cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5524/100620
title: Supporting data for "The integrated respiratory microbial gene catalogue facilitate the understanding of microbial aetiology in Mycoplasma pneumoniae pneumonia"

description: An imbalanced respiratory microbiota has been observed in pneumonia which caused high morbidity and mortality in childhood. Respiratory metagenomic analysis demands a comprehensive microbial gene catalogue which will significantly advance our understanding of host-microbiota interactions.<br>In this study, we collected 334 respiratory microbial samples from 171 healthy children and 76 pneumonia children. The established respiratory microbial gene catalogue (RMGC) comprised 2.25 million non-redundant microbial genes covering 90.52% prevalent genes. The core microbial species in the oropharynx (OP) of the healthy children mainly comprised Prevotella and Streptococcus. The OP microbial diversity and gene number in children with Mycoplasma pneumoniae pneumonia (MPP) decreased compared to that in healthy children, and the concurrence network of OP microbiota in patients is featured by Staphylococcus spp. and M. pneumoniae.
Functional orthologues, which are associated with the metabolism of various lipids, membrane transport and signal transduction, accumulated in the OP microbiome of sick children. Several antibiotics-resistance genes (ARGs) and virulence-factor genes (VFGs) were identified in M. pneumoniae as well as other 13 microbial draft genomes, which were reconstructed via metagenomic data. Though the common macrolides/beta-lactam-resistance genes were not identified in assembled M. pneumoniae genome, a SNP mutation (A2063G) related with macrolides resistance was identified in 23S rRNA gene.<br> This study will facilitate exploring unknown microbial components and host-microbiota interaction in respiratory microbiome studies as well as render further insights into the microbial aetiology of MPP.
DOI: 10.5524/100622
title: Chromosome level draft genomes of the fall armyworm, Spodoptera frugiperda (Lepidoptera: Noctuidae), an alien invasive pest in China

description: The fall armyworm (FAW), <i>Spodoptera frugiperda</i> (J.E. Smith) is a severely destructive pest native to the Americas, but has recently become an alien invasive species in Africa and Asia. With the very recent spread to China it has the potential to threaten food security and cause significant economic loss. To make effective management and control strategies, it is extremely useful to understand genomic architecture and its genetic background. In this work we have rapidly assembled two chromosome scale genomes of the fall armyworm, representing one male and one female individual procured from Yunnan province of China. The genome sizes were identified as 542.42 Mb with N50 of 14.16 Mb, and 530.77 Mb with N50 of 14.89 Mb for the male and female FAW, respectively. We predicted about 22,201 genes in the male genome. We found the expansion of cytochrome P450 and glutathione s-transferase gene families, which are functionally related to the intensified detoxification and pesticides tolerance. Further population analyses of corn strain (C strain) and rice strain (R strain) reveale that the Chinese fall armyworm has most likely invaded from Africa. This demographic information, genome features and possible invasion source described in this study should be extremely important for making effective strategies to manage the fall armyworms. And the data is being released here pre-publication to promote crowdsourcing and immediate utilisation to promote biocontrol strategies.
DOI: 10.5524/100626
title: Supporting data for "VAPPER: High-throughput Variant Antigen Profiling in African trypanosomes"

description: Analysing variant antigen gene families on a population scale is a difficult challenge for conventional methods of read mapping and variant calling due to the great variability in sequence, copy number and genomic loci. In African trypanosomes, hemoparasites of humans and animals, this is complicated by variant antigen repertoires containing hundreds of genes subject to various degrees of sequence recombination. <br>We introduce Variant Antigen Profiler (VAPPER), a tool that allows automated analysis of the variant surface glycoprotein repertoires of the most prevalent livestock African trypanosomes. VAPPER produces variant antigen profiles for any isolate of the veterinary pathogens Trypanosoma congolense and Trypanosoma vivax from genomic and transcriptomic sequencing data and delivers publication-ready figures that show how the queried isolate compares with a database of existing strains. VAPPER is implemented in Python. It can be installed to a local Galaxy instance from the ToolShed (https://toolshed.g2.bx.psu.edu/) or locally on a Linux platform via the command line (https://github.com/PGB-LIV/VAPPER). The documentation, requirements, examples, and test data are provided in the Github repository. <br>By establishing two different, yet comparable methodologies, our approach is the first to allow large-scale analysis of African trypanosome variant antigens, large multi-copy gene families that are otherwise refractory to high-throughput analysis.
DOI: 10.5524/100628
title: Supporting data for "The draft genome sequence of the spider Dysdera silvatica (Araneae, Dysderidae): A valuable resource for functional and evolutionary genomic studies in chelicerates"

