cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5524/102569
title: Supporting data for "MISIP: A data standard for the reuse and reproducibility of any stable isotope probing-derived nucleic acid sequence and experiment"

description: DNA/RNA-stable isotope probing (SIP) is a powerful tool to link <em>in situ </em>microbial activity to sequencing data. Every SIP dataset captures distinct information about microbial community metabolism, process rates, and population dynamics, offering valuable insights for a wide range of research questions. Data reuse maximizes the information derived from the labor and resource intensive SIP approaches. Yet, a review of publicly available SIP sequencing metadata showed that critical information necessary for reproducibility and reuse was often missing. Here, we outline the Minimum Information for any Stable Isotope Probing Sequence (MISIP) according to the Minimum Information for any (x) Sequence (MIxS) framework and include examples of MISIP reporting for common SIP experiments. Our objectives are to expand the capacity of MIxS to accommodate SIP-specific metadata and guide SIP users in metadata collection when planning and reporting an experiment. The MISIP standard requires five metadata fields: isotope, isotopolog, isotopolog label, labelling approach, and gradient position, and recommends several fields that represent best practices in acquiring and reporting SIP sequencing data (<em>e.g.</em> gradient density and nucleic acid amount). The standard is intended to be used in concert with other MIxS checklists to comprehensively describe the origin of sequence data, such as for marker genes (MISIP-MIMARKS) or metagenomes (MISIP-MIMS), in combination with metadata required by an environmental extension (<em>e.g.</em> soil). The adoption of the proposed data standard will improve the reuse of any sequence derived from a SIP experiment and, by extension, deepen understanding of <em>in situ</em> biogeochemical processes and microbial ecology.
DOI: 10.5524/102573
title: Supporting data for "High-speed whole-genome sequencing of a Whippet: Rapid chromosome-level assembly and annotation of an extremely fast dog’s genome"

description: The time required for sequencing and <i>de novo</i> assembly of genomes is highly dependent on the interaction between laboratory work, sequencing capacity, and the bioinformatics workflow. As a result, genome projects are often not only limited by financial, computational and sequencing platform resources, but also delayed by second party sequencing service providers. By bringing together academic biodiversity institutes and a medical diagnostics company with extensive sequencing capabilities and know-how, we aimed at generating a high-quality mammalian <i>de novo</i> genome in the shortest possible time period. Therefore, we streamlined all processes involved and chose a very fast dog as a role model: The Whippet. <br>We present the first chromosome-level genome assembly of the Whippet. We used PacBio long-read HiFi sequencing and reference-guided scaffolding to generate a high-quality genome assembly. The final assembly has a contig N50 of 55 Mbp and a scaffold N50 of 65.7 Mbp. The total assembly length is 2.47 Gbp, of which 2.43 Gpb were scaffolded into 39 chromosome-length scaffolds. In addition, we used available mammalian genomes and transcriptome data to annotate the genome assembly. The annotation resulted in 28,383 transcripts resembling a total of 90.9% complete BUSCO genes and identified a repeat content of 36.5%. <br>Sequencing, assembling, and scaffolding the chromosome-level genome of the Whippet took less than a week and adds a high-quality reference genome to the list of domestic dog breeds sequenced to date.
DOI: 10.5524/102576
title: Supporting data for "CoCoPyE: feature engineering for learning and prediction of genome quality indices"

description: The exploration of the microbial world has been greatly advanced by the reconstruction of genomes from metagenomic sequence data. However, the rapidly increasing number of metagenome-assembled genomes has also resulted in a wide variation in data quality. It is therefore essential to quantify the achieved completeness and possible contamination of a reconstructed genome before it is used in subsequent analyses. The classical approach for the estimation of quality indices solely relies on a relatively small number of universal single copy genes. Recent tools try to extend the genomic coverage of estimates for an increased accuracy. CoCoPyE is a fast tool based on a novel two-stage feature extraction and transformation scheme. First it identifies genomic markers and then refines the marker-based estimates with a machine learning approach. In our simulation studies, CoCoPyE showed a more accurate prediction of quality indices than the existing tools.
DOI: 10.5524/102548
title: Supporting data for "Innovative approach for high-throughput exploiting sex-specific markers in Japanese parrotfish <i>Oplegnathus fasciatus</i>"

