cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.sq7s3
title: Data from: Auxin steers root cell expansion via apoplastic pH regulation in Arabidopsis thaliana

description: Plant cells are embedded within cell walls, which provide structural
 integrity, but also spatially constrain cells, and must therefore be
 modified to allow cellular expansion. The long-standing acid growth theory
 postulates that auxin triggers apoplast acidification, thereby activating
 cell wall-loosening enzymes that enable cell expansion in shoots.
 Interestingly, this model remains heavily debated in roots, because of
 both the complex role of auxin in plant development as well as technical
 limitations in investigating apoplastic pH at cellular resolution. Here,
 we introduce 8-hydroxypyrene-1,3,6-trisulfonic acid trisodium salt (HPTS)
 as a suitable fluorescent pH indicator for assessing apoplastic pH, and
 thus acid growth, at a cellular resolution in Arabidopsis thaliana roots.
 Using HPTS, we demonstrate that cell wall acidification triggers cellular
 expansion, which is correlated with a preceding increase of auxin
 signaling. Reduction in auxin levels, perception, or signaling abolishes
 both the extracellular acidification and cellular expansion. These
 findings jointly suggest that endogenous auxin controls apoplastic
 acidification and the onset of cellular elongation in roots. In contrast,
 an endogenous or exogenous increase in auxin levels induces a transient
 alkalinization of the extracellular matrix, reducing cellular elongation.
 The receptor-like kinase FERONIA is required for this physiological
 process, which affects cellular root expansion during the gravitropic
 response. These findings pinpoint a complex, presumably
 concentration-dependent role for auxin in apoplastic pH regulation,
 steering the rate of root cell expansion and gravitropic response.
description: Barbez et
 al_2017_quantificationsThis file contains the
 quantifications of all experiments presented in the
 paper.FIGURE
 2raw
 image filesFIGURE
 1raw
 image filesFIGURE
 4raw
 image filesFIGURE
 5raw
 image filesFIGURE
 3raw
 image filesFIGURE-3.zipSI FIGURE S1and S2raw image filesSI_FIGURE_S1_and_S2.zipSI FIGURE S3-2raw image filesSI-FIGURE-S3-2.zipSI FIGURE S5raw image filesSI-FIGURE-S5.zipSI FIGURE S6raw image filesSI-FIGURE-S6.zip
DOI: 10.5061/dryad.81dg9
title: Data from: NGS library preparation may generate artifactual integration sites of AAV vectors

description: [No abstract entered]
description: rAAV_reference_sequencerAAV reference sequence in fasta, genbank and bed formatsFastq_Part1Part 1 of raw fastq dataFASTQ1.zipFastq_part2Part 2 of raw fastq dataFASTQ2.zipControl1_BAM_filesBAM files for Control1 obtained with FindMyVirusControl1.zipControl2_BAM_filesBAM files for Control1 obtained with FindMyVirusControl2.zipMouse1_BAM_FilesBAM files for Mouse1 obtained with FindMyVirusMouse1.zipMouse2_BAM_filesBAM files for Mouse2 obtained with FindMyVirusMouse2.zipMouse3_BAM_filesBAM files for Mouse3 obtained with FindMyVirusMouse3.zipMouse4_BAM_filesBAM files for Mouse4 obtained with FindMyVirusMouse4.zip
DOI: 10.5061/dryad.b9765
title: Data from: Is the Danube crested newt Triturus dobrogicus polytypic? A review and new nuclear DNA data

