{
 "Geometry" : [
 "POLYGON ((-94.79473 30.99125, -94.05903 30.99125, -94.05903 31.51662, -94.79473 31.51662, -94.79473 30.99125))"
 ]
}

 The dataset includes 292434 records from 184 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0067428-240626123714530/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.