cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.34636/dmportal/poknhd/obsh41
title: Table S9.docx

description: Gene Set Enrichment Analysis (GSEA) of differentially expressed genes (DEGs), considering the effect of eCO2 in Icatu and CL153, performed with WEB-based Gene SeT AnaLysis Toolkit (WebGestalt). Significantly enriched Gene Ontology (GO) terms from each category – Biological Process (BP), Molecular Function (MF) and Cellular Component (CC). Values indicate the number of DEGs annotated with each term and pathway (Counts), normalized enrichment scores (NES), p-value and False Discovery Rate (FDR 0.05; p 0.001).
DOI: 10.34636/dmportal/poknhd/sh8gtk
title: Figure S1.pdf

description: Principal component (PC) analysis of the raw reads generated by RNA-sequencing with (A) and without replicate 1C (B).
DOI: 10.34636/dmportal/poknhd/yf8wxz
title: Table S5.tab

description: List of down- and up-regulated CL153 DEGs when comparing to Icatu, at aCO2 with gene identification, protein name and fold-change (FC) values. Genes are sorted by fold-change in descending order.
DOI: 10.34636/dmportal/poknhd/d4sv6a
title: Table S4.tab

description: List of down- and up-regulated CL153 DEGs at eCO2 vs. aCO2 with gene identification, protein name and fold-change (FC) values.
DOI: 10.34636/dmportal/poknhd/w8x09x
title: Table S11.docx

description: Icatu and CL153 photosynthetic-related responsive DEGs to eCO2 . The searched GO-terms included: “Photosynthesis”, “Chlorophyll metabolic process”, “Ribulose-bisphosphate carboxylase activity”, “Antioxidant activity”, “Lipid metabolic process (LOX, FAD)”, “Cellular respiration”, “Malate dehydrogenase activity”, and “Pyruvate kinase activity”. Gene and protein annotation, main function(s) retrieved from UniprotKB, and respective fold-change. Blue indicates up-regulation and yellow indicates down-regulation.
DOI: 10.34636/dmportal/poknhd
title: Transcriptomic Leaf Profiling Reveals Differential Responses of the Two Most Traded Coffee Species to Elevated [CO2]

description: As atmospheric [CO2] continues to rise to unprecedented levels, understanding its impact on plants is imperative to improve crop performance and sustainability under future climate conditions. In this context, transcriptional changes promoted by elevated CO2 (eCO2) were studied in genotypes from the two major traded coffee species: the allopolyploid Coffea arabica (Icatu) and its diploid parent, C. canephora (CL153). While Icatu expressed more genes than CL153, a higher number of differentially expressed genes were found in CL153 as a response to eCO2. Although many genes were found to be commonly expressed by the two genotypes under eCO2, unique genes and pathways differed between them, with CL153 showing more enriched GO terms and metabolic pathways than Icatu. Divergent functional categories and significantly enriched pathways were found in these genotypes, which altogether supports contrasting responses to eCO2. A considerable number of genes linked to coffee physiological and biochemical responses were found to be affected by eCO2 with the significant upregulation of photosynthetic, antioxidant, and lipidic genes. This supports the absence of photosynthesis down-regulation and, therefore, the maintenance of increased photosynthetic potential promoted by eCO2 in these coffee genotypes.
DOI: 10.6084/m9.figshare.13177100
title: Faunal engineering stimulates landscape-scale accretion in southeastern US salt marshes

description: Data from "Faunal engineering stimulates landscape-scale accretion in southeastern US salt marshes" manuscript
DOI: 10.6084/m9.figshare.13177100.v4
title: Faunal engineering stimulates landscape-scale accretion in southeastern US salt marshes

description: Data from "Faunal engineering stimulates landscape-scale accretion in southeastern US salt marshes" manuscript
DOI: 10.6084/m9.figshare.13177100.v3
title: Faunal engineering stimulates landscape-scale accretion in southeastern US salt marshes