description: We present the draft genome sequence of <i>Dysdera silvatica</i>, a nocturnal ground dwelling spider from a genus that undergone a remarkable adaptive radiation in the Canary Islands. The draft assembly was obtained using short (illumina) and long (PacBio and Nanopore) sequencing reads. Our <i>de novo</i> assembly (1.36 Gb), that represents the 80% of the genome size estimated by flow-cytometry (1.7 Gb), is constituted by a high fraction of interspersed repetitive elements (53.8%). The assembly completeness, using BUSCO (benchmarking universal single-copy orthologs) and CEG (Core Eukaryotic genes), ranges from 90% to 96%. Functional annotations based on both ab initio and evidence-based information (including <i>D. silvatica</i> RNA-seq) yielded a total of 48 619 protein-coding sequences, of which 36 398 (74.9%) have the molecular hallmark of known protein domains, or sequence similarity with swissprot sequences. The <i>D. silvatica</i> assembly is the first representative of the superfamily Dysderoidea, and just the second available genome of Synspermiata, one of the major evolutionary lineages of the true spiders (Araneomorphae). Dysderoids, which are known for their numerous instances of adaptation to underground environments, include some of the few examples of trophic specialization within spiders and are excellent models for the study of cryptic female choice. This resource, will be therefore very useful as an starting point to study fundamental evolutionary and functional questions, including the molecular bases of the adaptation to extreme environments and ecological shifts, as well of the origin and evolution of relevant spider traits, such as the venom and silk.
DOI: 10.5524/100630
title: Supporting data for "To assemble or not to resemble – A validated Comparative Metatranscriptomics Workflow (CoMW)"

description: Metatranscriptomics has been used widely for investigation and quantification of microbial communities activity in response to external stimuli. By assessing the genes expressed, metatranscriptomics provide an understanding of the interactions between different major functional guilds and the environment. Here, we present de-novo assembly-based Comparative Metatranscriptomics Workflow (CoMW) implemented in a modular, reproducible structure, significantly improving the annotation and quantification of metatranscriptomes. Metatranscriptomics typically utilize short sequence reads, which can either be directly aligned to external reference databases (assembly-free approach) or first assembled into contigs before alignment (assembly-based approach). We also compare CoMW (assembly-based implementation) with assembly-free alternative workflow, using simulated and realworld metatranscriptomes from Arctic and Temperate terrestrial environments. We evaluate their accuracy in precision and recall using generic and specialized hierarchical protein databases. <br>CoMW provided significantly fewer false positives resulting in more precise identification and quantification of functional genes in metatranscriptomes. Using the comprehensive database M5nr, the assembly-based approach identified genes with only 0.6% false positives at thresholds ranging from inclusive to stringent compared to the assembly-free approach yielding up to 15% false positives. Using specialized databases (Carbohydrate Active-enzyme and Nitrogen Cycle), the assembly-based approach identified and quantified genes with 3-5x less false positives. We also evaluated the impact of both approaches on real-world datasets. <br> We present an open source de-novo assembly-based Comparative Metatranscriptomics Workflow (CoMW). Our benchmarking findings support the argument of assembling short reads into contigs before alignment to a reference database, since this provides higher precision and minimizes false positives.
DOI: 10.5524/100632
title: Supporting data for "Metabolic responses of rice source and sink organs during recovery from combined drought and heat stress in the field"