description: The utilization of sex-specific molecular markers has emerged as a significant technical approach to augment fish production and enhance economic value, while also establishing a fundamental basis for unraveling the intricate molecular mechanisms governing fish sex determination. In the past ten years, the field of genetic sex marker mining has primarily relied on first-generation development methods such as RFLP, RAPD, SSR, and AFLP, as well as second-generation techniques utilizing Illumina's SNP/InDel markers. However, the progress of sex-controlled breeding has been hindered by several factors, including the limited efficiency of the aforementioned methods, complex experimental procedures, high development costs, a high incidence of false positives, unstable markers, and inconvenient on-site testing. Nevertheless, the emergence and rapid advancement of third-generation sequencing technology offers new opportunities for overcoming these limitations. <br>Using male-female linear genomic information combined with Illumina survey and PacBio CLR/CCS data, a database of large-segment (&gt;100 bp) insertion-deletion genetic variants was constructed using a genome-wide variant site scanning method with bidirectional comparisons. A database of bulk primers and simulated PCR for the male-female variant loci were then constructed, employing primer design for the target region and e-PCR technology. Finally, the criteria for rapid identification of male and female differences were established based on agarose gel electrophoresis with two amplified bands for males and one amplified band for females. A high-throughput identification database of sex-specific markers for <i>Oplegnathus fasciatus</i> was constructed utilizing this method, yielding 3,645 (2,791 INS/854 DEL, <em> </em>as reference) and 3,872 (3,039 INS/833 DEL, <em> </em>as reference) genetic sex identification markers. Four differential loci were randomly selected from the database for validation, and the results met the criteria for male-female differences. Utilization of this technology will accelerate the identification of genetic sex markers for species, contributing to the rapid development of genetic breeding. <br>By utilizing the linear genomic information of male and female individuals acquired through PacBio sequencing, along with data from Illumina surveys and PacBio CLR/CCS. Our research extensively employed whole-genome variant site scanning and identification, high-throughput primer design for the target regions, and e-PCR batch amplification. By employing this comprehensive approach, which encompassed genome-wide variant site scanning, high-throughput primer design within the desired region, and e-PCR batch amplification and validation methodologies, we successfully developed a database encompassing insertion/deletion loci in large segments (&gt;100 bp) for both male and female <i>O. fasciatus</i>.
DOI: 10.5524/102549
title: Supporting data for "A Trade-off in Evolution: The Adaptive Landscape of Spiders without Venom Glands"

description: Venom glands play a key role in the predation and defense strategies of almost all spider groups. However, the spider family Uloboridae lacks venom glands and has evolved an adaptive strategy: They excessively wrap their prey directly with spider silk instead of paralyzing it first with toxins. This shift in survival strategy is very fascinating, but the genetic underpinnings behind it are poorly understood.br / Spanning multiple spider groups, we conducted multi-omics analyses on iOctonoba sinensis/i, and described the adaptive evolution of the Uloboridae family at the genome level. We observed the coding genes of myosin and twitchin in muscles are under positive selection, energy metabolism functions are enhanced, and gene families related to tracheal development and tissue mechanical strength are expanded or emerged, all of which are related to the unique anatomical structure and predatory behavior of spiders in the family Uloboridae. In addition, we also scanned the elements that are absent or under relaxed purifying selection, as well as toxin gene homologs in the genomes of two species in this family. The results show that the absence of regions and regions under relaxed selection in these spiders genomes are concentrated in areas related to development and neuro-system. The search for toxin homologs revealed possible gene function shift between toxins and non-toxins, and confirms that there are no reliable toxin genes in the genome of this group.br /This study demonstrates the trade-off between different predation strategies in spiders, either using chemical or physical strategy, and provides insights into the possible mechanism underlying this trade-off. Venomless spiders need to mobilize multiple developmental and metabolic pathways related to motor function and limb mechanical strength to cover the decline in adaptability caused by the absence of venom glands.
DOI: 10.5524/102552
title: Supporting data for "gNOMO2: a comprehensive and modular pipeline for integrated multi-omics analyses of microbiomes"