description: Data from "Faunal engineering stimulates landscape-scale accretion in southeastern US salt marshes" manuscript
DOI: 10.5281/zenodo.6668747
title: Small version of 01-08-22 OAS

description: Small version of OAS from 1st of August 2022. Size was reduced by removing sequences seen less than three times and sequences with unknown residues.
DOI: 10.5281/zenodo.7079547
title: Small version of 01-08-22 OAS

description: Small version of OAS from 1st of August 2022. Size was reduced by removing sequences seen less than three times and sequences with unknown residues.
DOI: 10.5281/zenodo.6668746
title: Small and tiny version of 11-01-23 OAS

description: Small and tiny version of OAS from September 2022. For the small version, size was reduced by removing sequences seen less than five times (previous versions used three times) and sequences with unknown residues. For the tiny version, starting from the small version, sequences missing residues at the first IMGT position was removed. Lastly, only one record was kept for identical sequences in the tiny version.
DOI: 10.5281/zenodo.7384311
title: Small and tiny version of 01-09-22 OAS

description: Small and tiny version of OAS from September 2022. For the small version, size was reduced by removing sequences seen less than three times and sequences with unknown residues. For the tiny version, starting from the small version, sequences missing residues at the first IMGT position was removed. Lastly, only one record was kept for identical sequences in the tiny version.
DOI: 10.5281/zenodo.7562025
title: Small and tiny version of 11-01-23 OAS

description: Small and tiny version of OAS from September 2022. For the small version, size was reduced by removing sequences seen less than five times (previous versions used three times) and sequences with unknown residues. For the tiny version, starting from the small version, sequences missing residues at the first IMGT position was removed. Lastly, only one record was kept for identical sequences in the tiny version.
DOI: 10.34636/dmportal/8x1xzb/jj98kg
title: Table_S9.pdf

description: Regulation pattern among differentially expressed genes (DEGs) related to catalytic activities, between plants of Coffea canephora cv. Conilon Clone CL153 (CL153) and C. arabica cv. Icatu (Icatu) submitted to moderate water deficit (MWD) and severe water deficit (SWD), relative to the control of well-watered (WW) plants. DEGs were selected if annotated with the Gene Ontology (GO) terms “phosphatase activity” (GO:0016791) and “protein kinase activity” (GO:0004672), or any of its respective child terms. Red rrepresents up-regulated DEGs and, blue represents down-regulated DEGs.
DOI: 10.34636/dmportal/8x1xzb/09zpag
title: Table_S5.tab

description: Full list of differentially expressed genes (DEGs) Coffea arabica cv. Icatu (Icatu) found between moderate water deficit (MWD) vs. well-watered (WW) plants. Gene identification and protein name according to Coffea canephora functional annotation retrieved from the Coffee Genome Hub (http://coffee-genome.org: 4 January 2020). DEGs were selected with DESeq2 and filtered by log2 fold change (FC) 6= 0 and false discovery rate (FDR) 0.01.
DOI: 10.34636/dmportal/8x1xzb/y0qj1n
title: Figure_S1.pdf

description: Principal component (PC) analysis of all log transformed gene expression data from Coffea canephora cv. Conilon Clone CL153 (CL153) and C. arabica cv. Icatu (Icatu) plants submitted to three different water availability conditions: well-watered (WW), moderate water deficit (MWD), and severe water deficit (SWD). A, B, C, D, and E correspond to biological replications. Each treatment is represented by the colors depicted in Figure 1 and contains three biological replicates, depicted in Table S1. The percentage of variance is indicated in each axis.
DOI: 10.34636/dmportal/8x1xzb/34by99
title: Table_S3.tab

