cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5524/100398
title: Supporting data for "Draft genome assembly of the Bengalese finch, Lonchura striata domestica, a model for motor skill variability and learning"

description: Vocal learning in songbirds has emerged as a powerful model for sensorimotor learning. Neurobehavioral
studies of Bengalese finch (Lonchura striata domestica) song, naturally more variable and plastic than songs of other finch species, have demonstrated the importance of behavioral variability
for initial learning, maintenance, and plasticity of vocalizations. However, the molecular and genetic
underpinnings of this variability, and the learning it supports, are poorly understood.

To establish a platform for the molecular analysis of behavioral variability and plasticity, we have
generated an initial draft assembly of the Bengalese finch genome from a single male animal to 151x
coverage and an N50 of 3.0 MB. Furthermore, we have developed an initial set of gene models using
RNA-seq data from eight samples that comprise liver, muscle, cerebellum, brainstem/midbrain and
forebrain tissue from juvenile and adult Bengalese finches of both sexes.

We provide a draft Bengalese finch genome and gene annotation to facilitate the study of the
molecular-genetic influences on behavioral variability and the process of vocal learning. These data
will directly support many avenues for the identification of genes involved in learning, including
differential expression analysis, comparative genomic analysis (through comparison to existing avian
genome assemblies), and derivation of genetic maps for linkage analysis. Bengalese finch gene
models and sequences will be essential for subsequent manipulation (molecular or genetic) of genes
and gene products, enabling novel mechanistic investigations into the role of variability in learned
behavior.
DOI: 10.5524/100400
title: Supporting data for “Quantitative super-resolution single molecule microscopy dataset of YFP-tagged growth factor receptors”

description: Super-resolution single molecule localization microscopy (SMLM) is a method for achieving resolution beyond the classical limit in optical microscopes (approx. 200 nm laterally). Yellow fluorescent protein (YFP) has been used for superresolution single molecule localization microscopy, but less frequently than other fluorescent probes. Working with YFP in SMLM is a challenge because a lower number of photons are emitted per molecule compared to organic dyes which are more commonly used. Publically available experimental data can facilitate development of new data analysis algorithms. Four complete, freely available single molecule super-resolution microscopy datasets on YFP-tagged growth factor receptors expressed in a human cell line are presented including both raw and analyzed data. We report methods for sample preparation, for data acquisition, and for data analysis, as well as examples of the acquired images. We also analyzed the SMLM data sets using a different method: super-resolution optical fluctuation imaging (SOFI). The two modes of analysis offer complementary information about the sample. A fifth single molecule super-resolution microscopy dataset acquired with the dye Alexa 532 is included for comparison purposes. This dataset has potential for extensive reuse. Complete raw data from SMLM experiments has typically not been published. The YFP data exhibits low signal to noise ratios, making data analysis a challenge. These data sets will be useful to investigators developing their own algorithms for SMLM, SOFI, and related methods. The data will also be useful for researchers investigating growth factor receptors such as ErbB3.
DOI: 10.5524/100401
title: Supporting data for "Analysis of the Aedes albopictus C6/36 genome provides insight into cell line utility for viral propagation"

description: The 50-year old Aedes albopictus C6/36 cell line is a resource for the detection, amplification, and analysis of mosquito-borne viruses including Zika, dengue, and chikungunya. The cell line is derived from an unknown number of larvae from an unspecified strain of Aedes albopictus mosquitoes. Toward improved utility of the cell line for research in virus transmission, we present an annotated assembly of the C6/36 genome. <br>
The C6/36 genome assembly has the largest contig N50 (3.3 Mbp) of any mosquito assembly, presents the sequences of both haplotypes for most of the diploid genome, reveals independent null mutations in both alleles of the Dicer locus, and indicates a male-specific genome. Gene annotation was computed with publicly available mosquito transcript sequences. Gene expression data from cell line RNA sequence identified enrichment of growth-related pathways and conspicuous deficiency in aquaporins and inward rectifier K+ channels. As a test of utility, RNA sequence data from Zika-infected cells was mapped to the C6/36 genome and transcriptome assemblies. Host subtraction reduced the data set by 89%, enabling faster characterization of non-host reads. <br>
The C6/36 genome sequence and annotation should enable additional uses of the cell line to study arbovirus vector interactions and interventions aimed at restricting the spread of human disease.
DOI: 10.5524/100403
title: Supporting data for "Single molecule, full-length transcript sequencing provides insight into the extreme metabolism of ruby-throated hummingbird Archilochus colubris"

