cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.15156/bio/sh168045.07fu
title: SH168045.07FU

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/sh168046.07fu
title: SH168046.07FU

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/sh168047.07fu
title: SH168047.07FU

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/sh168048.07fu
title: SH168048.07FU

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.21563882
title: Additional file 12 of Multicohort transcriptome analysis of whole blood identifies robust human response signatures in Plasmodium falciparum infections

description: Additional file 12: Table S3. The downregulated genes in malaria-infected relative to noninfected individuals in the discovery datasets.
DOI: 10.6084/m9.figshare.21563853
title: Additional file 10 of Systems biology approach reveals a common molecular basis for COVID-19 and non-alcoholic fatty liver disease (NAFLD)

description: Additional file 10: Table S9. Parameters of miRNAs-DEGs interaction network.
DOI: 10.6084/m9.figshare.21563856
title: Additional file 11 of Systems biology approach reveals a common molecular basis for COVID-19 and non-alcoholic fatty liver disease (NAFLD)

description: Additional file 11: Table S10. Parameters of the disease-DEGs network.
DOI: 10.6084/m9.figshare.21563862
title: Additional file 2 of Systems biology approach reveals a common molecular basis for COVID-19 and non-alcoholic fatty liver disease (NAFLD)

description: Additional file 2: Table S1. Differentially expressed genes for COVID-19.
DOI: 10.6084/m9.figshare.7932506
title: Phylogeny of Canadian ergot fungi and a detection assay by real-time polymerase chain reaction

description: The ergot disease of cereals has become increasingly important in agricultural areas of Canada since 1999. Generally, this disease is considered to be caused by <i>Claviceps purpurea</i>, but the taxonomy of <i>Claviceps</i> from these areas has not been well studied. The objectives of this study were (i) to determine the phylogenetic lineages (phylogenetic species) present in agricultural areas of Canada and (ii) to develop a molecular assay that can separate the lineages on crops from other lineages. Genetic diversity of <i>Claviceps</i> collected from agriculture areas in Canada were investigated using multilocus sequence typing. The loci sequenced include nuc rDNA internal transcribed spacer (ITS1-5.8S-ITS2 = ITS), partial fragments of translation elongation factor 1-α (<i>TEF1</i>), RNA polymerase II second largest subunit (<i>RPB2</i>), β-tubulin (<i>tubB</i>), and two ergot alkaloid synthesis genes (<i>easA, easE</i>). Based on individual locus and concatenated alignments, phylogenetic analyses revealed seven lineages within the premolecular concept of <i>C. purpurea</i>, of which five corresponded with undescribed species (G2b and G4–7). Although lineages G2–7 had narrow host ranges, lineage G1 (= <i>C. purpurea</i> s.s.) had a broad host range that overlapped with other lineages. A molecular diagnostic quantitative polymerase chain reaction (qPCR) assay was developed and validated with 185 samples from a wide range of host plants and geographic origins, including 10 phylogenetic species in <i>C</i>. sect. <i>Claviceps</i>, 8 in <i>C</i>. sect. <i>Pusillae</i>, 1 in <i>C</i>. sect. <i>Citrinae</i>, and 1–2 species from <i>Alternaria, Fusarium</i>, and <i>Penicillium</i>. The assay can detect lineage G1 at a concentration of 7.5 pg/μL and distinguish it from other <i>Claviceps</i> species and lineages. This facilitates disease management by detecting the inocula from nonagriculture host plants.
DOI: 10.6084/m9.figshare.22606945
title: Additional file 3 of Integrated multi-omics of the gastrointestinal microbiome and ruminant host reveals metabolic adaptation underlying early life development

description: Additional file 3: Table S3. Sequencing data of the 75 GIT samples of sika deer among the three stages. Table S4. The significantly changed metabolic pathways at KEGG level 1 in five GIT regions among the three time points. Table S5. The significantly changed metabolic pathways at KEGG level 3 in the rumen and colon among the three time points. Table S6. Enrichment analysis of the increased KOs in the rumen and colon microbiota between the comparison of Day 70 vs Day 1.
DOI: 10.6084/m9.figshare.7932506.v1
title: Phylogeny of Canadian ergot fungi and a detection assay by real-time polymerase chain reaction