description: In recent years, omics technologies have offered an exceptional chance to gain a deeper insight into the structural and functional characteristics of microbial communities. As a result, there is a growing demand for user friendly, reproducible, and versatile bioinformatic tools that can effectively harness multi-omics data to offer a holistic understanding of microbiomes. Previously, we introduced gNOMO, a bioinformatic pipeline tailored to analyze microbiome multi-omics data in an integrative manner. In response to the evolving demands within the microbiome field and the growing necessity for integrated multi-omics data analysis, we have implemented substantial enhancements to the gNOMO pipeline. <br>Here, we present gNOMO2, a comprehensive and modular pipeline that can seamlessly manage various omics combinations, ranging from two to four distinct omics data types including 16S rRNA gene amplicon sequencing, metagenomics, metatranscriptomics, and metaproteomics. Furthermore, gNOMO2 features a specialized module for processing 16S rRNA gene amplicon sequencing data to create a protein database suitable for metaproteomics investigations. Moreover, it incorporates new differential abundance, integration and visualization approaches, enhancing the toolkit for a more insightful analysis of microbiomes. The functionality of these new features is showcased through the use of four microbiome multi-omics datasets encompassing various ecosystems and omics combinations. gNOMO2 not only replicated most of the primary findings from these studies but also offered further valuable perspectives. <br>gNOMO2 enables the thorough integration of taxonomic and functional analyses in microbiome multi-omics data, offering novel insights in both host associated and free-living microbiome research. gNOMO2 is available freely at https://github.com/muzafferarikan/gNOMO2.
DOI: 10.5524/102553
title: Supporting data for "Get Free Copy: A Multi-Repository Search Platform for Biomedical Publications"

description: We introduce Get Free Copy, a web-based platform designed to streamline the search for biomedical literature across major repositories like arXiv, bioRxiv, medRxiv, and PubMed Central (PMC). Addressing challenges posed by paywalls and fragmented databases, it offers a unified interface for efficient retrieval of free, legitimate copies of biomedical literature. The platform's implementation involves a Node.js backend and dynamic front-end display, enhancing accessibility and research efficiency. As an open-source project, Get Free Copy represents a significant contribution to the open-access movement, inviting global researcher collaboration for further development.
DOI: 10.5524/102555
title: Supporting data for "Genomic insights into endangerment and conservation of the garlic-fruit tree (<i>Malania oleifera</i>), a plant species with extremely small populations"

description: Advanced whole genome sequencing techniques enable covering nearly all genome nucleotide variations, thus can provide deep insights into protecting endangered species. However, the use of genomic data to make conservation strategies is still rare, particularly for endangered plants. Here we performed comprehensive conservation genomic analysis for <i>Malania oleifera</i>, an endangered tree species with a high amount of nervonic acid. We used whole-genome resequencing data of 165 samples, covering 16 populations across the entire distribution range to investigate the formation reasons of its extremely small population sizes and to evaluate the possible genomic offsets and changes of ecology niche suitability under future climate change.<br>Although <i>M. oleifera</i> maintains relatively high genetic diversity among endangered woody plants ( = 3.87e3), high levels of inbreeding have been observed, which has reduced genetic diversity in three populations (JM, NP and BM2) and caused the accumulation of deleterious mutations. Repeated bottleneck events, recent inbreeding (~490 years ago) and anthropogenic disturbance to wild habitats have aggravated the fragmentation and endangered status of <i>M. oleifera</i>. Due to the significant effect of higher average annual temperature, populations distributed in low altitudes exhibit greater genomic offset. Furthermore, ecological niche modeling shows the suitable habitats for <i>M. oleifera</i> will decrease by 71.15% and 98.79% by 2100 under scenarios SSP126 and SSP585, respectively.<br>The basic realizations concerning the threats to <i>M. oleifera</i> provides a scientific foundation for defining management and adaptive units and prioritizing populations for genetic rescue. Meanwhile, we highlight the importance of integrating genomic offset and ecological niche modeling to make targeted conservation actions under future climate change. Overall, our study provides a paradigm for genomics-directed conservation.
DOI: 10.5524/102560
title: Supporting data for "RNAVirHost: a machine learning-based method for predicting hosts of RNA viruses through viral genomes"