description: Hummingbirds oxidize ingested nectar sugars directly to fuel foraging but cannot sustain this fuel use during fasting periods, such as during the night or during long-distance migratory flights. Instead, fasting hummingbirds switch to oxidizing stored lipids, derived from ingested sugars. The hummingbird liver plays a key role in moderating energy homeostasis and this remarkable capacity for fuel switching. Additionally, liver is the principle location of de novo lipogenesis, which can occur at exceptionally high rates, such as during premigratory fattening. Yet understanding how this tissue and whole organism moderates energy turnover is hampered by a lack of information regarding how relevant enzymes differ in sequence, expression, and regulation.
<br>
We generated a de novo transcriptome of the hummingbird liver using PacBio full-length cDNA sequencing (Iso-Seq), yielding a total of 8.6Gb of sequencing data, or 2.6M reads from 4 different size fractions. We analyzed data using the SMRTAnalysis v3.1 Iso-Seq pipeline, then clustered isoforms into gene families to generate de novo gene contigs using Cogent. We performed orthology analysis to identify closely related sequences between our transcriptome and other avian and human gene sets. Finally, we closely examined homology of critical lipid metabolism genes between our transcriptome data and avian and human genomes.
<br>
Our results leverage cutting-edge technology and a novel bioinformatics pipeline to provide a first direct look at the transcriptome of this incredible organism.
DOI: 10.5524/100404
title: Supporting data for "Improving the annotation of the Heterorhabditis bacteriophora genome"

description: Genome assembly and annotation remains an exacting task. As the tools available for these tasks improve, it is useful to return to data produced with earlier instances to
assess their credibility and correctness. The entomopathogenic nematode Heterorhabditis bacteriophora is widely used to control insect pests in horticulture. The genome sequence for this species was reported to encode an unusually high proportion of unique proteins and a paucity of secreted proteins compared to other related nematodes. We revisited the H. bacteriophora genome assembly and gene predictions to ask whether these unusual characteristics were biological or methodological in origin. We mapped an independent resequencing dataset to the genome and used the blobtools pipeline to identify potential contaminants. While present (0.2% of the genome span, 0.4% of predicted proteins), assembly contamination was not significant. Re-prediction of the gene set using BRAKER1 and published transcriptome data generated a predicted proteome that was very different from the published one. The new gene set had a much reduced complement of unique proteins, better completeness values that were in line with other related species'
genomes, and an increased number of proteins predicted to be secreted. It is thus likely that methodological issues drove the apparent uniqueness of the initial H.
bacteriophora genome annotation and that similar contamination and misannotation
issues affect other published genome assemblies.
DOI: 10.5524/100410
title: Supporting data for ‘Piggy: A Rapid, Large-Scale Pan-Genome Analysis Tool for Intergenic Regions in Bacteria’

description: Despite overwhelming evidence that variation in intergenic regions (IGRs) in bacteria can directly influence phenotypes, most current approaches for analysing pan-genomes focus exclusively on protein-coding sequences. To address this we present Piggy, a novel pipeline that emulates Roary except that it is based only on IGRs. We demonstrate the use of Piggy for pan-genome analyses of Staphylococcus aureus and Escherichia coli using large genome datasets. For S. aureus, we show that highly divergent (switched) IGRs are associated with differences in gene expression, and we establish a multi-locus reference database of IGR alleles (igMLST; implemented in BIGSdb). Piggy is available at https://github.com/harry-thorpe/piggy and registered with SciCrunch (RRID: SCR_015941).
DOI: 10.5524/100411
title: Supporting data for "The draft genome sequence of forest musk deer (Moschus berezovskii)"