description: The ergot disease of cereals has become increasingly important in agricultural areas of Canada since 1999. Generally, this disease is considered to be caused by <i>Claviceps purpurea</i>, but the taxonomy of <i>Claviceps</i> from these areas has not been well studied. The objectives of this study were (i) to determine the phylogenetic lineages (phylogenetic species) present in agricultural areas of Canada and (ii) to develop a molecular assay that can separate the lineages on crops from other lineages. Genetic diversity of <i>Claviceps</i> collected from agriculture areas in Canada were investigated using multilocus sequence typing. The loci sequenced include nuc rDNA internal transcribed spacer (ITS1-5.8S-ITS2 = ITS), partial fragments of translation elongation factor 1-α (<i>TEF1</i>), RNA polymerase II second largest subunit (<i>RPB2</i>), β-tubulin (<i>tubB</i>), and two ergot alkaloid synthesis genes (<i>easA, easE</i>). Based on individual locus and concatenated alignments, phylogenetic analyses revealed seven lineages within the premolecular concept of <i>C. purpurea</i>, of which five corresponded with undescribed species (G2b and G4–7). Although lineages G2–7 had narrow host ranges, lineage G1 (= <i>C. purpurea</i> s.s.) had a broad host range that overlapped with other lineages. A molecular diagnostic quantitative polymerase chain reaction (qPCR) assay was developed and validated with 185 samples from a wide range of host plants and geographic origins, including 10 phylogenetic species in <i>C</i>. sect. <i>Claviceps</i>, 8 in <i>C</i>. sect. <i>Pusillae</i>, 1 in <i>C</i>. sect. <i>Citrinae</i>, and 1–2 species from <i>Alternaria, Fusarium</i>, and <i>Penicillium</i>. The assay can detect lineage G1 at a concentration of 7.5 pg/μL and distinguish it from other <i>Claviceps</i> species and lineages. This facilitates disease management by detecting the inocula from nonagriculture host plants.
DOI: 10.6084/m9.figshare.21564137.v1
title: Additional file 10 of The phylogeny of Seseli (Apiaceae, Apioideae): insights from molecular and morphological data

description: Additional file 10: Table S9. Morphological data of the eighteen taxa in Selineae and Echinophoreae involved in this study.
DOI: 10.6084/m9.figshare.22606948
title: Additional file 4 of Integrated multi-omics of the gastrointestinal microbiome and ruminant host reveals metabolic adaptation underlying early life development

description: Additional file 4: Table S7. Summary of genome assembly of Sika deer. Table S8. Summary of RNA-seq data from 75 GIT epithelium samples of sika deer. Table S9. Enrichment analysis at KEGG level 3 of up regulated DEGs in rumen epithelium.
DOI: 10.6084/m9.figshare.21563883
title: Additional file 9 of Systems biology approach reveals a common molecular basis for COVID-19 and non-alcoholic fatty liver disease (NAFLD)

description: Additional file 9: Table S8. TFs-DEGs interaction network parameters.
DOI: 10.6084/m9.figshare.8981228
title: Additional file 10: of Genome survey and high-resolution backcross genetic linkage map construction of the ridgetail white prawn Exopalaemon carinicauda applications to QTL mapping of growth traits

description: Table S10. Markers of reverse Backcross linkage map anchored to transcriptome. (XLSX 39 kb)
DOI: 10.5281/zenodo.10627533
title: Dataset for DAWG Phylogenomics workshop

description: This page has the data for the DAWG Phylogenomics workshop
DOI: 10.5281/zenodo.10627534
title: Dataset for DAWG Phylogenomics workshop

description: This page has the data for the DAWG Phylogenomics workshop
DOI: 10.6084/m9.figshare.22612448.v1
title: Additional file 2 of Genome-wide identification and gene expression analysis of the 14–3-3 gene family in potato (Solanum tuberosum L.)

