cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.11497464.v1
title: MOESM2 of Prepartum dietary energy intake alters adipose tissue transcriptome profiles during the periparturient period in Holstein dairy cows

description: Additional file 2. Complete result datasets generated by the DIA analysis from transcript profiling analysis in bovine subcutaneous adipose tissue from end of pregnancy (− 14 d) through early lactation (1 and 14 d) in dairy cow fed a control diet prepartum (CTR) or relatively high energy diet prepartum (OVR). The KEGG pathways are sorted by category and subcategory. Blue bars represent the Impact, while red and green bars depict the Direction of the Impact (red = upregulation, green = downregulation)
DOI: 10.6084/m9.figshare.11497461
title: MOESM1 of Prepartum dietary energy intake alters adipose tissue transcriptome profiles during the periparturient period in Holstein dairy cows

description: Additional file 1. Complete database of differentially expressed genes (DEG) of bovine subcutaneous adipose tissue from end of pregnancy (− 14 d) through early lactation (1 and 14 d) in dairy cow fed a control diet prepartum (CTR) or relatively high energy diet prepartum (OVR).
DOI: 10.6084/m9.figshare.11497461.v1
title: MOESM1 of Prepartum dietary energy intake alters adipose tissue transcriptome profiles during the periparturient period in Holstein dairy cows

description: Additional file 1. Complete database of differentially expressed genes (DEG) of bovine subcutaneous adipose tissue from end of pregnancy (− 14 d) through early lactation (1 and 14 d) in dairy cow fed a control diet prepartum (CTR) or relatively high energy diet prepartum (OVR).
DOI: 10.6084/m9.figshare.11497443
title: MOESM8 of Using whole-genome SNP data to reconstruct a large multi-generation pedigree in apple germplasm

description: Additional file 8. Pedigree deduced from all relationships between diploid individuals inferred in the present work. The file can be opened using the Pedimap software [57]. Cultivar names are in their short version (Additional file 1: Table S1). The “indic” column indicates the level of information known for the individual(s) in the pedigree: 1, founders; 2, unknown individuals, with both parents known; 3, semi-founders (one parent known, one parent unknown); 4, known individuals with both parents known. (ZIP 13 kb)
DOI: 10.6084/m9.figshare.11497443.v1
title: MOESM8 of Using whole-genome SNP data to reconstruct a large multi-generation pedigree in apple germplasm

description: Additional file 8. Pedigree deduced from all relationships between diploid individuals inferred in the present work. The file can be opened using the Pedimap software [57]. Cultivar names are in their short version (Additional file 1: Table S1). The “indic” column indicates the level of information known for the individual(s) in the pedigree: 1, founders; 2, unknown individuals, with both parents known; 3, semi-founders (one parent known, one parent unknown); 4, known individuals with both parents known. (ZIP 13 kb)
DOI: 10.6084/m9.figshare.11497437
title: MOESM7 of Using whole-genome SNP data to reconstruct a large multi-generation pedigree in apple germplasm

description: Additional file 7: Table S6. Groups of grandparents, parent and offspring inferred with less than 100 Mendelian Errors (ME), indicating the preferred names of the offspring (Offspring), parent (Parent) and grandparents (GrandParent 1, GrandParent 2), i.e. parent couple of the missing parent, and their MUNQ (MUNQ O, MUNQ P, MUNQ GP1, MUNQ GP2), the number of ME in the 25 K SNP set (# ME 25 K) and in the 253 K SNP set (# ME 253 K), presupposed parents of the offspring (Parent1 from Literature, Parent 2 from Literature) and source of this documentation (Source_parents), consistency of inferred parent with literature (Ped_consistency), consistency of dates, i.e. offspring younger than its inferred grandparent(s), on the basis of documented dates indicated in Additional file 1: Table S1 (Date consistent GP1 and Date consistent GP2).
DOI: 10.6084/m9.figshare.11497437.v1
title: MOESM7 of Using whole-genome SNP data to reconstruct a large multi-generation pedigree in apple germplasm

description: Additional file 7: Table S6. Groups of grandparents, parent and offspring inferred with less than 100 Mendelian Errors (ME), indicating the preferred names of the offspring (Offspring), parent (Parent) and grandparents (GrandParent 1, GrandParent 2), i.e. parent couple of the missing parent, and their MUNQ (MUNQ O, MUNQ P, MUNQ GP1, MUNQ GP2), the number of ME in the 25 K SNP set (# ME 25 K) and in the 253 K SNP set (# ME 253 K), presupposed parents of the offspring (Parent1 from Literature, Parent 2 from Literature) and source of this documentation (Source_parents), consistency of inferred parent with literature (Ped_consistency), consistency of dates, i.e. offspring younger than its inferred grandparent(s), on the basis of documented dates indicated in Additional file 1: Table S1 (Date consistent GP1 and Date consistent GP2).
DOI: 10.6084/m9.figshare.11497428
title: MOESM5 of Using whole-genome SNP data to reconstruct a large multi-generation pedigree in apple germplasm

