cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5524/100365
title: Supporting data for "eHistology image and annotation data from the Kaufman Atlas of Mouse Development"

description: The Atlas of Mouse Development by Kaufman is a classic paper atlas that is the <em>de facto</em> standard for the definition of mouse embryo anatomy in the context of standard histological images. We have re-digitised the original H&E stained tissue sections used for the book at high resolution and transferred the hand-drawn annotations to digital form. We have augmented the annotations with standard ontological assignments (EMAPA anatomy) and made the data freely available. The dataset captures and preserves the definitive anatomical knowledge of the original atlas, provides a core image set for deeper community annotation and teaching, and delivers a unique high-quality set of high-resolution histological images through mammalian development for manual and automated analysis.
DOI: 10.5524/100389
title: Supporting data for "Snake fangs: 3D morphological and mechanical analysis by microCT, simulation and physical compression testing"

description: This data note provides data from an experimental campaign to analyse the detailed internal and external morphology and mechanical properties of venomous snake fangs. The aim of the experimental campaign was to investigate the evolutionary development of three fang phenotypes and investigate their mechanical behaviour. The study involved the use of load simulations to compare maximum Von Mises stress values, when a load is applied to the tip of the fang. The conclusions of this study have been published elsewhere, but in this data note we extend the analysis, providing morphological comparisons including details such as curvature comparisons, thickness, etc. Physical compression results of individual fangs, though reported in the original paper, were also extended here by calculating the effective elastic modulus of the entire snake fang structure including internal cavities for the first time. This elastic modulus of the entire fang is significantly lower than the locally-measured values previously reported from indentation experiments, highlighting the possibility that the elastic modulus is higher on the surface than in the rest of the material. The microCT data is presented both in image stacks and in the form of STL files, which simplifies the handling of the data and allow its re-use for future morphological studies. These fangs might also serve as bio-inspiration for future hypodermic needles.
DOI: 10.5524/100392
title: Supporting data for "Predicting plant biomass accumulation from image-derived parameters"

description: <br>Image-based high-throughput phenotyping technologies have been rapidly developed in plant science recently and they provide a great potential to gain more valuable information than traditionally destructive methods. Predicting plant biomass is regarded as a key purpose for plant breeders and ecologist. However, it is a great challenge to find a predictive biomass model across experiments.
<br>In the present study, we constructed four predictive models to examine the quantitative relationship between image-based features and plant biomass accumulation. Our methodology has been applied to three consecutive barley (<em>Hordeum vulgare</em>) experiments with control and stress treatments. The results proved that plant biomass can be accurately predicted from image-based parameters using a random forest model. The high prediction accuracy based on this model will contribute to relieve the phenotyping bottleneck in biomass measurement in breeding applications. The prediction performance is still relatively high cross experiments under similar conditions. The relative contribution of individual features for predicting biomass was further quantified, revealing new insights into the phenotypic determinants of plant biomass outcome. Furthermore, the methods could also be used to determine the most important image-based features related to plant biomass accumulation, which would be promising for subsequent genetic mapping to uncover the genetic basis of biomass.
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We have developed quantitative models to accurately predict plant biomass accumulation from image data. We anticipate that the analysis results will be useful to advance our views of the phenotypic determinants of plant biomass outcome, and the statistical methods can be broadly used for other plant species.
DOI: 10.5524/100402
title: Supporting data for "GeneSeqToFamily: a Galaxy workflow to find gene families based on the Ensembl Compara GeneTrees pipeline"

description: Gene duplication is a major factor contributing to evolutionary novelty, and the contraction or expansion of gene families has often been associated with morphological, physiological and environmental adaptations. The study of homologous genes helps us to understand the evolution of gene families. It plays a vital role in finding ancestral gene duplication events as well as identifying genes that have diverged from a common ancestor under positive selection. There are various tools available, such as MSOAR, OrthoMCL and HomoloGene, to identify gene families and visualise syntenic information between species, providing an overview of syntenic regions evolution at the family level. Unfortunately, none of them provide information about structural changes within genes, such as the conservation of ancestral exon boundaries amongst multiple genomes. The Ensembl GeneTrees computational pipeline generates gene trees based on coding sequences and provides details about exon conservation, and is used in the Ensembl Compara project to discover gene families.