description: Additional file 2. The similarities among StGRF proteins of potato.
DOI: 10.6084/m9.figshare.8981228.v1
title: Additional file 10: of Genome survey and high-resolution backcross genetic linkage map construction of the ridgetail white prawn Exopalaemon carinicauda applications to QTL mapping of growth traits

description: Table S10. Markers of reverse Backcross linkage map anchored to transcriptome. (XLSX 39 kb)
DOI: 10.6084/m9.figshare.8981234
title: Additional file 1: of Genome survey and high-resolution backcross genetic linkage map construction of the ridgetail white prawn Exopalaemon carinicauda applications to QTL mapping of growth traits

description: Table S1. Phenotypic data of sequenced individuals from BC1 and reverse BC1 families of E. carinicauda. (XLSX 24 kb)
DOI: 10.6084/m9.figshare.21564143
title: Additional file 2 of The phylogeny of Seseli (Apiaceae, Apioideae): insights from molecular and morphological data

description: Additional file 2: Table S1. Collection locality and voucher information of the eleven Seseli taxa.
DOI: 10.6084/m9.figshare.21564152
title: Additional file 5 of The phylogeny of Seseli (Apiaceae, Apioideae): insights from molecular and morphological data

description: Additional file 5: Table S4. The repeat sequences distribution in the eleven Seseli plastomes.
DOI: 10.6084/m9.figshare.21564155.v1
title: Additional file 6 of The phylogeny of Seseli (Apiaceae, Apioideae): insights from molecular and morphological data

description: Additional file 6: Table S5. Simple sequence repeats (SSRs) distribution in the eleven Seseli plastomes.
DOI: 10.6084/m9.figshare.8981261
title: Additional file 6: of Genome survey and high-resolution backcross genetic linkage map construction of the ridgetail white prawn Exopalaemon carinicauda applications to QTL mapping of growth traits

description: Table S6. Marker information of reverse Backcross linkage map. (XLSX 151 kb)
DOI: 10.6084/m9.figshare.21564137
title: Additional file 10 of The phylogeny of Seseli (Apiaceae, Apioideae): insights from molecular and morphological data

description: Additional file 10: Table S9. Morphological data of the eighteen taxa in Selineae and Echinophoreae involved in this study.
DOI: 10.6084/m9.figshare.8981270.v1
title: Additional file 8: of Genome survey and high-resolution backcross genetic linkage map construction of the ridgetail white prawn Exopalaemon carinicauda applications to QTL mapping of growth traits

description: Table S8. Markers of Backcross linkage map anchored to transcriptome. (XLSX 28 kb)
DOI: 10.21223/lqo3sp
title: Dataset for: Cytological characterization of potato wild relatives collected in Ecuador

description: A total of 91 accessions representing eight wild Solanum species (S. acaule, S. albicans, S. albornozii, S. andreanum, S. chilliasense, S.chomatophilum, S. colombianumand regnum and S. minutifoliolum) collected and preserved at the National Germplasm Bank, INIAP in Ecuador were comprehensive characterized for ploidy level by flow cytometry.
DOI: 10.21223/lqo3sp/8pnj0l
title: 02_Cytological characterization of wild potato_ECU.tab

description: :unav
DOI: 10.6084/m9.figshare.8981237.v1
title: Additional file 2: of Genome survey and high-resolution backcross genetic linkage map construction of the ridgetail white prawn Exopalaemon carinicauda applications to QTL mapping of growth traits

description: Table S2. The predicted genes from the genome survey of E. carinicauda. (XLSX 9232 kb)
DOI: 10.6084/m9.figshare.8981243
title: Additional file 3: of Genome survey and high-resolution backcross genetic linkage map construction of the ridgetail white prawn Exopalaemon carinicauda applications to QTL mapping of growth traits