description: Full list of differentially expressed genes (DEGs) in C. canephora cv. CL153 (CL153) found between moderate water deficit (MWD) vs. well-watered (WW) plants. Gene identification and protein name according to Coffea canephora functional annotation retrieved from the Coffee Genome Hub (http://coffee-genome.org: 4 January 2020). DEGs were selected with DESeq2 and filtered by log2 fold change (FC) 6= 0 and false discovery rate (FDR) 0.01.
DOI: 10.34636/dmportal/8x1xzb/9ttdrj
title: Table_S2.pdf

description: Number of total expressed genes, total differentially expressed genes (DEGs), and GO annotated DEGs in Coffea canephora cv. CL153 (CL153) and C. arabica cv. Icatu (Icatu) plants submitted to three different water availability conditions: well-watered (WW), moderate water deficit (MWD), and severe water deficit (SWD). DEGs represent the number of significant genes found to be differently expressed between each water treatment and the control (MWD vs. WW and SWD vs. WW, respectively), selected by DESeq2 and filtered by log2 fold change (FC) 6= 0 and a false discovery rate (FDR) 0.01.
DOI: 10.34636/dmportal/8x1xzb/gvdwr8
title: Table_S7.pdf

description: Regulation pattern of among differentially expressed genes (DEGs) related to photosynthesis and biochemical processes in plants of Coffea canephora cv. Conilon Clone CL153 (CL153) and C. arabica cv. Icatu (Icatu) submitted to moderate water deficit (MWD) and severe water deficit (SWD) relative to the control, well-watered (WW) plants. DEGs were selected if annotated with the direct or respective child Gene Ontology (GO) terms: “antioxidant activity” (GO:0016209) and “response to oxidative stress” (GO:0006979) under Antioxidant activity; “cellular respiration” (GO:0045333), “mitochondrion” (GO:0005739), “malate dehydrogenase activity” (GO:0016615), “pyruvate kinase activity” (GO:0004743) under Cellular respiration; “fatty acid metabolic process” (GO:0006631), LOX (GO:0004051, GO:0016702) under Lipid metabolism; and “photosynthesis” (GO:0015979), “photosystem” (GO:0009521), “photosynthetic electron transport chain” (GO:0009767), “photorespiration” GO:0009853) and “chlorophyll biosynthetic process” (GO:0015995) under hotosynthesis. Red represents up-regulated DEGs, and blue represent down-regulated DEGs.
DOI: 10.34636/dmportal/8x1xzb/nn1n0u
title: Table_S6.tab

description: Full list of differentially expressed genes (DEGs) in Coffea arabica cv. Icatu (Icatu) found between severe water deficit (SWD) vs. well-watered (WW) plants. Gene identification and protein name according to Coffea canephora functional annotation retrieved from the Coffee Genome Hub (http://coffee-genome.org: 4 January 2020). DEGs were selected with DESeq2 and filtered by log2 fold change (FC) 6= 0 and false discovery rate (FDR) 0.01.
DOI: 10.34636/dmportal/8x1xzb/jjigdk
title: Table_S4.tab

description: Full list of differentially expressed genes (DEGs) in C. canephora cv. CL153 (CL153) found between severe water deficit (SWD) vs. well-watered (WW) plants. Gene identification and protein name according to Coffea canephora functional annotation retrieved from the Coffee Genome Hub (http://coffee-genome.org: 4 January 2020). DEGs were selected with DESeq2 and filtered by log2 fold change (FC) 6= 0 and false discovery rate (FDR) 0.01.
DOI: 10.34636/dmportal/8x1xzb/tvic7f
title: Table_S8.pdf

description: Regulation pattern of transcription factors (TFs) found among differentially expressed genes (DEGs) in plants of Coffea canephora cv. Conilon Clone CL153 (CL153) and C. arabica cv. Icatu (Icatu) submitted to either moderate water deficit (MWD) or severe water deficit (SWD) in relation to well-watered (WW) plants. DEGs were selected if annotated with the Gene Ontology (GO) term “DNA-binding transcription factor” (GO:0003700). Red represents up-regulated DEGs, and blue represents down-regulated DEGs.
DOI: 10.34636/dmportal/8x1xzb/ke3ohq
title: Figure_S3.pdf