description: The Danube crested newt Triturus dobrogicus has been proposed to comprise
 two subspecies: T. d. dobrogicus and T. d. macrosoma. Uncertainty exists
 in the literature over their distribution and diagnosability. We conduct a
 multilocus phylogeographical survey and review published data to determine
 whether a two taxon treatment is warranted. Newly produced and published
 nuclear DNA data suggest intraspecific variation in the Pannonian Plain
 part of the range, but with extensive genetic admixture, whereas
 mitochondrial DNA data shows a lack of geographical structuring in T.
 dobrogicus altogether. None of the studied morphological characters
 suggest the presence of two geographical groups in T. dobrogicus
 unequivocally. Although Danube Delta newts do have relatively short bodies
 compared to the remainder of the range (the Pannonian and Lower Danube
 Plains and the Dnepr Delta), we argue that this finding can be explained
 by phenotypic plasticity – particularly in light of the incongruent
 evolutionary scenario suggested by genetic data. We conclude that the
 total body of evidence does not support the two subspecies hypothesis and
 recommend that T. dobrogicus is treated as a monotypic species.
description: Input and output
 files.Input and output files
 for Network, FSTAT, BAPS, TESS and POPTREE.Tdob_input_output.zipIon torrent dataRaw Ion Torrent reads in FASTQ format; scripts associated with the bioinformatics pipeline; BWA alignments in SAM format; raw SNP reports in VCF and BCF format; the filtered SNP report used to construct consensus sequences; an overview of the number of reads in total and per marker and/or individual; nuclear DNA data in genotypic format; nuclear DNA sequence alignments.Tdob_IonTorrent.zip
DOI: 10.5061/dryad.td03h
title: Data from: Estimating colony sizes of emerging bats using acoustic recordings

description: The decline of bats demands more widespread monitoring of populations for
 conservation and management. Current censusing methods are either prone to
 bias or require costly equipment. Here, we report a new method using
 passive acoustics to determine bat count census from overall acoustic
 amplitude of the emerging bat stream. We recorded the video and audio of
 an emerging colony of Mexican free-tailed bats from two cave locations
 across multiple nights. Instantaneous bat counts were calculated from the
 video frames, and the bat stream’s acoustic amplitude corresponding to
 each video frame was determined using three different methods for
 calculating acoustic intensity. We found a significant link between all
 three acoustic parameters and bat count, with the highest R2 of 0.742
 linking RMS pressure and bat count. Additionally, the relationship between
 acoustics and population size at one cave location could accurately
 predict the population size at another cave location. The data were
 gathered with low-cost, easy-to-operate equipment, and the data analysis
 can be easily accomplished using automated scripts or with open-source
 acoustic software. These results are a potential first step towards
 creating an acoustic model to estimate bat population at large cave
 colonies worldwide.
description: North_Video_FramesVideo frames for the North Cave, grouped into folders by dayNorth_Acoustic_Files_aNorth Cave Acoustic Files: First half of experimental daysNorth_Acoustic_Files_bNorth Cave Acoustic Files: Second Half of Experimental DaysSouth_Video_FramesVideo frames for the South Cave, grouped into folders by daySouth_Acoustic_Data_aSouth Cave Acoustic Files: First half of experimental daysSouth_Acoustic_Data_bSouth Cave Acoustic Files: Second half of experimental daysData File InformationInformation about the data
DOI: 10.5061/dryad.84d4j
title: Data from: De novo sequencing and variant calling with nanopores using PoreSeq

description: The accuracy of sequencing single DNA molecules with nanopores is
 continually improving, but de novo genome sequencing and assembly using
 only nanopore data remain challenging. Here we describe PoreSeq, an
 algorithm that identifies and corrects errors in nanopore sequencing data
 and improves the accuracy of de novo genome assembly with increasing
 coverage depth. The approach relies on modeling the possible sources of
 uncertainty that occur as DNA transits through the nanopore and finds the
 sequence that best explains multiple reads of the same region. PoreSeq
 increases nanopore sequencing read accuracy of M13 bacteriophage DNA from
 85% to 99% at 100× coverage. We also use the algorithm to assemble
 Escherichia coli with 30× coverage and the λ genome at a range of
 coverages from 3× to 50×. Additionally, we classify sequence variants at
 an order of magnitude lower coverage than is possible with existing
 methods.
description: M13 sequencing run, part
 1PORESEQ_M13.zipM13 sequencing run, part 2PORESEQ_M13.z01Lambda sequencing run, part 1PORESEQ_LAMBDA.zipLambda sequencing run, part 2PORESEQ_LAMBDA.z01DNA_CS sequencing runPORESEQ_DNA_CS.zipOriginal submission codePORESEQ_CODE.zip
DOI: 10.5061/dryad.j05n0
title: Data from: Identifying pathogenicity of human variants via paralog-based yeast complementation

