cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.57907/mirri/zysavh
title: MIRRI0075888

description: Organism type: Filamentous Fungi ; Taxon name: Ramularia miae ; Collection: CBS 120121 ; Country: South Africa
DOI: 10.15468/dl.783b9x
title: Occurrence Download

description: A dataset containing 322026 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Saxicola caprata)",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 "License is one of (CC-BY 4.0, CC0 1.0)"
 ]
}

 The dataset includes 322026 records from 34 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0067431-250717081556266/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.3535/vh5-a8g-0ra
title: Teucrium polium L.

description: Digital Specimen for the physical specimen hosted at University of Graz.
DOI: 10.57907/mirri/0smllz/pajksq
title: MIRRI0076719.json

description: Strain json file
DOI: 10.57907/mirri/714lty/cmzzeu
title: MIRRI0076378.json

description: Strain json file
DOI: 10.57907/mirri/9bw5fs/kdrv9w
title: MIRRI0076380.json

description: Strain json file
DOI: 10.57907/mirri/wk3cbm
title: MIRRI0076421

description: Organism type: Filamentous Fungi ; Taxon name: Trichoderma asperellum ; Collection: CBS 120898 ; Country: Cameroon
DOI: 10.57907/mirri/yfmu6n
title: MIRRI0076441

description: Organism type: Filamentous Fungi ; Taxon name: Phytophthora infestans ; Collection: CBS 120920 ; Country: Netherlands
DOI: 10.57907/mirri/yfmu6n/o7osxf
title: MIRRI0076441.json

description: Strain json file
DOI: 10.57907/mirri/zac70x
title: MIRRI0076357

description: Organism type: Filamentous Fungi ; Taxon name: Fusarium veterinarium ; Collection: CBS 120760 ; Country: Netherlands
DOI: 10.15468/dl.4vxs4e
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Bromus catharticus",
 "Country is Bosnia and Herzegovina",
 "HasCoordinate is true"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0067466-250717081556266/datasets/export for details.
DOI: 10.3535/2ff-hsd-l17
title: Equisetum ramosissimum Desf.

description: Digital Specimen for the physical specimen hosted at University of Graz.
DOI: 10.3535/t88-yy5-ekk
title: Festuca altissima All.

description: Digital Specimen for the physical specimen hosted at University of Graz.
DOI: 10.57907/mirri/00fll7
title: MIRRI0076437

description: Organism type: Filamentous Fungi ; Taxon name: Pythium rostratum ; Collection: CBS 120916 ; Country: France
DOI: 10.57907/mirri/dpetuq
title: MIRRI0075952

description: Organism type: Filamentous Fungi ; Taxon name: Tetracladium marchalianum ; Collection: CBS 120214 ; Country: Germany
DOI: 10.57907/mirri/gwrgvs/ps83nn
title: MIRRI0075955.json

description: Strain json file
DOI: 10.57907/mirri/ih6ls8/g78yaq
title: MIRRI0075967.json

description: Strain json file
DOI: 10.57907/mirri/pjb4hq/wpueik
title: MIRRI0076405.json

description: Strain json file
DOI: 10.57907/mirri/q66dbc/f0smzn
title: MIRRI0076401.json

description: Strain json file
DOI: 10.57907/mirri/rnjpz4/u5bkcc
title: MIRRI0076375.json

description: Strain json file
DOI: 10.57907/mirri/shtycv/utwpdm
title: MIRRI0076422.json

description: Strain json file
DOI: 10.3535/2tg-lhp-ajr
title: Anthoxanthum australe (Schrad.) Veldkamp

description: Digital Specimen for the physical specimen hosted at University of Graz.
DOI: 10.3535/6vf-7tf-6l8
title: Carex elata All.