A certain amount of expertise is required to configure and run the Ensembl Compara GeneTrees pipeline via command line. Therefore, we have converted the command line Ensembl Compara GeneTrees pipeline into a Galaxy workflow, called GeneSeqToFamily, and provided additional functionality. This workflow uses existing tools from the Galaxy ToolShed, as well as providing additional wrappers and tools that are required to run the workflow.

GeneSeqToFamily represents the Ensembl Compara pipeline as a set of interconnected Galaxy tools, so they can be run interactively within the Galaxys user-friendly workflow environment while still providing the flexibility to tailor the analysis by changing configurations and tools if necessary. Additional tools allow users to subsequently visualise the gene families produced by the workflow, using the Aequatus.js interactive tool, which has been developed as part of the Aequatus software project.
DOI: 10.5524/100406
title: Supporting data for "Genome-wide determination of on-target and off-target characteristics for RNA-guided DNA Methylation by dCas9 methyltransferases"

description: Fusion of DNA methyltransferase domains to the nuclease-deficient clustered regularly interspaced short palindromic repeat (CRISPR) associated protein 9 (dCas9) has been used for epigenome editing, but the specificities of these dCas9 methyltransferases have not been fully investigated. 
<br>We generated CRISPR-guided DNA methyltransferases by fusing the catalytic domain of DNMT3A or DNMT3B to the C terminus of the dCas9 protein from S. pyogenes and validated its on-target and global off-target characteristics. Using targeted quantitative bisulfite pyrosequencing, we prove that dCas9-BFP-DNMT3A and dCas9-BFP-DNMT3B can efficiently methylate the CpG dinucleotides flanking its target sites at different genomic loci (uPA and TGFBR3) in human embryonic kidney cells (HEK293T). Furthermore, we conducted whole genome bisulfite sequencing (WGBS) to address the specificity of our dCas9 methyltransferases. WGBS revealed that although dCas9-BFP-DNMT3A and dCas9-BFP-DNMT3B did not cause global methylation changes, a substantial number (over 1000) of off-target differentially methylated regions (DMRs) were identified. The off-target DMRs, which were hypermethylated in cells expressing dCas9 methyltransferase and gRNAs, were predominantly found in promoter regions, 5 untranslated regions, CpG islands, and DNase I hypersensitivity sites, whereas, unexpected hypomethylated off-target DMRs were significantly enriched in repeated sequences. Through chromatin immunoprecipitation with massive parallel DNA sequencing analysis, we further revealed that these off-target DMRs were weakly correlated with dCas9 off-target binding sites. Using qPCR, RNA sequencing and fluorescence reporter cells, we also found that dCas9-BFP-DNMT3A and dCas9-BFP-DNMT3B can mediate transient inhibition of gene expression, which might be caused by dCas9-mediated de novo DNA methylation as well as interference with transcription.
DOI: 10.5524/100407
title: Supporting data for "The genome sequence and transcriptome of Potentilla micrantha and their comparison to Fragaria vesca (the woodland strawberry)"

description: The genus Potentilla is closely related to that of Fragaria, the economically important strawberry genus. Potentilla micrantha is a species that does not develop berries, but shares numerous morphological and ecological characteristics with F. vesca. These similarities make P. micrantha an attractive choice for comparative genomics studies with F. vesca. <br>In this study, the Potentilla micrantha genome was sequenced and annotated, and RNA-Seq data from the different developmental stages of flowering and fruiting were used to develop a set of gene predictions. A 327 Mbp sequence and annotation of the genome of P. micrantha, spanning 2,674 sequence contigs, with an N50 size of 335,712, estimated to cover 80% of the total genome size of the species was developed. <br>The genus Potentilla has a characteristically larger genome size than Fragaria, but the recovered sequence scaffolds were remarkably collinear at the microsyntenic level with the genome of F. vesca, its closest sequenced relative. A total of 33,602 genes were predicted, and 95.1% of BUSCO genes were complete within the presented sequence. Thus, we argue that the majority, of the gene-rich regions of the genome have been sequenced. Comparisons of RNA-Seq data from the stages of floral and fruit development revealed genes differentially expressed between P. micrantha and F. vesca. The data presented are a valuable resource for future studies of berry development in Fragaria and the Rosaceae and they also shed light on the evolution of genome size and organization in this family.
DOI: 10.5524/100409
title: Supporting data for ‘Draft Genome of the Protandrous Chinese Black Porgy, <em>Acanthopagrus schlegelii’</em>