description: To better understand the health implications of personal genomes, we now
 face a largely unmet challenge to identify functional variants within
 disease-associated genes. Functional variants can be identified by
 trans-species complementation, e.g., by failure to rescue a yeast strain
 bearing a mutation in an orthologous human gene. Although orthologous
 complementation assays are powerful predictors of pathogenic variation,
 they are available for only a few percent of human disease genes. Here we
 systematically examine the question of whether complementation assays
 based on paralogy relationships can expand the number of human disease
 genes with functional variant detection assays. We tested over 1,000
 paralogous human-yeast gene pairs for complementation, yielding 34
 complementation relationships, of which 33 (97%) were novel. We found that
 paralog-based assays identified disease variants with success on par with
 that of orthology-based assays. Combining all homology-based assay
 results, we found that complementation can often identify pathogenic
 variants outside the homologous sequence region, presumably because of
 global effects on protein folding or stability. Within our search space,
 paralogy-based complementation more than doubled the number of human
 disease genes with a yeast-based complementation assay for disease
 variation.
description: Negative
 ResultsThis data include all
 the functional complementation assay pictures showing negative
 results.Negative_Results.zip
DOI: 10.5061/dryad.8723t
title: Data from: Effective polyploidy causes phenotypic delay and influences bacterial evolvability

description: Whether mutations in bacteria exhibit a noticeable delay before expressing
 their corresponding mutant phenotype was discussed intensively in the
 1940s to 1950s, but the discussion eventually waned for lack of supportive
 evidence and perceived incompatibility with observed mutant distributions
 in fluctuation tests. Phenotypic delay in bacteria is widely assumed to be
 negligible, despite the lack of direct evidence. Here, we revisited the
 question using recombineering to introduce antibiotic resistance mutations
 into E. coli at defined time points and then tracking expression of the
 corresponding mutant phenotype over time. Contrary to previous
 assumptions, we found a substantial median phenotypic delay of three to
 four generations. We provided evidence that the primary source of this
 delay is multifork replication causing cells to be effectively polyploid,
 whereby wild-type gene copies transiently mask the phenotype of recessive
 mutant gene copies in the same cell. Using modeling and simulation
 methods, we explored the consequences of effective polyploidy for mutation
 rate estimation by fluctuation tests and sequencing-based methods. For
 recessive mutations, despite the substantial phenotypic delay, the
 per-copy or per-genome mutation rate is accurately estimated. However, the
 per-cell rate cannot be estimated by existing methods. Finally, with a
 mathematical model, we showed that effective polyploidy increases the
 frequency of costly recessive mutations in the standing genetic variation
 (SGV), and thus their potential contribution to evolutionary adaptation,
 while drastically reducing the chance that de novo recessive mutations can
 rescue populations facing a harsh environmental change such as antibiotic
 treatment. Overall, we have identified phenotypic delay and effective
 polyploidy as previously overlooked but essential components in bacterial
 evolvability, including antibiotic resistance evolution.
description: Microscopy data - Part
 1Zipped microscopy data
 split by Mac OS, 8 parts in total.xaaMicroscopy data - Part 2Zipped microscopy data split by Mac OS, 8 parts in total.xabMicroscopy data - Part 3Zipped microscopy data split by Mac OS, 8 parts in total.xacMicroscopy data - Part 4Zipped microscopy data split by Mac OS, 8 parts in total.xadMicroscopy data - Part 5Zipped microscopy data split by Mac OS, 8 parts in total.xaeMicroscopy data - Part 6Zipped microscopy data split by Mac OS, 8 parts in total.xafMicroscopy data - Part 7Zipped microscopy data split by Mac OS, 8 parts in total.xagMicroscopy data - Part 8Zipped microscopy data split by Mac OS, 8 parts in total.xahCode and simulation dataZipped folder with code and simulation data.code and sim data for deposit.zipREADME_computer_codeThis file describes how to use the deposited code and simulation data to reproduce the manuscript figures.
DOI: 10.5061/dryad.1m1hg
title: Data from: The Carpathians hosted extra-Mediterranean refugia-within-refugia during the Pleistocene Ice Age: genomic evidence from two newt genera