description: Digital Specimen for the physical specimen hosted at University of Graz.
DOI: 10.57907/mirri/3bibxc/ydjtwm
title: MIRRI0076012.json

description: Strain json file
DOI: 10.57907/mirri/5ijd1i
title: MIRRI0076753

description: Organism type: Filamentous Fungi ; Taxon name: Alternaria incomplexa ; Collection: CBS 121330 ; Country: United States of America
DOI: 10.57907/mirri/6ojll1
title: MIRRI0076886

description: Organism type: Filamentous Fungi ; Taxon name: Exophiala pisciphila ; Collection: CBS 121505 ; Country: Germany
DOI: 10.57907/mirri/a7tujj/hwhykl
title: MIRRI0076563.json

description: Strain json file
DOI: 10.57907/mirri/bm9eew/tjk1oe
title: MIRRI0076851.json

description: Strain json file
DOI: 10.57907/mirri/bwwpvc
title: MIRRI0076536

description: Organism type: Filamentous Fungi ; Taxon name: Trametes gibbosa ; Collection: CBS 121041 ; Country: Czech Republic
DOI: 10.57907/mirri/bzze3o
title: MIRRI0075977

description: Organism type: Filamentous Fungi ; Taxon name: Massariosphaeria maxima ; Collection: CBS 120240 ; Country: Japan
DOI: 10.57907/mirri/de02e4/fueno2
title: MIRRI0076411.json

description: Strain json file
DOI: 10.57907/mirri/epivfa/isjqgt
title: MIRRI0075984.json

description: Strain json file
DOI: 10.57907/mirri/fox5jl/qnd90t
title: MIRRI0076738.json

description: Strain json file
DOI: 10.5524/100565
title: Supporting data for "A Hybrid de novo Assembly of the Sea Pansy (<i>Renilla muelleri</i>) Genome"

description: Over 3,000 species of octocorals (Cnidaria, Anthozoa) inhabit an expansive range of environments, from shallow tropical seas to the deep-ocean floor. They are important foundation species that create coral forests, which provide unique niches and three-dimensional living space for other organisms. The octocoral genus <i>Renilla</i> inhabits sandy, continental shelves in the subtropical and tropical Atlantic and eastern Pacific Oceans. <i>Renilla</i> is especially interesting because it produces secondary metabolites for defense, exhibits bioluminescence, and produces a luciferase that is widely used in dual-reporter assays in molecular biology. Although several cnidarian genomes are currently available, the majority of these are hexacorals. Here, we present a de novo assembly of an azooxanthellate shallow-water octocoral, <i>R. muelleri</i>. <br>We generated a hybrid de novo assembly using the Maryland Super-Read Celera Assembler v.3.2.6 (MaSuRCA). The final assembly included 4,825 scaffolds and a haploid genome size of 172 Mb. A BUSCO assessment found 88% of metazoan orthologs present in the genome. An Augustus ab initio gene prediction found 23,660 genes, of which 66% (15,635) had detectable similarity to annotated genes from the starlet sea anemone, <i>Nematostella vectensis</i> or to the Uniprot database. Although the <i>R. muelleri</i>genome may be smaller (172 Mb minimum size) than other publicly available coral genomes (256-448 Mb), the <i>R. muelleri</i> genome is similar to other coral genomes in terms of the number of complete metazoan BUSCOs and predicted gene models.<br> The <i>R. mueller</i>i hybrid genome provides a novel resource for researchers to investigate the evolution of genes and gene families within Octocorallia and more widely across Anthozoa. It will be a key resource for future comparative genomics with other corals and for understanding the genomic basis of coral diversity.
DOI: 10.5524/100516
title: 1000 Genomes phase 3, phased and annotated data for use in plink2.0 worked examples

description: Lightly processed 1000 Genomes phase 3 dataset, directly derived from http://ftp.1000genomes.ebi.ac.uk/vol1/ftp/release/20130502/ . We have corrected a few errors in the official pedigree using the method described in Manichaikul A, Mychaleckyj JC, Rich SS, Daly K, Sale M, Chen WM (2010) Robust relationship inference in genome-wide association studies, however the most notable property of these data are their size: they are ~78% smaller without throwing away any relevant information. This has been achieved by using the latest pre-release version of PLINK (plink2), which can now act as a new form of genomic compression technology. The manuscript describing the new PLINK release is currently in preparation, these data are being made available pre-publication due to demand. <br>Please refer to the 1000 Genomes website for additional sample information, data usage rules,, and citation instructions. <br>
DOI: 10.5524/100517
title: Supporting data for "Comprehensive evaluation of RNA-Seq analysis pipelines in diploid and polyploid species"

