cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5524/100463
title: Supporting data for "High quality assembly of the reference genome for scarlet sage, Salvia splendens, an economically important ornamental plant"

description: Salvia splendens Ker-Gawler, scarlet or tropical sage, is a tender herbaceous perennial widely introduced and seen in public gardens all over the world. With few molecular resources, breeding is still restricted to traditional phenotypic selection, and the genetic mechanisms underlying phenotypic variation still remain unknown. Hence, a high quality reference genome will be very valuable for marker assisted breeding, genome editing or molecular genetics. We generated 66 gigabases (Gb) and 37 Gb of raw DNA sequences, respectively, from whole-genome sequencing of a largely homozygous scarlet sage inbred line using PacBio Single-Molecule Real-Time (SMRT) and Illumina HiSeq sequencing platforms. PacBio de novo assembly yielded a final genome with a scaffold N50 size of 3.12 megabases (Mb), and a total length of 808 Mb. The repetitive sequences identified accounted for 57.52% of the genome sequence and 54,008 protein-coding genes were predicted collectively with ab initio and homology-based gene prediction from the masked genome. The divergence time between S. splendens and S. miltiorrhiza was estimated with 28.21 million years ago (Mya). Moreover, 3,797 species-specific genes and 1,187 expanded gene families were identified for the scarlet sage genome. We provide the first genome sequence and gene annotation for the scarlet sage. The availability of these resources will be of great importance for further breeding strategies, genome editing and also for comparative genomics among related species.
DOI: 10.5524/100464
title: Supporting data for "Leveraging multiple transcriptome assembly methods for improved gene structure annotation"

description: The performance of RNA-Seq aligners and assemblers varies greatly across different organisms and experiments, and often the optimal approach is not known beforehand. Here we show that the accuracy of transcript reconstruction can be boosted by combining multiple methods, and we present a novel algorithm to integrate multiple RNA-Seq assemblies into a coherent transcript annotation. Our algorithm can remove redundancies and select the best transcript models according to user-specified metrics, while solving common artefacts such as erroneous transcript chimerisms. We have implemented this method in an open-source Python3 and Cython program, Mikado, available at https://github.com/lucventurini/Mikado.
DOI: 10.5524/100465
title: Supporting data for "A near complete, chromosome-scale assembly of the black raspberry (Rubus occidentalis) genome"

description: The fragmented nature of most draft plant genomes has hindered downstream gene discovery, trait mapping for breeding, and other functional genomics applications. There is a pressing need to improve or finish draft plant genome assemblies. Here we present a chromosome-scale assembly of the black raspberry genome using single-molecule real-time (SMRT) PacBio sequencing and Hi-C genome scaffolding. The updated V3 assembly has a contig N50 of 5.1 Mb, representing a ~200-fold improvement over the previous Illumina-based version. Each of the 235 contigs was anchored and oriented into seven chromosomes, correcting several major misassemblies. Black raspberry V3 contains 47 Mb of new sequences including large pericentromeric regions and thousands of previously unannotated protein-coding genes. Among the new genes are hundreds of expanded tandem gene arrays that were collapsed in the Illumina-based assembly. Detailed comparative genomics with the high quality V4 woodland strawberry genome (Fragaria vesca) revealed near perfect 1:1 synteny with dramatic divergence in tandem gene array composition. Lineage-specific tandem gene arrays in black raspberry are related to agronomic traits such as disease resistance and secondary metabolite biosynthesis. The improved resolution of tandem gene arrays highlights the need to reassemble these highly complex and biologically important regions in draft plant genomes. The updated, high-quality black raspberry reference genome will be useful for comparative genomics across the horticulturally important Rosaceae family and enable the development of marker assisted breeding in Rubus.
DOI: 10.5524/100470
title: Supporting data for "Establishment of a <i>Macaca fascicularis</i> gut microbiome gene catalog and comparison with the human, pig and mouse gut microbiomes"