description: Additional file 5: Table S4. Oriented Parent-Offspring duos inferred with less than 600 Mendelian Errors (ME), indicating the preferred name of the offspring (Preferred Name Offspring) and its MUNQ (MUNQ O), the preferred name of the parent (Preferred Name P) and its MUNQ (MUNQ P), the number of ME (# ME), presupposed parents of the offspring (Parent1 from Literature, Parent 2 from Literature) and source of this documentation (Source_parents), consistency of inferred parent with literature (one parent confirmed), consistency of dates, i.e. offspring younger than its inferred parent, on the basis of documented dates indicated in Additional file 1: Table S1 (Date consistent). The duos for which presupposed parents were identified are listed in the first 25 lines, while the remaining are below. In each part, the duos are sorted alphabetically according to the preferred name of the offspring.
DOI: 10.6084/m9.figshare.11497431
title: MOESM6 of Using whole-genome SNP data to reconstruct a large multi-generation pedigree in apple germplasm

description: Additional file 6: Table S5. Non-Oriented Parent-Offspring duos inferred with less than 600 Mendelian Errors (ME), indicating the preferred name of the two individuals of the pair (Preferred Name Ind1, Preferred Name Ind2) and their MUNQ (MUNQ Ind1, MUNQ Ind2, the number of ME (# ME), MUNQ of supposed offspring (Supposed Offspring) and supposed parent (Supposed parent) in the pair when available with indication of the source of the supposed orientation (oriented using), presupposed parents of both individuals (Ind1_Parent1 from Literature, Ind1_Parent 2 from Literature, Ind2_Parent1 from Literature, Ind2_Parent 2 from Literature) and source of these documentation (Source_parents_ind1, Source_parents_ind2), documented dates of ind1 and ind2 as indicated in Additional file 1: Table S1, and indication of possibility of orientation according to date (Date consistency). The duos which were oriented based on documented parentage (ped-lit in column “oriented using”) are listed in the first 44 lines, and are sorted alphabetically according to the preferred name of the supposed offspring. The duos which were oriented based on documented dates of the two individuals are listed in the next 161 lines and are sorted from the oldest to the most recent supposed parent; next are listed the 43 duos which were oriented because one individual of the duos was supposed a child in a duo oriented according to previously documented parentage or dates; these are sorted from the oldest to the most recent supposed parent; next are listed two duos which were oriented in a second round. Next are listed 51 duos for which a date was listed for one individual only: this individual was then attributed to be Ind2 and all these duos are sorted from the oldest to the most recent Ind2. Next are listed seven duos for which a date was available for both individuals but was too imprecise or too old to enable orientation. The remaining 22 duos for which neither dates nor parentage documentation were found, are listed at the end; individuals that appeared most frequently in these duos were attributed to be Ind2 and all these duos are sorted alphabetically according to the preferred name of Ind2.
DOI: 10.6084/m9.figshare.11497428.v1
title: MOESM5 of Using whole-genome SNP data to reconstruct a large multi-generation pedigree in apple germplasm

description: Additional file 5: Table S4. Oriented Parent-Offspring duos inferred with less than 600 Mendelian Errors (ME), indicating the preferred name of the offspring (Preferred Name Offspring) and its MUNQ (MUNQ O), the preferred name of the parent (Preferred Name P) and its MUNQ (MUNQ P), the number of ME (# ME), presupposed parents of the offspring (Parent1 from Literature, Parent 2 from Literature) and source of this documentation (Source_parents), consistency of inferred parent with literature (one parent confirmed), consistency of dates, i.e. offspring younger than its inferred parent, on the basis of documented dates indicated in Additional file 1: Table S1 (Date consistent). The duos for which presupposed parents were identified are listed in the first 25 lines, while the remaining are below. In each part, the duos are sorted alphabetically according to the preferred name of the offspring.
DOI: 10.6084/m9.figshare.11497431.v1
title: MOESM6 of Using whole-genome SNP data to reconstruct a large multi-generation pedigree in apple germplasm