description: The forest musk deer, Moschus berezovskii, is one of seven musk deer (Moschus spp.) and is distributed in Southwest China. Akin to other musk deer, the forest musk deer has been traditionally, and is currently, hunted for its musk (i.e. global perfume industry). Considerable hunting pressure and habitat loss has caused significant population declines and therefore the Chinese government commenced captive breeding programs for musk harvesting in the 1950s. However, the prevalence of fatal diseases is considerably restricting population increases. Disease severity and extent is exacerbated by inbreeding and genetic diversity declines in captive musk deer populations. It is essential for the physical and genetic health of captive and wild forest musk deer populations to improve knowledge of its immune system and genome. We have thus sequenced the whole genome of the forest musk deer, completed the genomic assembly and annotation, and performed preliminary bioinformatic analyses. A total of 407 Gb raw reads from whole-genome sequencing was generated by the Illumina Hiseq4000 platform. The final assembly genome is around 2.72 Gb, with a contig N50 length of 22.6 kb and a scaffold N50 length 2.85 Mb. We identified 24,352 genes, and found 42.05% of the genome is composed of repetitive elements. We also detected 1,236 olfactory receptor genes. The genome-wide phylogenetic tree indicated that the forest musk deer was within the order Artiodactyla, and it appeared as the sister clade of four members of family Bovidae. In total, 576 genes were under positive selection in the forest musk deer lineage. We provide the first genome sequence and gene annotation for the forest musk deer. The availability of these resources will be very useful for the conservation and captive breeding for this Endangered and economically important species, and for reconstructing the evolutionary history of the order Artiodactyla.
DOI: 10.5524/100390
title: Supporting data for "Mammalian genomic regulatory regions predicted by utilizing human genomics, transcriptomics and epigenetics data"

description: Genome sequences for hundreds of mammalian species are available, but an understanding of their genomic regulatory regions, which control gene expression, is only beginning. A comprehensive prediction of potential active regulatory regions is necessary to functionally study the roles of the majority of genomic variants in evolution, domestication, and animal production. We developed a computational method to predict regulatory DNA sequences (promoters, enhancers and transcription factor binding sites) in production animals (cows and pigs) and extended its broad applicability to other mammals. The method utilizes human regulatory features identified from thousands of tissues, cell lines, and experimental assays to find homologous regions that are conserved in sequences and genome organization and are enriched for regulatory elements in the genome sequences of other mammalian species. Importantly, we developed a filtering strategy, including a machine learning classification method, to utilize a very small number of species-specific experimental datasets available to select for the likely active regulatory regions. The method finds the optimal combination of sensitivity and accuracy to unbiasedly predict regulatory regions in mammalian species. Furthermore, we demonstrated the utility of the predicted regulatory datasets in cattle for prioritizing variants associated with multiple production and climate change adaptation traits, and identifying potential genome editing targets.
DOI: 10.5524/100391
title: Supporting data for "A catalog of microbial genes from the bovine rumen reveals the determinants of herbivory"

description: The rumen microbiome is responsible for the unique nature of ruminants. A thorough knowledge of the genetic potential of rumen symbiotic microbes is therefore crucial for the sustainability of ruminant production systems. Using deep metagenome sequencing we identified 13,825,880 non-redundant prokaryote genes from the bovine rumen and constructed 324 high quality metagenomic species. These metagenomic species were prevalent in the rumen of 77 cattle fed various diets whereas known rumen microbial genomes were less abundant. Compared to human, pig and mouse gut metagenome catalogs, the rumen is richer in functions and microbial species associated to the degradation of lignocellulosic material and production of methane. Genes coding for enzymes that deconstruct lignocellulosic substrates showed a particularly high richness that is otherwise impossible to infer from available genomes or shallow metagenomics sequencing. These data bring new insights on functions, enzymes and microbes of the rumen, critical to understand phenotypes and biological processes.
DOI: 10.5524/100397
title: Supporting data for "Finding Nemo: Hybrid assembly with Oxford Nanopore and Illumina reads greatly improves the Clownfish (Amphiprion ocellaris) genome assembly"