description: As one of the most popular and valuable commercial marine fishes in China and East Asian countries, the Chinese black porgy (<em>Acanthopagrus schlegelii</em>) also known as the blackhead seabream, has some attractive characteristics, such as fast growth rate, good meat quality, resistance to diseases and excellent adaptability to various environments. Furthermore, the black porgy is a good model for investigating sex changes in fish due to its protandrous hermaphrodite. Here, we obtained a high-quality genome assembly of this interesting teleost species and performed a genomic survey on potential genes associated with the sex-change phenomenon. We generated 175.4 gigabases (Gb) of clean sequence reads using a whole-genome shotgun sequencing strategy. The final genome assembly is approximately 688.1 megabases (Mb), accounting for 93% of the estimated genome size (739.6 Mb). The achieved scaffold N50 is 7.6 Mb, reaching a relatively high level among sequenced fish species. Meanwhile, we identified 19,465 protein-coding genes, which had an average transcript length of 17.3 kb. By performing a comparative genomic analysis, we found three types of genes potentially associated with sex change, which are useful for the prediction of related genetic basis for the interesting protandrous hermaphrodite. We provided a draft genome assembly of the Chinese black porgy and discussed about the potential genetic mechanisms of sex change. These data are also an important resource for studying the biology and facilitating the molecular breeding of this economically important fish.
DOI: 10.5524/100328
title: Supporting data for "Novel transcriptome resources for three scleractinian coral species from the Indo-Pacific"

description: Transcriptomic resources for coral species can provide insight into coral evolutionary history and stress-response physiology. Goniopora columna, Galaxea astreata and Galaxea acrhelia are scleractinian corals of the Indo-Pacific, representing a diversity of morphologies and life-history traits. G. columna and G. astreata are common and cosmopolitan, while G. acrhelia is largely restricted to the coral triangle and Great Barrier Reef. Reference transcriptomes for these species were assembled from replicate colony fragments exposed to elevated (31°C) and ambient (27°C) temperature.<br>
Trinity was used to create de novo assemblies for each species from 92-102 million raw Illumina Hiseq 2 x 150 bp reads. Host-specific assemblies contained 65,460-72,405 contigs, representing 26,693-37,894 isogroups (~genes) with an average N50 of 2,254. Gene name and/or gene ontology annotations were possible for 58% of isogroups on average. Transcriptomes contained 93.1-94.3% of KOGs comprising the core eukaryotic gene set and 89.98-91.92% of the single-copy metazoan core gene set orthologs were complete, indicating fairly comprehensive assemblies.
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This work expands the complement of transcriptomic resources available for scleractinian coral species, including the first reference for a representative of Goniopora spp. as well as species with novel morphology.
DOI: 10.5524/100329
title: De novo genome assembly and annotation data for the Murray cod (Maccullochella peelii), Australia's largest freshwater fish

description: One of the most iconic Australian fish is the Murray cod, Maccullochella peelii (Mitchell, 1838), a freshwater species that can grow to ~1.8 metres in length and live 48 years of age. The Murray cod is of conservation concern as a result of strong population contractions, but is also popular for recreational fishing and is of growing aquaculture interest. In this study, we report the whole genome sequence of the Murray cod to support ongoing population genetics, conservation and management-related research, as well as to understand better the evolutionary ecology and history of the species.
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A draft Murray cod genome of 633 Mbp (N50=109,974bp; BUSCO and CEGMA completeness of 94.2% and 91.9%, respectively) with an estimated 148 Mbp of putative repetitive sequences was assembled from the combined sequencing data of two fish individuals with an identical maternal lineage. 47.2 Gb of Illumina HiSeq data and 804 Mb of Nanopore data were generated from the first individual while 23.2 Gb of Illumina MiSeq data were from the second individual. The inclusion of Nanopore reads for scaffolding followed by subsequent gap-closing using Illumina data led to a 29% reduction in the number of scaffolds and a 55% and 54% increase in the scaffold and contig N50, respectively. We also report the first transcriptome of Murray cod that was subsequently used to annotate the Murray cod genome leading to the identification of 26,539 protein-coding genes.
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We present the whole genome of the Murray cod and anticipate this will be a catalyst for a range of genetic, genomic and phylogenetic studies of the Murray cod and more generally other fish species of Percichthydae family.
DOI: 10.5524/100336
title: Supporting data for "Proteomic landscape of the primary somatosensory cortex upon sensory deprivation"