description: The high-throughput sequencing technologies have revolutionized the identification of novel RNA viruses. Given that viruses are infectious agents, identifying hosts of these new viruses carries significant implications for public health and provides valuable insights into the dynamics of the microbiome. However, determining the hosts of these newly discovered viruses is not always straightforward, especially in the case of viruses detected in environmental samples. Even for host-associated samples, it is not always correct to assign the sample origin as the host of the identified viruses. The process of assigning hosts to RNA viruses remains challenging due to their high mutation rates and vast diversity.<br>In this study, we introduce RNAVirHost, a machine learning-based tool that predicts the hosts of RNA viruses solely based on viral genomes. RNAVirHost is a hierarchical classification framework that predicts hosts at different taxonomic levels. We demonstrate the superior accuracy of RNAVirHost in predicting hosts of RNA viruses through comprehensive comparisons with various state-of-the-art techniques. When applying to viruses from novel genera, RNAVirHost achieved the highest accuracy of 84.3%, outperforming the alignment-based strategy by 12.1%.<br>The application of machine learning models has proven beneficial in predicting hosts of RNA viruses. By integrating genomic traits and sequence homologies, RNAVirHost provides a cost-effective and efficient strategy for host prediction. We believe that RNAVirHost can greatly assist in RNA virus analyses and contribute to pandemic surveillance
DOI: 10.5524/102563
title: Supporting data for "The first high-altitude autotetraploid haplotype-resolved genome assembled (<i>Rhododendron nivale</i> subsp. <i>boreale</i>) provides new insights into mountaintop adaptation"

description: <i>Rhododendron nivale</i> subsp. <i>boreale</i> Philipson et M. N. Philipson is an alpine woody species with ornamental qualities that serve as the predominant species in mountainous scrub habitats found at an altitude of ~4200 m. As a high-altitude woody polyploid, this species may serve as a model to understand how plants adapt to alpine environments. Despite its ecological significance, the lack of genomic resources has hindered a comprehensive understanding of its evolutionary and adaptive characteristics in high-altitude mountainous environments.<br>We sequenced and assembled the genome of <i>R. nivale</i> subsp. <i>boreale</i>, an assembly of the first subgenus <i>Rhododendron</i> and the first high-altitude woody flowering tetraploid, contributing an important genomic resource for alpine woody flora. The assembly included 52 pseudochromosomes (scaffold N50=42.93 Mb; BUSCO=98.8%; QV=45.51; S-AQI=98.69), which belonged to 4 haplotypes, harboring 127,810 predicted protein-coding genes. Conjoint <i>k-mer</i> analysis, collinearity assessment, and phylogenetic investigation corroborated autotetraploid identity. Comparative genomic analysis revealed that <i>R. nivale</i> subsp. <i>boreale</i> originated as a neopolyploid of <i>R. nivale</i> and underwent two rounds of ancient polyploidy events. Transcriptional expression analysis showed that differences in expression between alleles were common and randomly distributed in the genome. We identified extended gene families and signatures of positive selection that are involved not only in adaptation to the mountaintop ecosystem (response to stress and developmental regulation) but also in autotetraploid reproduction (meiotic stabilization). Additionally, the expression levels of the (Group VII ethylene response factor transcription factors) <i>ERF VIIs</i> were significantly higher than the mean global gene expression. We suspect that these changes have enabled the success of this species at high altitudes.<br>We assembled the first high-altitude autopolyploid genome and achieved chromosome-level assembly within the subgenus <i>Rhododendron</i>. In addition, a high-altitude adaptation strategy of <i>R. nivale</i> subsp. <i>boreale</i> was reasonably speculated. This study provides valuable data for the exploration of alpine mountaintop adaptations and the correlation between extreme environments and species polyploidization.
DOI: 10.5524/102564
title: Supporting data for "Whole-genome sequencing of the invasive golden apple snail Pomacea canaliculata from Asia reveals rapid expansion and adaptive evolution"