description: Part of Europe’s temperate species survived the Pleistocene glacial cycles
 in refugia north of the Mediterranean peninsulas. For one such
 extra-Mediterranean refugia, the Carpathians, an intricate
 ‘refugia-within-refugia’ scenario has been suggested, involving species
 surviving in multiple discrete glacial refugia. We test the Carpathian
 refugia-within-refugia hypothesis, employing genome-wide multilocus data
 sets for two newt species (Triturus cristatus and Lissotriton montandoni).
 We first use Bayesian clustering to delineate intraspecific evolutionary
 lineages. The number of intraspecific lineages identified, and the
 allocation of localities to these lineages, were used to construct
 testable hypotheses on the spatial arrangement of glacial refugia in both
 newt species. Next we employ approximate Bayesian computation to date
 whether these lineages are of Holocene (&lt; 12 Ka) or Pleistocene
 (&gt; 12 Ka) origin. We identify three intraspecific evolutionary
 lineages for T. cristatus and two for L. montandoni. For both newt
 species, intraspecific divergence is rooted in the Pleistocene, in line
 with species survival in distinct range fragments during the last glacial
 period. Hence, our findings firmly support the Carpathian
 refugia-within-refugia hypothesis. Furthermore, we show that mitochondrial
 DNA overestimates the age of intraspecific evolutionary lineages and we
 urge caution in basing refugia-within-refugia scenarios on mitochondrial
 DNA alone.
description: LocalitiesThe localities as a kmz file.Locs_kmz.zipScripts for Lissotriton montandoniThe scripts used for Lissotriton montandoni.Lm_scripts.zipABC analysisFiles associated with the ABC analysis.ABCanalysis.zipIon Torrent processed output, alignments and scriptsThe Ion Torrent processed output, alignments and scripts for Triturus cristatus.Ion_Torrent_processed_output_alignments_scripts.zipIon Torrent unprocessed AUnprocessed Ion Torrent data for Triturus cristatus part A.Ion_Torrent_raw_output_A.zipIon Torrent unprocessed BUnprocessed Ion Torrent data for Triturus cristatus part B.Ion_Torrent_raw_output_B.zipIon Torrent filtered AFiltered Ion Torrent data for Triturus cristatus part A.Ion_Torrent_filtered_output_A.zipIon Torrent filtered BFiltered Ion Torrent data for Triturus cristatus part B.Ion_Torrent_filtered_output_B.zipIon Torrent filtered C.Filtered Ion Torrent data for Triturus cristatus part C.Ion_Torrent_filtered_output_C.zipStructure analysesFiles associated with the Structure analyses.Structure_Clumpak.zip
DOI: 10.5061/dryad.5r774
title: Data from: The genetic basis for ecological adaptation of the Atlantic herring revealed by genome sequencing

description: Ecological adaptation is of major relevance to speciation and sustainable
 population management, but the underlying genetic factors are typically
 hard to study in natural populations due to genetic differentiation caused
 by natural selection being confounded with genetic drift in subdivided
 populations. Here, we use whole genome population sequencing of Atlantic
 and Baltic herring to reveal the underlying genetic architecture at an
 unprecedented detailed resolution for both adaptation to a new niche
 environment and timing of reproduction. We identify almost 500 independent
 loci associated with a recent niche expansion from marine (Atlantic Ocean)
 to brackish waters (Baltic Sea), and more than 100 independent loci
 showing genetic differentiation between spring- and autumn-spawning
 populations irrespective of geographic origin. Our results show that both
 coding and non-coding changes contribute to adaptation. Haplotype blocks,
 often spanning multiple genes and maintained by selection, are associated
 with genetic differentiation.
description: cluhar_rc6_codingGene_GOonGene.gffIndividual.GATK.filtered.only.SNPs.vcfPool_20.filtered.vcf
DOI: 10.5061/dryad.222j0
title: Data from: Brazilian sugarcane ethanol as an expandable green alternative to crude oil use