description: Additional file 6: Table S5. Non-Oriented Parent-Offspring duos inferred with less than 600 Mendelian Errors (ME), indicating the preferred name of the two individuals of the pair (Preferred Name Ind1, Preferred Name Ind2) and their MUNQ (MUNQ Ind1, MUNQ Ind2, the number of ME (# ME), MUNQ of supposed offspring (Supposed Offspring) and supposed parent (Supposed parent) in the pair when available with indication of the source of the supposed orientation (oriented using), presupposed parents of both individuals (Ind1_Parent1 from Literature, Ind1_Parent 2 from Literature, Ind2_Parent1 from Literature, Ind2_Parent 2 from Literature) and source of these documentation (Source_parents_ind1, Source_parents_ind2), documented dates of ind1 and ind2 as indicated in Additional file 1: Table S1, and indication of possibility of orientation according to date (Date consistency). The duos which were oriented based on documented parentage (ped-lit in column “oriented using”) are listed in the first 44 lines, and are sorted alphabetically according to the preferred name of the supposed offspring. The duos which were oriented based on documented dates of the two individuals are listed in the next 161 lines and are sorted from the oldest to the most recent supposed parent; next are listed the 43 duos which were oriented because one individual of the duos was supposed a child in a duo oriented according to previously documented parentage or dates; these are sorted from the oldest to the most recent supposed parent; next are listed two duos which were oriented in a second round. Next are listed 51 duos for which a date was listed for one individual only: this individual was then attributed to be Ind2 and all these duos are sorted from the oldest to the most recent Ind2. Next are listed seven duos for which a date was available for both individuals but was too imprecise or too old to enable orientation. The remaining 22 duos for which neither dates nor parentage documentation were found, are listed at the end; individuals that appeared most frequently in these duos were attributed to be Ind2 and all these duos are sorted alphabetically according to the preferred name of Ind2.
DOI: 10.6084/m9.figshare.11497416
title: MOESM2 of Using whole-genome SNP data to reconstruct a large multi-generation pedigree in apple germplasm

description: Additional file 2: Table S2. List of the 253,095 robust SNPs used in the study, with their chromosome location, and position on chromosome, in bp. SNPs located on chromosome 18 are those located on contigs or scaffold that could not be attributed to a chromosome. SNPs located on chromosome 19 are those for which no clear position could be found (either no BLAST results for the probe, or several equivalent results). Inclusion of a SNP in the 25 K subset is indicated by a “yes” in column “in.25 K.subset”.
DOI: 10.6084/m9.figshare.11497416.v1
title: MOESM2 of Using whole-genome SNP data to reconstruct a large multi-generation pedigree in apple germplasm

description: Additional file 2: Table S2. List of the 253,095 robust SNPs used in the study, with their chromosome location, and position on chromosome, in bp. SNPs located on chromosome 18 are those located on contigs or scaffold that could not be attributed to a chromosome. SNPs located on chromosome 19 are those for which no clear position could be found (either no BLAST results for the probe, or several equivalent results). Inclusion of a SNP in the 25 K subset is indicated by a “yes” in column “in.25 K.subset”.
DOI: 10.6084/m9.figshare.11497419
title: MOESM3 of Using whole-genome SNP data to reconstruct a large multi-generation pedigree in apple germplasm

description: Additional file 3: Table S3. Complete parent-offspring trios inferred with less than 600 Mendelian Errors (ME), indicating the preferred name of the offspring (Preferred Name Offspring) and its MUNQ (MUNQ O), the preferred names of the parents (Preferred Name P1, Preferred Name P2) and their MUNQ (MUNQ P1, MUNQ P2), the number of ME (# ME), presupposed parents (Parent1 from Literature, Parent 2 from Literature) and source of this documentation (Source_parents), consistency of inferred parents with literature (P1_confirmed and P2_confirmed), consistency of dates, i.e. offspring younger than its inferred parent(s), on the basis of documented dates indicated in Additional file 1: Table S1 (Date consistent P1 and Date consistent P2). The trios for which presupposed parent(s) were identified are listed in the first 143 lines, while the remaining are below. In each part, the trios are sorted alphabetically according to the preferred name of the offspring. When presupposed parents were identified, parents considered as P1 and P2 were sorted according to literature. For the remaining trios, parents were attributed to P1 and P2 arbitrarily.
DOI: 10.6084/m9.figshare.11497413
title: MOESM1 of Using whole-genome SNP data to reconstruct a large multi-generation pedigree in apple germplasm