description: Clustered heat map and dendrogram of the differentially expressed genes (DEGs) associated with drought, in plants of Coffea arabica cv. Icatu (Icatu) and C. canephora cv. Conilon Clone CL153 (CL153) submitted to either moderate water deficit (MWD) or severe water deficit (SWD) in relation to well-watered (WW) plants. DEGs were selected if annotated with the Gene Ontology (GO) terms “response to water deprivation” (GO:0009414) and “response to desiccation” (GO:0009269). Hot colors represent up-regulated DEGs, and cold colors represent down-regulated DEGs. Numbers in the right column indicate the chromosome of the retrieved DEGs.
DOI: 10.34636/dmportal/8x1xzb/p2ixrg
title: Figure_S2.pdf

description: The effect of moderate (MWD) and severe (SWD) water deficit on the number of up- and down-regulated DEGs in plants of Coffea canephora cv. Conilon Clone CL153 (CL153) and C. arabica cv. Icatu (Icatu).
DOI: 10.34636/dmportal/8x1xzb/sw5as9
title: Table_S1.pdf

description: Summary of sequencing and mapping of reads from Coffea canephora cv. CL153 (CL153) and C. arabica cv. Icatu (Icatu) samples. A, B, C, D, and E correspond to biological replications. Plants were grown in two different stress water conditions, mild water deficit (MWD) and severe water deficit (SWD) and the control well-watered plants (WW). RAW READS: number of reads obtained after sequencing. CLEAN READS: number of reads passing the Illumina quality filters and downstream filters. CLEAN %: percentage of reads passing filters compared to the number of raw reads. UNIQUE: number of reads aligned to a unique position. UNIQUE %: proportion of reads aligned to a unique position compared to the number of clean reads. MULTIPLE MAP: number of reads aligned to exons of several overlapping genes. MULTIPLE MAP %: proportion of reads aligned to exons of several overlapping genes compared to the number of clean reads. UNMAPPED %: proportion of non-aligning reads compared to the number of clean reads.
DOI: 10.34636/dmportal/8x1xzb
title: Understanding the Impact of Drought in Coffea Genotypes: Transcriptomic Analysis Supports a Common High Resilience to Moderate Water Deficit but a Genotype Dependent Sensitivity to Severe Water Deficit

description: Water scarcity is the most significant factor limiting coffee production, although some cultivars can still have important drought tolerance. This study analyzed leaf transcriptomes of two coffee cultivars with contrasting physiological responses, Coffea canephora cv. CL153 and Coffea. arabica cv. Icatu, subjected to moderate (MWD) or severe water deficits (SWD). We found that MWD had a low impact compared with SWD, where 10% of all genes in Icatu and 17% in CL153 reacted to drought, being mainly down-regulated upon stress. Drought triggered a genotype-specific response involving the up-regulation of reticuline oxidase genes in CL153 and heat shock proteins in Icatu. Responsiveness to drought also included desiccation protectant genes, but primarily, aspartic proteases, especially in CL153. A total of 83 Transcription Factors were found engaged in response to drought, mainly up-regulated, especially under SWD. Together with the enrollment of 49 phosphatases and 272 protein kinases, results suggest the involvement of ABA-signaling processes in drought acclimation. The integration of these findings with complementing physiological and biochemical studies reveals that both genotypes are more resilient to moderate drought than previously thought and suggests the existence of post-transcriptional mechanisms modulating the response to drought.
DOI: 10.5517/ccdc.csd.cc20rpdw
title: CCDC 1869808: Experimental Crystal Structure Determination

description: Related Article: Justin B. Diccianni, Chunhua T. Hu, Tianning Diao|2019|Angew.Chem.,Int.Ed.|58|13865|doi:10.1002/anie.201906005
description: Related Article: Justin B. Diccianni,  Joseph Katigbak,  Chunhua Hu,  Tianning Diao|2019|J.Am.Chem.Soc.|141|1788|doi:10.1021/jacs.8b13499
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc21jkkq
title: CCDC 1892753: Experimental Crystal Structure Determination