description: Reduction of CO2 emissions will require a transition from fossil fuels to
 alternative energy sources. Expansion of Brazilian sugarcane ethanol1, 2
 provides one near-term scalable solution to reduce CO2 emissions from the
 global transport sector. In contrast to corn ethanol, the Brazilian
 sugarcane ethanol system may offset 86% of CO2 emissions compared to oil
 use, and emissions resulting from land-use change to sugarcane are paid
 back in just 2–8 years3, 4. But, it has been uncertain how much further
 expansion is possible given increasing demand for food and animal feed,
 climate change impacts and protection of natural ecosystems. We show that
 Brazilian sugarcane ethanol can provide the equivalent of
 3.63–12.77 Mb d−1 of crude oil by 2045 under projected climate change
 while protecting forests under conservation5 and accounting for future
 land demand for food and animal feed production. The corresponding range
 of CO2 offsets is 0.55–2.0 Gigatons yr−1. This would displace 3.8–13.7% of
 crude oil consumption and 1.5–5.6% of net CO2 emission globally relative
 to data for 20146, 7.
description: Estimates of Land Area
 for Sugarcane Expansion in BrazilThis is a zipped
 shapefile with data on land area for 557 microregions of
 Brazillandavailability.zipSugarcane yield and production projection in Brazilzipped file contains four different shapefiles. One is for sugarcane yield projection under historical and future projection of climate in Brazil. Remaining three shapefiles correspond to production or delivery of biomass at the mill under the three different land use scenarios.yield_and_production.zipAnalyses in RThis folder provides codes, inputs, and output data and output Figures which were generated during this study.analyses.zipGitHub djaiswal/SugarcaneBrazillR packages required for running the analyses
DOI: 10.5061/dryad.706df
title: Data from: Revision of Icacinaceae from the Early Eocene London Clay flora based on X-ray micro-CT

description: The Early Eocene (Ypresian) London Clay Formation contains one of the most
 important fruit and seed assemblages from the Paleogene, including a large
 diversity of taxa (&gt;350 spp.) preserved as pyrite
 permineralizations retaining 3D structure as well as anatomical detail.
 Despite the importance of the flora for understanding angiosperm
 biogeographic and evolutionary history, the majority of the fossil
 material has not been revisited since the original taxonomic treatments by
 E.M. Reid and M.E.J. Chandler. Given subsequent advances in our
 understanding of angiosperm phylogeny and fruit morphology, coupled with
 technological advances in imaging/visualizing fossil material, many of the
 taxa represented in the flora deserve further study. Here we present a
 revision of the pantropical family Icacinaceae using X-ray micro-computed
 tomography (micro-CT) images of 21 species from the flora. Based on the
 results, four new combinations are made, a new fossil-genus is established
 for a distinctive species with affinities to the Phytocreneae, and emended
 diagnoses are provided for eight taxa. Of the seven genera recognized from
 the flora, only one, Iodes Blume, is extant. This study offers important
 insights on the biogeographic and evolutionary history of Icacinaceae,
 which is one of the most abundant and diverse components of the flora from
 the London Clay Formation.
description: CT scans of Icacinaceae
 fossils: Faboidea and PalaeophytocreneX-Ray micro-CT scans of
 Faboidea and Palaeophytocrene fossils (Icacinaceae) from the Early Eocene
 London Clay floraFab_Palaeo.zipCT scans of Icacinaceae fossils: Icacinicarya spp. 1X-ray micro-CT scans of Icacinicarya spp. (Icacinaceae) from the Early Eocene London Clay floraIcacinicarya_1.zipCT scans of Icacinaceae fossils: Icacinicarya spp. 2X-ray micro-CT scans of Icacinicarya fossils (Icacinaceae) from the Early Eocene London Clay floraIcacinicarya_2.zipCT scans of Icacinaceae fossils: Iodes spp. 1X-ray micro-CT scans of Iodes fossil (Icacinaceae) from the Early Eocene London Clay floraIodes_1.zipCT scans of Icacinaceae fossils: Iodes spp. 2X-ray micro-CT scans of Iodes fossils (Icacinaceae) from the Early Eocene London Clay floraIodes_2.zipCT scans of Icacinaceae fossils: Spaeriodes and StizocaryaX-ray micro-CT scans of Spaeriodes and Stizocarya fossils (Icacinaceae) from the Early Eocene London Clay floraSphaer_Stizo.zip
DOI: 10.5061/dryad.9mq14
title: Data from: BrAD-seq: Breath Adapter Directional sequencing: a streamlined, ultra-simple and fast library preparation protocol for strand specific mRNA library construction