description: Additional file 1: Table S1. List of the 1433 unique Malus domestica individuals (MUNQ) involved in the study, with the accession number of the accession used to represent the MUNQ in genotyping (Accession code), the preferred name attributed to the MUNQ (Preferred Name), and its short version (Preferred Name Short), the original reason for genotyping the MUNQ (Origin), their ploidy level (Ploidy), the date of origin, first description, introduction, recording or inclusion in collections of cultivars corresponding to the preferred name (Date), and reference(s) enabling to document the date (Source for date).
DOI: 10.6084/m9.figshare.11497419.v1
title: MOESM3 of Using whole-genome SNP data to reconstruct a large multi-generation pedigree in apple germplasm

description: Additional file 3: Table S3. Complete parent-offspring trios inferred with less than 600 Mendelian Errors (ME), indicating the preferred name of the offspring (Preferred Name Offspring) and its MUNQ (MUNQ O), the preferred names of the parents (Preferred Name P1, Preferred Name P2) and their MUNQ (MUNQ P1, MUNQ P2), the number of ME (# ME), presupposed parents (Parent1 from Literature, Parent 2 from Literature) and source of this documentation (Source_parents), consistency of inferred parents with literature (P1_confirmed and P2_confirmed), consistency of dates, i.e. offspring younger than its inferred parent(s), on the basis of documented dates indicated in Additional file 1: Table S1 (Date consistent P1 and Date consistent P2). The trios for which presupposed parent(s) were identified are listed in the first 143 lines, while the remaining are below. In each part, the trios are sorted alphabetically according to the preferred name of the offspring. When presupposed parents were identified, parents considered as P1 and P2 were sorted according to literature. For the remaining trios, parents were attributed to P1 and P2 arbitrarily.
DOI: 10.6084/m9.figshare.11497407
title: MOESM12 of Using whole-genome SNP data to reconstruct a large multi-generation pedigree in apple germplasm

description: Additional file 12: Table S7. Relationships identified for triploids inferred with less than 300 Mendelian Errors (ME) for duos and trios, and less than 1200 tri-hom/di-het with the parent giving a diploid gamete, indicating the preferred name of the triploid offspring (Triploid Offspring) and its MUNQ (MUNQ O), the preferred name of the parent giving a diploid gamete (2n-gamete Parent) and its MUNQ (MUNQ 2n P), the number of ME for the duo triploid-2n-gamete parent (#ME 2n P), the number of tri-hom/di-het SNPs for the duo triploid-2n-gamete parent (# Hom-Het), the preferred name of the parent giving a haploid gamete (n-gamete Parent) and its MUNQ (MUNQ n P), the number of ME for the duo triploid-n-gamete parent (#ME n P), and when available, the number of ME for the trio (# ME trio).
DOI: 10.6084/m9.figshare.11497413.v1
title: MOESM1 of Using whole-genome SNP data to reconstruct a large multi-generation pedigree in apple germplasm

description: Additional file 1: Table S1. List of the 1433 unique Malus domestica individuals (MUNQ) involved in the study, with the accession number of the accession used to represent the MUNQ in genotyping (Accession code), the preferred name attributed to the MUNQ (Preferred Name), and its short version (Preferred Name Short), the original reason for genotyping the MUNQ (Origin), their ploidy level (Ploidy), the date of origin, first description, introduction, recording or inclusion in collections of cultivars corresponding to the preferred name (Date), and reference(s) enabling to document the date (Source for date).
DOI: 10.6084/m9.figshare.11497407.v1
title: MOESM12 of Using whole-genome SNP data to reconstruct a large multi-generation pedigree in apple germplasm

description: Additional file 12: Table S7. Relationships identified for triploids inferred with less than 300 Mendelian Errors (ME) for duos and trios, and less than 1200 tri-hom/di-het with the parent giving a diploid gamete, indicating the preferred name of the triploid offspring (Triploid Offspring) and its MUNQ (MUNQ O), the preferred name of the parent giving a diploid gamete (2n-gamete Parent) and its MUNQ (MUNQ 2n P), the number of ME for the duo triploid-2n-gamete parent (#ME 2n P), the number of tri-hom/di-het SNPs for the duo triploid-2n-gamete parent (# Hom-Het), the preferred name of the parent giving a haploid gamete (n-gamete Parent) and its MUNQ (MUNQ n P), the number of ME for the duo triploid-n-gamete parent (#ME n P), and when available, the number of ME for the trio (# ME trio).
DOI: 10.6084/m9.figshare.11497389
title: MOESM7 of Evolutionary superscaffolding and chromosome anchoring to improve Anopheles genome assemblies

description: Additional file 7. Anchored scaffolds and superscaffolds. Definitive chromosome anchoring data.
DOI: 10.6084/m9.figshare.11497389.v1
title: MOESM7 of Evolutionary superscaffolding and chromosome anchoring to improve Anopheles genome assemblies