description: Related Article: He Huang, Zack M. Strater, Michael Rauch, James Shee, Thomas J. Sisto, Colin Nuckolls, Tristan H. Lamb|2019|Angew.Chem.,Int.Ed.|58|13318|doi:10.1002/anie.201906381
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc20rpgy
title: CCDC 1869810: Experimental Crystal Structure Determination

description: Related Article: Justin B. Diccianni, Chunhua T. Hu, Tianning Diao|2019|Angew.Chem.,Int.Ed.|58|13865|doi:10.1002/anie.201906005
description: Related Article: Justin B. Diccianni,  Joseph Katigbak,  Chunhua Hu,  Tianning Diao|2019|J.Am.Chem.Soc.|141|1788|doi:10.1021/jacs.8b13499
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc20rphz
title: CCDC 1869811: Experimental Crystal Structure Determination

description: Related Article: Justin B. Diccianni, Chunhua T. Hu, Tianning Diao|2019|Angew.Chem.,Int.Ed.|58|13865|doi:10.1002/anie.201906005
description: Related Article: Justin B. Diccianni,  Joseph Katigbak,  Chunhua Hu,  Tianning Diao|2019|J.Am.Chem.Soc.|141|1788|doi:10.1021/jacs.8b13499
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc229wfq
title: CCDC 1916123: Experimental Crystal Structure Determination

description: Related Article: Justin B. Diccianni, Chunhua T. Hu, Tianning Diao|2019|Angew.Chem.,Int.Ed.|58|13865|doi:10.1002/anie.201906005
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc229wgr
title: CCDC 1916124: Experimental Crystal Structure Determination

description: Related Article: Justin B. Diccianni, Chunhua T. Hu, Tianning Diao|2019|Angew.Chem.,Int.Ed.|58|13865|doi:10.1002/anie.201906005
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc229whs
title: CCDC 1916125: Experimental Crystal Structure Determination

description: Related Article: Justin B. Diccianni, Chunhua T. Hu, Tianning Diao|2019|Angew.Chem.,Int.Ed.|58|13865|doi:10.1002/anie.201906005
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc229wjt
title: CCDC 1916126: Experimental Crystal Structure Determination

description: Related Article: Justin B. Diccianni, Chunhua T. Hu, Tianning Diao|2019|Angew.Chem.,Int.Ed.|58|13865|doi:10.1002/anie.201906005
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc229wkv
title: CCDC 1916127: Experimental Crystal Structure Determination

description: Related Article: Justin B. Diccianni, Chunhua T. Hu, Tianning Diao|2019|Angew.Chem.,Int.Ed.|58|13865|doi:10.1002/anie.201906005
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc22bk22
title: CCDC 1916763: Experimental Crystal Structure Determination

description: Related Article: Guillaume Bélanger-Chabot, Holger Braunschweig|2019|Angew.Chem.,Int.Ed.|58|14270|doi:10.1002/anie.201906666
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc229wlw
title: CCDC 1916128: Experimental Crystal Structure Determination

description: Related Article: Justin B. Diccianni, Chunhua T. Hu, Tianning Diao|2019|Angew.Chem.,Int.Ed.|58|13865|doi:10.1002/anie.201906005
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc22bk33
title: CCDC 1916764: Experimental Crystal Structure Determination

description: Related Article: Guillaume Bélanger-Chabot, Holger Braunschweig|2019|Angew.Chem.,Int.Ed.|58|14270|doi:10.1002/anie.201906666
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc22bk44
title: CCDC 1916765: Experimental Crystal Structure Determination

description: Related Article: Guillaume Bélanger-Chabot, Holger Braunschweig|2019|Angew.Chem.,Int.Ed.|58|14270|doi:10.1002/anie.201906666
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.