description: Experience-dependent plasticity (EDP) powerfully shapes neural circuits by inducing long-lasting molecular changes in the brain. Molecular mechanisms of EDP have been traditionally studied by identifying single or small subsets of targets along the biochemical pathways that link synaptic receptors to nuclear processes. Recent technological advances in large-scale analysis of gene transcription and translation now allow systematic observation of thousands of molecules simultaneously. Here we employed label-free quantitative mass spectrometry to address experience-dependent changes in the proteome after sensory deprivation of the primary somatosensory cortex.br /
Cortical column- and layer-specific tissue samples were collected from control animals, with all whiskers intact, and animals whose C-row whiskers were bilaterally plucked for 11-14 days. 33 samples from cortical layers (L) 2/3 and L4 spanning across control, deprived, 1st and 2nd order spared columns yielded at least 10,000 peptides mapping to ~5000 protein groups. Of these, 4,676 were identified with high confidence and 3000 are found in all samples.
This comprehensive database provides a snapshot of the proteome after whisker deprivation, a protocol that has been widely used to unravel the synaptic, cellular and network mechanisms of EDP. Complementing the recently made available transcriptome for identical experimental conditions (see DOI:10.5524/100296), the database can be used to (1) mine novel targets whose translation is modulated by sensory organ use, (2) cross-validate experimental protocols from the same developmental time point, and (3) statistically map the molecular pathways of cortical plasticity at a columnar and laminar resolution.
DOI: 10.5524/100340
title: Supporting data for "Long-read sequencing of the coffee bean transcriptome reveals the diversity of full length transcripts"

description: Polyploidization contributes to the complexity of gene expression resulting in numerous related but different transcripts. This study explored the transcriptome diversity and complexity of tetraploid Arabica coffee (Coffea arabica) bean. Long-read sequencing (LRS) by Pacbio Isoform sequencing (Iso-seq) was used to obtain full-length transcripts without the difficulty and uncertainty of assembly required for reads from short read technologies. The tetraploid transcriptome was annotated and compared with data from the sub-genome progenitors. Caffeine and sucrose genes were targeted for case analysis.
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An isoform-level tetraploid coffee bean reference transcriptome with 95,995 distinct transcripts (average 3,236 bp) was obtained. A total of 88,715 sequences (92.42%) were annotated with BLASTx against NCBI non-redundant plant proteins, including 34,719 high quality annotations. Further BLASTn to NCBI non-redundant nucleotide sequences, C. canephora coding sequences with UTR, C.arabica ESTs and Rfam resulted in 1,213 sequences without hits, were potential novel genes in coffee. Longer UTRs were captured, especially in the 5'UTRs, facilitating the identification of upstream ORFs (uORFs). The LRS also revealed more and longer transcript variants in key caffeine and sucrose metabolism genes from this polyploid genome. Long sequences (&gt;10kb) were poorly annotated.
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DOI: 10.5524/100345
title: Transcriptome assemblies of three Bauhinia species.