description: Drought and heat stress effects on rice have been extensively studied, in particular during the sensitive flowering and grain-filling stages. However, in the field these stresses usually occur together because reduced transpirational cooling under drought conditions results in increased plant tissue temperature. In addition, environmental stresses are usually transient and the ability to efficiently recover from stress may be at least as important for overall stress tolerance as the direct stress response itself. Nevertheless, nothing is known about recovery mechanisms after drought and heat stress in rice under field conditions. <br>We have used gas chromatography-mass spectrometry (GC-MS)-based metabolomics to elucidate the metabolic responses of flag leaves, flowering spikelets and developing seeds from three rice cultivars differing in their drought and heat tolerance to rewatering after stress in the field. Within 60 h after rewatering, many stressresponsive metabolites returned to their control levels, although recovery was not complete. In addition, control plants showed developmental differences that were revealed by metabolite profiles during 60 h of post-stress sampling, in particular in developing seeds. Correlation analysis identified several metabolites as marker candidates for the stability of grain yield or quality under conditions of combined drought and heat stress. <br> The rewatering responses of stressed plants seemed to be a combination of the reversal of stress effects and reinitiation of development after stress relief. The identified potential markers can be useful in efforts to breed stress-tolerant rice germplasm to ensure food availability under changing climate conditions.
DOI: 10.5524/100639
title: Supporting data for "Genomic evidence of neo-sex chromosomes in the Eastern Yellow Robin"

description: Understanding sex-biased natural selection can be greatly enhanced by access to well-annotated chromosomes including ones inherited in sex-specific fashions. The Eastern Yellow Robin (EYR) is an endemic Australian songbird inferred to have experienced climate-driven sex-biased selection and is a prominent model for studying mitochondrial-nuclear interactions in the wild. However, the lack of an EYR reference genome containing both sex chromosomes (in birds, a female bearing Z and W chromosomes) is limiting current efforts to understand the mechanisms of these processes. Here, we assemble the genome for a female EYR and use low depth (10 ×) genome resequencing data from 19 individuals of known sex to identify chromosome fragments with sex-specific inheritance. <br> MaSurCA hybrid assembly using Nanopore and Illumina reads generated a 1.22 Gb EYR genome in 20,702 scaffolds (94.2% BUSCO completeness). Scaffolds were tested for W-linked (female-only) inheritance using a k-mer approach, and for Zlinked inheritance using median read-depth test in male and female reads (read-depths must indicate haploid female and diploid male representation). This resulted in 2,372 W-linked scaffolds (total length: 97,872,282 bp, N50: 81,931 bp) and 586 Z-linked scaffolds (total length: 121,817,358 bp, N50: 551,641 bp). Anchoring of the sex-linked EYR scaffolds to the reference genome of a female Zebra Finch revealed two categories of sex-linked genome region. First, 653 W-linked scaffolds (25.7 Mb) were anchored to the W sex chromosome and 215 Z-linked scaffolds (74.4 Mb) to the Z. Second, 1138 W-linked scaffolds (70.9 Mb), and 179 Z-linked scaffolds (51.0 Mb), were anchored to a large section (coordinates ~5 to ~60 Mb) of Zebra Finch chromosome 1A. The first ~5 Mb and last ~14 Mb of the reference chromosome 1A had only autosomally-behaving EYR scaffolds mapping to them. <br>We report a female (W-chromosome containing) EYR genome and provide genomic evidence for a neo-sex (neo-W and neo-Z) chromosome system in EYR, involving most of a large chromosome (1A) previously only reported to be autosomal in passerines.
DOI: 10.5524/100644
title: Supporting data for "Pseudo-chromosome length genome assembly of a double haploid 'Bartlett' pear (Pyrus communis L.)"

description: We report an improved assembly and scaffolding of the European pear (<i>Pyrus communis</i> L.) genome (referred to as BartlettDHv2.0), obtained using a combination of Pacific Biosciences RSII Long read sequencing (PacBio), Bionano optical mapping, chromatin interaction capture (Hi-C), and genetic mapping. A total of 496.9 million bases (Mb) corresponding to 97% of the estimated genome size were assembled into 494 scaffolds. Hi-C data and a high-density genetic map allowed us to anchor and orient 87% of the sequence on the 17 chromosomes of the pear genome. About 50% (247 Mb) of the genome consists of repetitive sequences. Comparison with previous assemblies of <i>Pyrus communis</i> and <i>Pyrus x bretschneider</i>i confirmed the presence of 37,445 protein-coding genes, which is 13% fewer than previously predicted.
DOI: 10.5524/100648
title: 3D printing data from enlarged museum specimens