description: Additional file 7. Anchored scaffolds and superscaffolds. Definitive chromosome anchoring data.
DOI: 10.6084/m9.figshare.11497383
title: MOESM6 of Evolutionary superscaffolding and chromosome anchoring to improve Anopheles genome assemblies

description: Additional file 6. Adjacency and superscaffold data. Reconciled sets of scaffold adjacencies and corresponding superscaffolds.
DOI: 10.6084/m9.figshare.11497383.v1
title: MOESM6 of Evolutionary superscaffolding and chromosome anchoring to improve Anopheles genome assemblies

description: Additional file 6. Adjacency and superscaffold data. Reconciled sets of scaffold adjacencies and corresponding superscaffolds.
DOI: 10.6084/m9.figshare.11497374
title: MOESM5 of Evolutionary superscaffolding and chromosome anchoring to improve Anopheles genome assemblies

description: Additional file 5. Chromosome mapping data. Reconciled chromosome-mapped scaffolds.
DOI: 10.6084/m9.figshare.11497374.v1
title: MOESM5 of Evolutionary superscaffolding and chromosome anchoring to improve Anopheles genome assemblies

description: Additional file 5. Chromosome mapping data. Reconciled chromosome-mapped scaffolds.
DOI: 10.6084/m9.figshare.11497368
title: MOESM4 of Evolutionary superscaffolding and chromosome anchoring to improve Anopheles genome assemblies

description: Additional file 4. Physical mapping data. Input datasets of the physically mapped scaffolds.
DOI: 10.6084/m9.figshare.11497368.v1
title: MOESM4 of Evolutionary superscaffolding and chromosome anchoring to improve Anopheles genome assemblies

description: Additional file 4. Physical mapping data. Input datasets of the physically mapped scaffolds.
DOI: 10.6084/m9.figshare.11497359
title: MOESM3 of Evolutionary superscaffolding and chromosome anchoring to improve Anopheles genome assemblies

description: Additional file 3. Orthology anchor data. Input data for the synteny analyses of orthology relationships and genomic locations of annotated genes.
DOI: 10.6084/m9.figshare.11497359.v1
title: MOESM3 of Evolutionary superscaffolding and chromosome anchoring to improve Anopheles genome assemblies

description: Additional file 3. Orthology anchor data. Input data for the synteny analyses of orthology relationships and genomic locations of annotated genes.
DOI: 10.6084/m9.figshare.11497350
title: MOESM2 of Evolutionary superscaffolding and chromosome anchoring to improve Anopheles genome assemblies

description: Additional file 2. Chromosome arm assignments. Lists of scaffold assignments to chromosome arms.
DOI: 10.6084/m9.figshare.11497350.v1
title: MOESM2 of Evolutionary superscaffolding and chromosome anchoring to improve Anopheles genome assemblies

description: Additional file 2. Chromosome arm assignments. Lists of scaffold assignments to chromosome arms.
DOI: 10.6084/m9.figshare.11497329
title: MOESM6 of A detailed in silico analysis of secondary metabolite biosynthesis clusters in the genome of the broad host range plant pathogenic fungus Sclerotinia sclerotiorum

description: Additional file 6: Table S5.Â Results from OrthoFinder showing the nodes to which orthogroups correspond along with all genes in the orthogroups.
DOI: 10.6084/m9.figshare.11497332
title: MOESM7 of A detailed in silico analysis of secondary metabolite biosynthesis clusters in the genome of the broad host range plant pathogenic fungus Sclerotinia sclerotiorum

description: Additional file 7: Table S6. Proteomes used in Orthofinder analysis.
DOI: 10.6084/m9.figshare.11497332.v1
title: MOESM7 of A detailed in silico analysis of secondary metabolite biosynthesis clusters in the genome of the broad host range plant pathogenic fungus Sclerotinia sclerotiorum

description: Additional file 7: Table S6. Proteomes used in Orthofinder analysis.
DOI: 10.6084/m9.figshare.11497323
title: MOESM5 of A detailed in silico analysis of secondary metabolite biosynthesis clusters in the genome of the broad host range plant pathogenic fungus Sclerotinia sclerotiorum

description: Additional file 5: Table S4. Results from MultiGeneBlast analysis.
DOI: 10.6084/m9.figshare.11497329.v1
title: MOESM6 of A detailed in silico analysis of secondary metabolite biosynthesis clusters in the genome of the broad host range plant pathogenic fungus Sclerotinia sclerotiorum

description: Additional file 6: Table S5.Â Results from OrthoFinder showing the nodes to which orthogroups correspond along with all genes in the orthogroups.