description: Table S3. The SNP marker number and the read depth of each genotyped marker in the backcross mapping family. (XLSX 15 kb)
DOI: 10.6084/m9.figshare.21564146
title: Additional file 3 of The phylogeny of Seseli (Apiaceae, Apioideae): insights from molecular and morphological data

description: Additional file 3: Table S2. GenBank accession numbers of DNA sequences used in this study. The accession numbers of DNA sequences from our lab were in bold.
DOI: 10.6084/m9.figshare.8981261.v1
title: Additional file 6: of Genome survey and high-resolution backcross genetic linkage map construction of the ridgetail white prawn Exopalaemon carinicauda applications to QTL mapping of growth traits

description: Table S6. Marker information of reverse Backcross linkage map. (XLSX 151 kb)
DOI: 10.6084/m9.figshare.14224170.v1
title: Identification of differentially expressed microRNAs in ovulatory and subordinate follicles in Dazu black goats

description: How multiple ovulations happen in prolific goats is still unknown even though studies on ovarian physiology and folliculogenesis have made extensive progress. MicroRNAs (miRNAs) are a class of endogenous regulatory factors and regulate structural gene expression mainly at the post-transcriptional level. In this study, in the follicular phase, six large follicles were collected from prolific Dazu black goat and used to generate RNA libraries for RNA sequencing. Based on the litter size and average number of ovulatory follicles in Dazu black goats, the largest three follicles were sorted as ovulatory follicles, and the remaining as subordinate ones. In total, 418 known miRNAs and 110 novel miRNAs were found, and the expression of six randomly selected miRNAs was validated by quantitative PCR analysis. Nine miRNAs were differently expressed between the ovulatory and subordinate follicles (<i>p</i> &lt; 0.01). Chi-miR-582-5p, novel-130, chi-miR-214-3p, and chi-miR-500-5p were upregulated in the ovulatory group, and chi-miR-383, chi-miR-130b-5p, chi-miR-92a-3p, chi-miR-125b-5p, and novel-9 were downregulated in the same group. Chi-miR-130b-5p and chi-miR-214-3p were predicted to target at <i>LHR</i> (XM_013967581.1), <i>GDF9</i> (NM_001285708.1), <i>BMP15</i> (NM_001285588.1), and <i>CYP19A1</i> (XM_013967046.1). In conclusion, nine miRNAs were differently expressed between ovulatory and subordinate follicles, and chi-miR-130b-5p and chi-miR-214-3p were predicted to regulate the expression of genes involved in gonadotropin hormone signaling and oocyte-derived growth factors. Additional studies are needed to confirm these findings.
DOI: 10.6084/m9.figshare.21564149.v1
title: Additional file 4 of The phylogeny of Seseli (Apiaceae, Apioideae): insights from molecular and morphological data

description: Additional file 4: Table S3. Gene contents of the eleven Seseli plastomes.
DOI: 10.6084/m9.figshare.8981267.v1
title: Additional file 7: of Genome survey and high-resolution backcross genetic linkage map construction of the ridgetail white prawn Exopalaemon carinicauda applications to QTL mapping of growth traits

description: Table S7. Markers of Backcross linkage map anchored to scaffolds. (XLSX 151 kb)
DOI: 10.6084/m9.figshare.21564158
title: Additional file 7 of The phylogeny of Seseli (Apiaceae, Apioideae): insights from molecular and morphological data

description: Additional file 7: Table S6. Nucleotide diversity (Pi) of coding and non-coding regions.
DOI: 10.6084/m9.figshare.8981279.v1
title: Additional file 9: of Genome survey and high-resolution backcross genetic linkage map construction of the ridgetail white prawn Exopalaemon carinicauda applications to QTL mapping of growth traits

description: Table S9. Markers of reverse Backcross linkage map anchored to scaffolds. (XLSX 227 kb)
DOI: 10.6084/m9.figshare.14224170
title: Identification of differentially expressed microRNAs in ovulatory and subordinate follicles in Dazu black goats