description: The usual analysis of RNA-Seq reads is based on an existing reference genome and annotated gene models. However, when a reference for the sequenced species is not available, alternatives include using a reference genome from a related species or reconstructing transcript sequences with de novo assembly. In addition, researchers are faced with many options for RNA-Seq data processing and limited information on how their decisions will impact the final outcome. Using both a diploid and polyploid species with a distant reference genome, we have tested the influence of different tools at various steps of a typical RNA-Seq analysis workflow on the recovery of useful processed data available for downstream analysis. At the preprocessing step, we found error correction has a strong influence on de novo assembly but not on mapping results. After trimming, a greater percentage of reads were able to be used in downstream analysis by selecting gentle quality trimming performed with Skewer instead of strict quality trimming with Trimmomatic. This availability of reads correlated with size, quality and completeness of de novo assemblies, and number of mapped reads. When selecting a reference genome from a related species to map reads, outcome was significantly improved when using mapping software tolerant of greater sequence divergence, such as Stampy or GSNAP. The selection of bioinformatic software tools for RNA-Seq data analysis can maximize quality parameters on de novo assemblies and availability of reads in downstream analysis.
DOI: 10.5524/100519
title: Supporting data for "Efficient and accurate detection of splice junctions from RNA-Seq with Portcullis"

description: Next generation sequencing (NGS) technologies enable rapid and cheap genome-wide transcriptome analysis, providing vital information about gene structure, transcript
expression and alternative splicing. Key to this is the the accurate identification of exon-exon junctions from RNA sequenced (RNA-Seq) reads. A number of RNA-Seq aligners capable of splitting reads across these splice junctions (SJs) have been developed, however, it has been shown that while they correctly identify most genuine SJs available in a given sample, they also often produce large numbers of incorrect SJs. <br> Herein we describe the extent of this problem using popular RNA-Seq mapping tools, and present a new method, called Portcullis, to rapidly filter false SJs junctions derived from spliced alignments. We show that Portcullis distinguishes between genuine and false positive junctions to a high-degree of accuracy across different species, samples, expression levels, error profiles and read lengths. Portcullis is portable, efficient and to our knowledge is currently the only SJ prediction tool that reliably scales for use with large RNA-Seq datasets and large, highly-fragmented genomes, whilst delivering accurate SJs
DOI: 10.5524/100521
title: Supporting data for "Comparative analyses identify genomic features potentially involved in the evolution of birds-of-paradise."

description: The diverse array of phenotypes and courtship displays exhibited by birds-of-paradise have long fascinated scientists and laymen alike. Remarkably, almost nothing is known about the genomics of this iconic radiation. There are 41 species in 16 genera currently recognized within the birds-of-paradise family (Paradisaeidae), most of which are endemic to the island of New Guinea. In this study, we sequenced genomes of representatives from all five major clades within this family to characterize genomic changes that may have played a role in the evolution of the groups extensive phenotypic diversity. We found genes important for coloration, morphology, feather and eye development to be under positive selection. In birds-of-paradise with complex lekking systems and strong sexual dimorphism, the core birds-of-paradise, we found GO categories for startle response and olfactory receptor activity to be enriched among the gene families expanding significantly faster compared to the other birds in our study. Furthermore, we found novel families of retrovirus-like retrotransposons active in all three de novo genomes since the early diversification of the birds-of-paradise group, which might have played a role in the evolution of this fascinating group of birds.
DOI: 10.5524/100523
title: Supporting data for "Rice Galaxy: an open resource for plant science"