description: Next Generation Sequencing (NGS) is driving rapid advancement in
 biological understanding and RNA-sequencing (RNA-seq) has become an
 indispensable tool for biology and medicine. There is a growing need for
 access to these technologies although preparation of NGS libraries remains
 a bottleneck to wider adoption. Here we report a novel method for the
 production of strand specific RNA-seq libraries utilizing inherent
 properties of double-stranded cDNA to capture and incorporate a sequencing
 adapter. Breath Adapter Directional sequencing (BrAD-seq) reduces sample
 handling and requires far fewer enzymatic steps than most available
 methods to produce high quality strand-specific RNA-seq libraries. The
 method we present is optimized for 3-prime Digital Gene Expression (DGE)
 libraries and can easily extend to full transcript coverage shotgun (SHO)
 type strand-specific libraries and is modularized to accommodate a
 diversity of RNA and DNA input materials. BrAD-seq offers a highly
 streamlined and inexpensive option for RNA-seq libraries.
description: SHO.FQ.tar.gzCompressed file containing Tomato RNA-seq reads from BrAD-seq shotgun (SHO) type strand-specific libraries (SHO_22.fastq, SHO_23.fastq, SHO_24.fastq).S_HTR.FQ.tar.gzCompressed file containing Tomato SAM RNA-seq reads from HTR-method libraries (S_HTR_A5.fastq, S_HTR_A6.fastq, S_HTR_B6.fastq, S_HTR_B7.fastq)L_HTR.FQ.tar.gzCompressed file containing Tomato leaf RNA-seq reads from HTR-method libraries (L_HTR_A4.fastq, L_HTR_B5.fastq, L_HTR_C6.fastq, L_HTR_D7.fastq)L_DGE.FQ2.tar.gzCompressed file containing Tomato leaf RNA-seq reads from BrAd-seq DGE libraries (L_DGE_E7.fastq, L_DGE_E8.fastq, L_DGE_F1.fastq)S_DGE.FQ1.tar.gzCompressed file containing Tomato SAM RNA-seq reads from BrAd-seq DGE libraries (S_DGE_A5.fastq, S_DGE_A6.fastq, S_DGE_B7.fastq, S_DGE_C7.fastq)L_DGE.FQ1.tar.gzCompressed file containing Tomato leaf RNA-seq reads from BrAd-seq DGE libraries (L_DGE_B5.fastq, L_DGE_C6.fastq, L_DGE_D7.fastq)S_DGE.FQ2.tar.gzCompressed file containing Tomato SAM RNA-seq reads from BrAd-seq DGE libraries (S_DGE_D8.fastq, S_DGE_E1.fastq, S_DGE_F2.fastq)READMELinks to detailed information regarding (1) sample and library preparation and (2) bioinformatic methods