description: Some of the most widely recognised coral-reef fishes are clownfish or anemonefishes, members of the family Pomacentridae (subfamily: Amphiprioninae). They are popular aquarium species due to their bright colours, adaptability to captivity and fascinating behavior. Their breeding biology (sequential hermaphrodites) and symbiotic mutualism with sea anemones have attracted much scientific interest. Moreover, there are some curious geographic-based phenotypes which warrant investigation. Leveraging on the advancement in Nanopore long read technology, we report the first hybrid assembly of the clown anemonefish (Amphiprion ocellaris) genome utilizing Illumina and Nanopore reads, further demonstrating the substantial impact of modest long read sequencing data sets on improving genome assembly statistics. We generated 43 Gb of short Illumina reads and 9 Gb of long Nanopore reads representing an approximate genome coverage of 54× and 11×, respectively, based on the range of estimated k-mer-predicted genome sizes of between 791 to 967 Mbp. The final assembled genome size is contained in 6,404 scaffolds with an accumulated length of 880 Mb (96.3% BUSCO-calculated genome completeness). Compared to the Illumina-only assembly, the hybrid approach generated 94% fewer scaffolds with 18-fold increase in N50 length (401 kb) and increased the genome completeness by an additional 16%. A total of 27,240 high quality protein-coding genes were predicted from the clown anemonefish, 26,211 (96%) of which were annotated functionally with information from either sequence homology or protein signature searches. We present the first genome of any anemonefish and demonstrate the value of low coverage (~11×) long Nanopore reads sequencing in improving both genome assembly contiguity and completeness. The near-complete assembly of the A. ocellaris genome will be an invaluable molecular resource for supporting a range of genetic, genomic and phylogenetic studies specifically for clownfish and more generally for other related fish species of the family Pomacentridae.
DOI: 10.5524/100399
title: Supporting data for "Advanced lesion symptom mapping analyses and implementation as BCBtoolkit"

description: Patients with brain lesions provide a unique opportunity to understand the functioning of the human mind. However, even when focal, brain lesions have local and remote effects that impact functionally and structurally connected circuits. Similarly, function emerges from the interaction between brain areas rather than their sole activity. For instance, category fluency requires the association between executive, semantic and language functions. Here we provide, for the first time, a set of complementary solutions to measure the impact of a given lesion upon the neuronal circuits. Our methods, which were applied to 37 patients with a focal frontal brain lesion, revealed a large set of directly and indirectly disconnected brain regions that had significantly impacted category fluency performance. The directly disconnected regions corresponded to areas that are classically considered as functionally engaged in verbal fluency and categorization tasks. These regions were also organized into larger directly and indirectly disconnected functional networks, including the left ventral fronto-parietal network, whose cortical thickness correlated with performance on category fluency. The combination of structural and functional connectivity together with cortical thickness estimates reveal the remote effects of brain lesions, provide for the identification of the affected networks and strengthen our understanding of their relationship with cognitive and behavioural measures. The methods presented are available and freely accessible in the BCBtoolkit as supplementary software (http://toolkit.bcblab.com).
DOI: 10.5524/100405
title: Draft genomes of two blister beetles Hycleus cichorii and Hycleus phaleratus