description: How multiple ovulations happen in prolific goats is still unknown even though studies on ovarian physiology and folliculogenesis have made extensive progress. MicroRNAs (miRNAs) are a class of endogenous regulatory factors and regulate structural gene expression mainly at the post-transcriptional level. In this study, in the follicular phase, six large follicles were collected from prolific Dazu black goat and used to generate RNA libraries for RNA sequencing. Based on the litter size and average number of ovulatory follicles in Dazu black goats, the largest three follicles were sorted as ovulatory follicles, and the remaining as subordinate ones. In total, 418 known miRNAs and 110 novel miRNAs were found, and the expression of six randomly selected miRNAs was validated by quantitative PCR analysis. Nine miRNAs were differently expressed between the ovulatory and subordinate follicles (<i>p</i> &lt; 0.01). Chi-miR-582-5p, novel-130, chi-miR-214-3p, and chi-miR-500-5p were upregulated in the ovulatory group, and chi-miR-383, chi-miR-130b-5p, chi-miR-92a-3p, chi-miR-125b-5p, and novel-9 were downregulated in the same group. Chi-miR-130b-5p and chi-miR-214-3p were predicted to target at <i>LHR</i> (XM_013967581.1), <i>GDF9</i> (NM_001285708.1), <i>BMP15</i> (NM_001285588.1), and <i>CYP19A1</i> (XM_013967046.1). In conclusion, nine miRNAs were differently expressed between ovulatory and subordinate follicles, and chi-miR-130b-5p and chi-miR-214-3p were predicted to regulate the expression of genes involved in gonadotropin hormone signaling and oocyte-derived growth factors. Additional studies are needed to confirm these findings.
DOI: 10.6084/m9.figshare.21564132.v1
title: Additional file 2 of Identification of key gene networks related to the freezing resistance of apricot kernel pistils by integrating hormone phenotypes and transcriptome profiles

description: Additional file 2: Table S2. The expression information of genes in the transcriptome of two apricot kernel cultivars.
DOI: 10.6084/m9.figshare.21564138
title: Additional file 4 of Identification of key gene networks related to the freezing resistance of apricot kernel pistils by integrating hormone phenotypes and transcriptome profiles

description: Additional file 4: Table S5. The expression level of DEGs related to plant hormone signaling transduction in two apricot kernel cultivars under freezing stress.
DOI: 10.6084/m9.figshare.21564138.v1
title: Additional file 4 of Identification of key gene networks related to the freezing resistance of apricot kernel pistils by integrating hormone phenotypes and transcriptome profiles

description: Additional file 4: Table S5. The expression level of DEGs related to plant hormone signaling transduction in two apricot kernel cultivars under freezing stress.
DOI: 10.6084/m9.figshare.8981234.v1
title: Additional file 1: of Genome survey and high-resolution backcross genetic linkage map construction of the ridgetail white prawn Exopalaemon carinicauda applications to QTL mapping of growth traits

description: Table S1. Phenotypic data of sequenced individuals from BC1 and reverse BC1 families of E. carinicauda. (XLSX 24 kb)
DOI: 10.6084/m9.figshare.8981243.v1
title: Additional file 3: of Genome survey and high-resolution backcross genetic linkage map construction of the ridgetail white prawn Exopalaemon carinicauda applications to QTL mapping of growth traits

description: Table S3. The SNP marker number and the read depth of each genotyped marker in the backcross mapping family. (XLSX 15 kb)
DOI: 10.6084/m9.figshare.21564132
title: Additional file 2 of Identification of key gene networks related to the freezing resistance of apricot kernel pistils by integrating hormone phenotypes and transcriptome profiles

description: Additional file 2: Table S2. The expression information of genes in the transcriptome of two apricot kernel cultivars.
DOI: 10.6084/m9.figshare.21564135.v1
title: Additional file 3 of Identification of key gene networks related to the freezing resistance of apricot kernel pistils by integrating hormone phenotypes and transcriptome profiles

description: Additional file 3: Table S4. The raw expression information of DEGs in two apricot kernel cultivars under freezing stress.