description: Museums are embracing new technologies and one of these is the use of 3D printing. 3D printing allows for creating physical replicas of items which may, due to great value or significance, not be handled by the public, or which are too small or fragile to be handled or even seen with the naked eye. One such application of new technologies has been welcomed by the National Museum in Bloemfontein, Free Sate. Here, blown-up (enlarged) Museum specimens were 3D printed for various interactive exhibits that are aimed at increasing the accessibility of their permanent displays for visually impaired visitors who rely greatly on touch as a source of observation. A selection of scorpions, pseudoscorpions, mites and archetypal bird skulls were scanned, processed and 3D printed to produce enlarged, highly functional nylon models. This data paper provides the raw micro Computed Tomography (micro-CT) scan data and print ready STL files processed from this data. The STL files may be used in their current format and details of the printing are provided.
DOI: 10.5524/100653
title: Supporting data for "Chromosomal-level reference genome of Chinese peacock butterfly (Papilio bianor) based on third-generation DNA sequencing and Hi-C analysis"

description: <i>Papilio bianor</i> Cramer, 1777 (i.e. Chinese peacock) (Insecta, Lepidoptera, Papilionidae) is a widely distributed swallowtail butterfly with a large number of geographic populations from the Southeast of Russia to China, Japan, India, Vietnam, Myanmar and Thailand. Its wing color consists of both pigmentary colored scales (black, reddish) and structural colored scales (iridescent blue or green dust). A highquality reference genome of <i>P. bianor</i> is thus important for investigating iridescent color evolution, phylogeography, and evolution of swallowtail butterflies. <br>Here, we obtained a chromosome-level de novo genome assembly of the high heterozygous Chinese peacock (<i>Papilio bianor</i>) (1.81%) using long Pacific Biosciences (PacBio) sequencing reads (43.19 Gb) and high-through chromosome conformation capture (Hi-C) technology. The final assembly is 402.00 Mb on 30 chromosomes (29 autosomes and 1 sex chromosomes W) with 5.50 Mb contig N50 and 12.51 Mb scaffold N50. Totally 15,375 protein-coding genes and 222.29 Mb (55.30%) of repetitive sequences were identified. The phylogenetic trees of representative species of butterflies and moths constructed using one to one single-copy orthologous genes indicate that the Chinese peacock was separated from a common ancestor of swallowtails about 23.69-36.04 million years ago (mya). Demographic history inferred using the Pairwise Sequentially Markovian Coalescence (PSMC) analysis suggested that the population expansion of this species from the last interglacial period to the last glacial maximum possibly resulted from its decreased natural enemies and its adaptation to climate diversity during glacial period. <br>We present a high-quality chromosome-level reference genome of the Chinese peacock (<i>Papilio bianor</i>) using long-read single-molecule sequencing and Hi-C-based chromatin interaction maps. Our results lay the foundation for exploring genetic basis of special biological features of the Chinese peacock butterfly, and also provide a useful datasource for comparative genomics and phylogenomics among butterflies and moths.
DOI: 10.5524/100656
title: Supporting data for "RepeatFiller newly identifies megabases of aligning repetitive sequences and improves annotations of conserved non-exonic elements"

description: Transposons and other repetitive sequences make up a large part of complex genomes. Repetitive sequences can be co-opted into a variety of functions and thus provide a source for evolutionary novelty. However, comprehensively detecting ancestral repeats that align between species is difficult since considering all repeat-overlapping seeds in alignment methods that rely on the seed-and-extend heuristic results in prohibitively high runtimes. Here, we show that ignoring repeat-overlapping alignment seeds when aligning entire genomes misses numerous alignments between repetitive elements. We present a tool RepeatFiller that improves genome alignments by incorporating previously-undetected local alignments between repetitive sequences. By applying RepeatFiller to genome alignments between human and 20 other representative mammals, we uncover between 22 and 84 megabases of previously-undetected alignments that mostly overlap transposable elements. We further show that the increased alignment coverage improves the annotation of conserved non-exonic elements, both by discovering numerous novel transposon-derived elements that evolve under constraint and by removing thousands of elements that are not under constraint in placental mammals. In conclusion, RepeatFiller contributes to comprehensively aligning repetitive genomic regions, which facilitates studying transposon co-option and genome evolution.
DOI: 10.5524/100663
title: Supporting data for "A Galaxy-based training resource for single-cell RNA-seq quality control and analyses"