description: Commonly known as blister beetles or <em>Spanish fly</em>, there are more than 1,500 species in the Meloidae family (Hexapoda:Coleoptera:Tenebrionoidea) that produce the potent defensive blistering agent cantharidin. Cantharidin and its derivatives have been used to treat cancers, such as liver, stomach, lung and esophageal cancers.<em> Hycleus cichorii</em> and <em>Hycleus phaleratus</em> are the most commercially important blister beetles due to their ability to biosynthesize this potent vesicant. However, there is a lack of genome reference, which has hindered development of studies on the biosynthesis of cantharidin and a better understanding of its biology and pharmacology. We report two draft genomes and quantified gene sets for blister beetles<em> H. cichorii</em> and <em>H. phaleratus</em>, two complex genomes with &gt;72 % repeats and ~1 % heterozygosity, using Illumina sequencing data. An integrated assembly pipeline was performed for assembly and most of the coding regions were obtained. BUSCO assessment showed that our assembly obtained more than 98 % of the Endopterygota universal single-copy orthologs. Comparison analysis showed that the completeness of coding gene in our assembly was comparable to other beetle genomes such as <em>Dendroctonus ponderosae</em> and <em>Agrilus planipennis</em>. Gene annotation yielded 13,813 and 13,725 protein-coding genes in <em>H. cichorii</em> and <em>H. phaleratus</em>, of which ~89 % were functionally annotated. BUSCO assessment showed that ~86 and 84 % of the Endopterygota universal single-copy orthologs were annotated completely in these two gene sets, whose completeness is comparable to that of <em>D. ponderosae</em> and <em>A. planipennis</em>. Assembly of the both blister beetle genomes provide a valuable resource for future biosynthesis of cantharidin and comparative genomic studies of blister beetles and other beetles.
DOI: 10.5524/100408
title: Supporting data for ‘Whole-genome sequences of 89 Chinese sheep suggest role of <em>RXFP2</em> in the development of unique horn phenotype as response to semi-feralization’

description: Animal domestication has been extensively studied but the process of feralization remains poorly understood. Here, we performed whole-genome sequencing of 99 sheep and identified a primary genetic divergence between two heterogeneous populations in the Tibetan Plateau, including one semi-feral lineage. Selective sweep and candidate gene analysis revealed the local adaptations of these sheep associated with sensory perception, muscle strength, eating habit, mating process and aggressive behavior. In particular, a horn-related gene <em>RXFP2</em> showed signs of rapid evolution specifically in the semi-feral breeds. A unique haplotype and repressed horn-related-tissue expressions of <em>RXFP2</em> were correlated with higher horn length, as well as spiral and horizontally extended horn shape. Semi-feralization has an extensive impact on diverse phenotypic traits of sheep. By acquiring features like those of their wild ancestors, semi-feral sheep were able to re-gain fitness in frequent contact with wild surroundings and rare human interventions. The present study provides a new insight into the evolution of domestic animals when human interventions are no longer dominant.
DOI: 10.5524/100363
title: Supporting data for "Filling reference gaps via assembling DNA barcodes using high-throughput sequencing - moving toward barcoding the world"

description: Over the past decade, biodiversity scientists have dedicated tremendous efforts in constructing DNA reference barcodes for rapid species registration and identification. Although analytical cost for standard DNA barcoding has been significantly reduced since early 2,000, further dramatic reduction on barcoding costs is unlikely because the Sanger sequencing is approaching its limits in throughput and chemistry cost. Constraints in barcoding cost not only led to unbalanced barcoding efforts around the globe, but also refrained High-Throughput-Sequencing (HTS) based taxonomic identification from applying binomial species names, which provide crucial linkages to biological knowledge. We developed an Illumina-based pipeline, HIFI-Barcode, to produce full-length COI barcodes from pooled PCR amplicons generated by individual specimens. The new pipeline generated accurate barcode sequences that were comparable to Sanger standards, even for different haplotypes of the same species that were only a few nucleotides different from each other. Additionally, the new pipeline was much more sensitive in recovering amplicons at low quantity. The HIFI-Barcode pipeline successfully recovered barcodes from over 78% of the PCR reactions that didn't show clear bands on the electrophoresis gel. Moreover, sequencing results based on the single molecular sequencing platform, Pacbio, confirmed the accuracy the HIFI-Barcode results. Altogether, the new pipeline can provide an improved solution to produce full-length reference barcodes at about 1/10 of the current cost, enabling construction of comprehensive barcode libraries for local fauna, leading to a feasible direction for DNA barcoding global biomes.