description: Rice molecular genetics, breeding, genetic diversity, and allied research (such as rice-pathogen interaction) have adopted sequencing technologies and high density genotyping platforms for genome variation analysis and gene discovery. Germplasm collections representing rice diversity, improved varieties and elite breeding materials are accessible through rice gene banks for use in research and breeding, with many having genome sequences and high density genotype data available. Combining phenotypic and genotypic information on these accessions enables genome-wide association analysis, which is driving quantitative trait loci (QTL) discovery and molecular marker development. Comparative sequence analyses across QTL regions facilitate the discovery of novel alleles. Analyses involving DNA sequences and large genotyping matrices for thousands of samples, however, pose a challenge to non-computer savvy rice researchers. We adopted the Galaxy framework to build the federated Rice Galaxy resource, with shared datasets, tools, and analysis workflows relevant to rice research. The shared datasets include high density genotypes from the 3,000 Rice Genomes project and sequences with corresponding annotations from nine published rice genomes. Rice Galaxy includes tools for designing single nucleotide polymorphism (SNP) assays, analyzing genome-wide association studies, population diversity, rice-bacterial pathogen diagnostics, and a suite of published genomic prediction methods. A prototype Rice Galaxy compliant to Open Access, Open Data, and Findable, Accessible, Interoperable, and Reproducible principles is also presented. Rice Galaxy is a freely available resource that empowers the plant research community to perform state-of-the-art analyses and utilize publicly available big datasets for both fundamental and applied science.
DOI: 10.5524/100527
title: Supporting data for " Prot-SpaM: Fast alignment-free phylogeny reconstruction based on whole-proteome sequences"

description: Word-based or `alignment-free' sequence comparison has become an active research area in bioinformatics. While previous word-frequency approaches calculated rough measures of sequence similarity or dissimilarity, some new alignment-free methods are able to accurately estimate phylogenetic distances between genomic sequences. One of these approaches is Filtered Spaced Word Matches. Herein, we extend this approach to estimate evolutionary distances between complete or incomplete proteomes; our implementation of this approach is called Prot-SpaM. We compare the performance of Prot-SpaM to other alignment-free methods on simulated sequences and on various groups of eukaryotic and prokaryotic taxa. Prot-SpaM can be used to calculate high-quality phylogenetic trees for dozens of whole-proteome sequences in a matter of seconds or minutes and often outperforms other alignment-free approaches. The source code of our software is available through Github: https://github.com/jschellh/ProtSpaM
DOI: 10.5524/100540
title: Supporting data for "LR_Gapcloser: a tiling path-based gap closer that uses long reads to complete genome assembly"

description: Completing a genome is an important goal of genome assembly. However, many assemblies, including reference assemblies, are unfinished and have a number of gaps. Long reads obtained from third-generation sequencing (TGS) platforms can help close these gaps and improve assembly contiguity. However, current gap-closure approaches using long reads require extensive runtime and high memory usage. Thus, a fast and memory-efficient approach using long reads is needed to obtain complete genomes. <br>We developed LR_Gapcloser to rapidly and efficiently close the gaps in genome assembly. This tool utilizes long reads generated from TGS sequencing platforms. Tested on de novo assembled-gaps, repeat-derived gaps, and real gaps, LR_Gapcloser closed a higher number of gaps faster, with a lower error rate and a much lower memory usage than two existing, state-of-the art tools. This tool utilized raw reads to fill more gaps than when using error-corrected reads. It is applicable to gaps in the assemblies by different approaches and from large and complex genomes. After performing gap-closure using this tool, the contig N50 size of the human CHM1 genome was improved from 143 kb to 19 Mb, a 132-fold increase. We also closed the gaps in the Triticum urartu genome, a large genome rich in repeats, and the contig N50 size was increased by 40%. Further, we evaluated the contiguity and correctness of six hybrid assembly strategies by combining the optimal TGS-based and NGS-based assemblers with LR_Gapcloser. A proposed and optimal hybrid strategy generated a new human CHM1 genome assembly with marked contiguity. The contig N50 value was over 28 Mb, which is larger than previous non-reference assemblies of the diploid human genome. <br>The software is available at http://www.fishbrowser.org/software/LR_Gapcloser/.
DOI: 10.5524/100544
title: Supporting data for "A Near-Chromosome Scale Genome Assembly of the Gemsbok (Oryx gazella): An Iconic Antelope of the Kalahari Desert"