description: It is not a trivial step to move from single-cell RNA-seq (scRNA-seq) data production to data analysis. There is a lack of intuitive training materials and easy-to-use analysis tools, and researchers can find it difficult to master the basics of scRNA-seq quality control and the later analysis.<br>We have developed a range of practical scripts, together with their corresponding Galaxy wrappers, that make scRNA-seq training and quality-control accessible to researchers previously daunted by the prospect of scRNA-seq analysis. We implement a visualise-filter-visualise paradigm through simple command-line tools that use the Loom format to exchange data between the tools. The point-and-click nature of Galaxy makes it easy to assess, visualise, and filter scRNA-seq data from short-read sequencing data. <br> We have developed a suite of scRNA-seq tools that can be used for both training and more in-depth analyses.
DOI: 10.5524/100665
title: Supporting data for "Accessible and reproducible mass spectrometry imaging data analysis in Galaxy"

description: Mass spectrometry imaging is increasingly used in biological and translational research as it has the ability to determine the spatial distribution of hundreds of analytes in a sample. Being at the interface of proteomics/metabolomics and imaging, the acquired data sets are large and complex and often analyzed with proprietary software or in-house scripts, which hinder reproducibility. Open source software solutions that enable reproducible data analysis often require programming skills and are therefore not accessible to many MSI researchers. <br>We have integrated 18 dedicated mass spectrometry imaging tools into the Galaxy framework to allow accessible, reproducible, and transparent data analysis. Our tools are based on Cardinal, MALDIquant, and scikit-image and enable all major MSI analysis steps such as quality control, visualization, preprocessing, statistical analysis, and image coregistration. Further, we created hands-on training material for use cases in proteomics and metabolomics. To demonstrate the utility of our tools, we re-analyzed a publicly available N-linked glycan imaging dataset. By providing the entire analysis history online, we highlight how the Galaxy framework fosters transparent and reproducible research.<br> The Galaxy framework has emerged as a powerful analysis platform for the analysis of MSI data with ease of use and access together with high levels of reproducibility and transparency.
DOI: 10.5524/100619
title: Supporting data for "A high-quality genome assembly of the endangered golden snub-nosed monkey Rhinopithecus roxellana"

description: The golden snub-nosed monkey (Rhinopithecus roxellana), is an endangered colobine monkey species endemic to China. This species has several distinctive traits, and it is an ideal model for analysing evolutionary development of the social structure due to its unique social organization. Although there has been reported a genome assembly of the subspecies R. roxellana hubeiensis, the assembly is incomplete and fragmented due to employing short reads sequencing technology. This drawback may lose information, such as structural variation and repeat sequences which are important for understanding this endangered species. Therefore, to have a better understanding of evolutionary history and genetic-specific signatures, a high-quality reference genome of the taxon is need. To obtain a high-quality chromosome assembly of R. roxellana qinlingensis, we combined a total of five techniques including Pacific Biosciences single-molecule real-time sequencing, Illuminas paired-end sequencing, BioNano optical maps, 10X Genomics link-reads and high-throughput chromosome conformation capture. The results indicate the assembled genome is about 3.04 Gb with a contig N50 of 5.72 Mbp and a scaffold N50 of 144.56 Mbp, which have made a 10-fold improvement compared to past published. It is shown that a total of 22497 protein coding genes were predicted, of which 22053 were functionally annotated. Moreover, gene family analysis shows that 993 and 2745 gene families are expanded and contracted in the R. roxellana genome, respectively. We present the updated high-quality genome assembly of R. roxellana with superior continuity and accuracy. The assembled genome can be used as reference for future genetic studies of the species. Also, the updated genome assembly may contribute to our comprehensive understanding of the species, which is particularly helpful in the conservation of this endangered species. Furthermore, such genome with superior continuity and accuracy can provide a new standard reference for Colobine primates.