description: <i>Pomacea canaliculata</i> an invasive species native to South America, is recognized for its broad geographic distribution and adaptability to a variety of ecological conditions. The details concerning the evolution and adaptation of <i>P. canaliculate</i> remains unclear due to a lack of whole-genome re-sequencing data.<br>We examined 173 <i>P. canaliculata</i> genomes representing 17 geographic populations in East and Southeast Asia. Interestingly, <i>P. canaliculata</i> showed a higher level of genetic diversity than other mollusks, and our analysis suggested that the dispersal of <i>P. canaliculata</i> could have been driven by climate changes and human activities. Notably, we identified a set of genes associated with low-temperature adaptation, including Csde1, a cold shock protein-coding gene. Further RNA-seq analysis and RT-qPCR experiments demonstrated the genes dynamic pattern and biological functions during cold exposure. Moreover, both positive selection and balancing selection are likely to have contributed to the rapid environmental adaptation of <i>P. canaliculata</i> populations. In particular, genes associated with energy metabolism and stress response were undergoing positive selection, while a large number of immune-related genes showed strong signatures of balancing selection. Our study has advanced our understanding of the evolution of <i>P. canaliculata</i> and has provided a valuable resource concerning an invasive species.
DOI: 10.6084/m9.figshare.26047735.v4
title: Assembly and annotation of <i>Rhododendron</i> sp. genome (Rhonb_v1)

description: Assembly and annotation of <i>Rhododendron</i> sp. genome (Rhonb_v1)
DOI: 10.5524/102547
title: Supporting data for "Impact of reference design on estimating SARS-CoV-2 lineage abundances from wastewater sequencing data"

description: Sequencing of SARS-CoV-2 RNA from wastewater samples has emerged as a valuable tool for detecting the presence and relative abundances of SARS-CoV-2 variants in a community. By analyzing the viral genetic material present in wastewater, public health officials can gain early insights into the spread of the virus and inform timely intervention measures. The construction of reference datasets from known SARS-CoV-2 lineages and their mutation pro­les has become state-of-the-art for assigning viral lineages and their relative abundances from wastewater sequencing data. However, the selection of reference sequences or mutations directly affects the predictive power. <br>Here, we show the impact of a <i>mutation-</i> and <i>sequence-</i> based reference reconstruction for SARS-CoV-2 abundance estimation. We benchmark three data sets: 1) synthetic spike-in mixtures, 2) German samples from early 2021, mainly comprising Alpha, and 3) samples obtained from wastewater at an international airport in Germany from the end of 2021, including ­rst signals of Omicron. The two approaches differ in sub-lineage detection, with the marker-mutation-based method, in particular, being challenged by the increasing number of mutations and lineages. However, the estimations of both approaches depend on selecting representative references and optimized parameter settings. By performing parameter escalation experiments, we demonstrate the effects of reference size and alternative allele frequency cutoffs for abundance estimation. We show how different parameter settings can lead to different results for our test data sets, and illustrate the effects of virus lineage composition of wastewater samples and references. <br>Here, we compare a <i>mutation-</i> and <i>sequence-</i> based reference construction and assignment for SARS-CoV-2 abundance estimation from wastewater samples. Our study highlights current computational challenges, focusing on the general reference design, which signi­ficantly and directly impacts abundance allocations. We illustrate advantages and disadvantages that may be relevant for further developments in the wastewater community and in the context of higher standardization.