description: The gemsbok (Oryx gazella) is one of the largest antelopes in Africa. Gemsbok are heterothermic and thus highly adapted to live in the desert, changing their feeding behavior when faced with extreme drought and heat. A high-quality genome sequence of this species will assist efforts to elucidate these and other important traits of gemsbok and facilitate research on conservation efforts. Using 180 Gbp of Illumina paired-end and mate-pair reads, a 2.9 Gbp assembly with scaffold N50 of 1.48 Mbp was generated using SOAPdenovo. Scaffolds were extended using Chicago library sequencing, which yielded an additional 114.7 Gbp of DNA sequence. The HiRise assembly using SOAPdenovo + Chicago library sequencing produced a scaffold N50 of 47 Mbp and a final genome size of 2.9 Gbp, representing 90.6% of the estimated genome size and including 93.2% of expected genes according to BUSCO analysis. The Reference-Assisted Chromosome Assembly tool (RACA) was used to generate a final set of 47 predicted chromosome fragments with N50 of 86.25 Mbp and containing 93.8% of expected genes. A total of 23,125 protein-coding genes and 1.14 Gbp of repetitive sequences were annotated using de novo and homology-based predictions. Our results provide the first high-quality, chromosome-scale genome sequence assembly for gemsbok, which will be a valuable resource for studying adaptive evolution of this species and other ruminants.
DOI: 10.5524/100554
title: Supporting data for "Integrating genomic resources to present full gene and putative promoter capture probe sets for bread wheat"

description: Whole genome shotgun re-sequencing of wheat is expensive because of its large, repetitive genome. Moreover, sequence data can fail to map uniquely to the reference genome making it difficult to unambiguously assign variation. Re-sequencing using target capture enables sequencing of large numbers of individuals at high coverage to reliably identify variants associated with important agronomic traits. Previous studies have implemented cDNA/exon or gene-based probe sets where promoter and intron sequence is largely missing alongside newly characterized genes from the recent improved reference sequences. We present and validate two gold standard capture probe sets for hexaploid bread wheat, a gene and a putative promoter capture, which are designed using recently developed genome sequence and annotation resources. The captures can be combined or used independently. We demonstrate that the capture probe sets effectively enrich the high confidence genes and putative promoter regions that were identified in the genome alongside a large proportion of the low confidence genes and associated promoters. Finally, we demonstrate successful sample multiplexing that allows generation of adequate sequence coverage for SNP calling while significantly reducing cost per sample for gene and putative promoter capture. We show that a capture design employing an island strategy can enable analysis of the large gene/putative promoter space of wheat with only 2x160 Mb probe sets. Furthermore, these assays extend the regions of the wheat genome that are amenable to analyses beyond its exome, providing tools for detailed characterization of these regulatory regions in large populations.
DOI: 10.5524/100555
title: Supporting data for "CropSight: a scalable and open-source information management system for distributed plant phenotyping and IoT-based crop management."

description: High-quality plant phenotyping and climate data lay the foundation of phenotypic analysis and genotype-environment interaction, providing important evidence not only for plant scientists to understand the dynamics between crop performance, genotypes, and environmental factors, but also for agronomists and farmers to closely monitor crops in fluctuating agricultural conditions. With the rise of Internet of Things technologies (IoT) in recent years, many IoT-based remote sensing devices have been applied to plant phenotyping and crop monitoring, which are generating terabytes of biological datasets every day. However, it is still technically challenging to calibrate, annotate, and aggregate the big data effectively, especially when they were produced in multiple locations, at different scales. <br>CropSight is a PHP and SQL based server platform, which provides automated data collation, storage, and information management through distributed IoT sensors and phenotyping workstations. It provides a two-component solution to monitor biological experiments through networked sensing devices, with interfaces specifically designed for distributed plant phenotyping and centralised data management. Data transfer and annotation are accomplished automatically though an HTTP accessible RESTful API installed on both device-side and server-side of the CropSight system, which synchronise daily representative crop growth images for visual-based crop assessment and hourly microclimate readings for GxE studies. CropSight also supports the comparison of historical and ongoing crop performance whilst different experiments are being conducted.<br>As a scalable and open-source information management system, CropSight can be used to maintain and collate important crop performance and microclimate datasets captured by IoT sensors and distributed phenotyping installations. It provides near real-time environmental and crop growth monitoring in addition to historical and current experiment comparison through an integrated cloud-ready server system. Accessible both locally in the field through smart devices and remotely in an office using a personal computer, CropSight has been applied to field experiments of bread wheat prebreeding since 2016 and speed breeding since 2017. We believe that the CropSight system could have a significant impact on scalable plant phenotyping and IoT-style crop management to enable smart agricultural practices in the near future.