description: <em>Bauhinia blakeana Dunn</em> commonly known as the Hong Kong Orchid Tree, was adopted as the city flower of Hong Kong in 1965 and became the official emblem of the Hong Kong Special Administrative Region (HKSAR) in 1997. It was first discovered in the 1880s and is now planted all over the territory. It has long been suspected that <em>Bauhinia blakeana</em> is the sterile hybrid of two related species, <em>B. purpurea</em> and <em>B. variegata</em>, although limited genetic information of this plant has been available to confirm this. In this study utilizing crowdfunded data from the Bauhinia Genome project, unigenes of <em>B. blakeana</em> (94,755), <em>B. purpurea</em> (111,976) and <em>B. variegata</em> (81,757) were obtained after de novo transcriptome assembly of the three species leaves. We also pooled the reads of flowers and leaves from <em>B. blakeana</em>, resulting in 123,668 clusters. Data from mapping reads of the tested species to chloroplast sequences demonstrates that <em>B. purpurea</em> is the maternal parent. Differential expressed genes up-regulated in <em>B. blakeana</em> vs <em>B. purpurea</em> and <em>B. variegata</em> showed more specific bacterial and pathogen resistance, UV tolerance and drought avoidance. Using SNP parentage testing, a total of 79,302 SNPs were observed in 27 possible scenarios, in which 65,159 SNPs follow Mendelian law and yielded 82.17% in support of their parentage relationship. Raw data (see: GigaDB:100245) and RNA-extraction protocols (see: DOI:10.17504/protocols.io.gsnbwde) have already been published, and included here are the transcriptome assemblies, annotations and SNPs, along with other materials and results supporting this research. For more information see Buahinia Project pages.
DOI: 10.5524/100347
title: Supporting data for "The genome draft of Coconut (Cocos nucifera)"

description: Coconut palm (Cocos nucifera, 2n = 32), a member of genus Cocos and family Arecaceae (Palmaceae), is an important tropical fruit and oil crop. Currently, coconut palm is cultivated in 93 countries, including Central and South America, East and West Africa, Southeast Asia and the Pacific island, with a total growth area of more than 12 million hectares (www.fao.org/faostat/en/). Coconut palm is generally classified into two main categories: "Tall" (flowering 8-10 years after planting) and "Dwarf" (flowering 4-6 years after planting), based on morphological characteristics and breeding habits. This Palmae species has a long growth period before reproductive years which hinders conventional breeding progress. In spite of initial successes, improvements made by conventional breeding have been very slow. In the present study, we obtained de novo sequences of Cocos nucifera genome: a major genomic resource which could be used to facilitate molecular breeding in Cocos nucifera and accelerating the breeding process in this important crop.
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A total of 419.67 gigabases (Gb) of raw reads were generated by the IlluminaHiSeq 2000 platform using a series of paired-end and mate-pair libraries, covering the predicted Cocos nucifera genome length (2.42Gb, variety "Hainan Tall") to an estimated 173.32× read depth. A total scaffold length of 2.20 Gb was generated (N50 418 Kb), representing 90.91% of the genome. The coconut genome was predicted to harbor 28,039 protein-coding genes, which is less than in Phoenix dactylifera (PDK30 variety: 28,889), Phoenix dactylifera (DPV01 variety: 41,660) and Elaeis guineensis (34,802). BUSCO evaluation demonstrated the obtained scaffold sequences covered 90.8% of the coconut genome, and that the genome annotation was 74.1% complete. Genome annotation results revealed that 72.75% of the coconut genome was consisted of transposable elements. of which long-terminal repeat retrotransposons elements (LTRs) accounted for the largest proportion (92.23%). Comparative analysis of the antiporter gene family and ion channel gene families between C. nucifera and Arabidopsis thaliana indicated that significant gene expansion may occurred in coconut involving Na+/H+ antiporter, Carnitine/acylcarnitine translocase, Potassium-dependent sodium-calcium exchanger, and potassium channel genes.
DOI: 10.5524/100349
title: Supporting software for "Indexcov: fast coverage quality control for whole-genome sequencing"

description: The BAM and CRAM formats provide a supplementary linear index that facilitates rapid access to sequence alignments in arbitrary genomic regions. Comparing consecutive entries in a BAM or CRAM index allows one to infer the number of alignment records per genomic region for use as an effective proxy of sequence depth in each genomic region. Based on these properties, we have developed indexcov, an efficient estimator of whole-genome sequencing coverage to rapidly identify samples with aberrant coverage profiles, reveal large scale chromosomal anomalies, recognize potential batch effects, and infer the sex of a sample. Indexcov is available at: https://github.com/brentp/goleft under the MIT license.