description: <i>Macaca fascicularis</i>, the cynomolgus macaque, is a widely used model in biomedical research and drug development as its genetics and physiology are close to humans. Detailed information on the cynomolgus macaque gut microbiota, the functional interplay between the gut microbiota and host physiology, and possible similarities to humans and other mammalians is very limited. The aim of this study was to construct the first cynomolgus macaque gut microbial gene catalog and compare this catalog to the human, pig, and mouse gut microbial gene catalogs. We performed metagenomic sequencing on fecal samples from twenty cynomolgus macaques and identified in total 1.9 million non-redundant bacterial genes of which 39.49% and 25.45% are present in the human and pig gut bacterial gene catalogs, respectively, whereas only 0.6% of the genes are present in the mouse gut bacterial gene catalog. By contrast, at the functional levels, more than 76% KOs are shared between the gut microbiota of all four mammalians. Thirty-two highly abundant bacterial genera could be defined as core genera of these mammalians. We demonstrated significant differences in the composition and functional potential of the gut microbiota as well as in the distribution of predicted bacterial phages sequences in cynomolgus macaques fed either a low-fat/high fiber diet or a high-fat/low fiber diet. Interestingly, the gut microbiota of cynomolgus macaques fed the high-fat/low fiber diet became more similar to the gut microbiota of humans.
DOI: 10.5524/100472
title: Supporting data for "KREAP: An automated Galaxy Platform to Quantify Re-Epithelialization Kinetics"

description: In vitro scratch assays have been widely used to study the influence of bioactive substances on the processes of cell migration and proliferation that are involved in re-epithelialization. The development of high-throughput microscopy and image analysis has enabled scratch assays to become compatible with high-throughput research. However, effective processing and in-depth analysis of such high-throughput image-datasets is far from trivial and requires integration of multiple image processing and data extraction software tools.<br>We developed and implemented a Kinetic Re-Epithelialization Analysis Pipeline (KREAP) in Galaxy. The KREAP toolbox incorporates freely available image analysis tools and automatically performs image segmentation and feature extraction of each image series, followed by automatic quantification of cells inside and outside the scratched area over time. The enumeration of infiltrating cells over time is modelled to extract three biologically relevant parameters that describe re-epithelialization kinetics. The output of the tools is organized, displayed, and saved in the Galaxy environment for future consultation. <br>The Galaxy KREAP toolbox provides an open-source, easy-to-use, web-based platform for reproducible image processing and data analysis of high-throughput scratch assays. The KREAP toolbox could assist a broad scientific community in the discovery of compounds that are able to modulate re-epithelialization kinetics.
DOI: 10.5524/100475
title: Supporting data for "Entering the era of conservation genomics: Cost-effective assembly of the African wild dog genome using linked reads"

description: A high-quality reference genome assembly is a valuable tool for the study of non-model organisms across disciplines. Genomic techniques can provide important insights about past population sizes, local adaptation, and even aid in the development of breeding management plans. This information can be particularly important for fields like conservation genetics, where endangered species require critical and immediate attention. However, funding for genomic-based methods can be sparse for conservation projects, as costs for general species management can consume budgets. Here we report the generation of high-quality reference genomes for the African wild dog (Lycaon pictus) at a low cost, thereby facilitating future studies of this endangered canid. We generated assemblies for three individuals from whole blood samples using the linked-read 10x Genomics Chromium system. The most continuous assembly had a scaffold N50 of 21 Mb, a contig N50 of 83 Kb, and completely reconstructed 95% of conserved mammalian genes as reported by BUSCO v2, indicating a high assembly quality. Thus, we show that 10x Genomics Chromium data can be used to effectively generate high-quality genomes of mammal species from Illumina short-read data of intermediate coverage (~25-50x). Interestingly, the wild dog shows a much higher heterozygosity than other species of conservation concern, possibly as a result of its behavioral ecology. The availability of reference genomes for non-model organisms will facilitate better genetic monitoring of threatened species such as the African wild dog and help researchers and conservationists to better understand the ecology and adaptability of those species in a changing environment.
DOI: 10.5524/100486
title: Supporting data for "Comparative genomics and transcriptomics of Chrysolophus provide insights into the evolution of complex plumage coloration"

description: As one of the most recognizable characteristics in birds, plumage colour has a high impact on understanding the evolution and mechanisms of colouration. Feather and skin are ideal tissues to explore the genomics and complexity of colour patterns in vertebrates. Two species of the genus Chrysolophus, golden pheasant (Chrysolophus pictus) and Lady Amhersts pheasant (Chrysolophus amherstiae), exhibit brilliant colours in their plumage, but with extreme phenotypic differences, making these two species great models to investigate plumage colouration mechanisms in birds.<br>We sequence and assemble a genome of golden pheasant with high-coverage and annotate 15,552 protein-coding genes. The genome of Lady Amherst's pheasant is sequenced with low coverage. Based on the feather pigment identification, a series of genomic and transcriptomic comparisons are conducted to investigate the complex features of plumage colouration. Through identifying the lineage-specific sequence variations in Chrysolophus and golden pheasant, against different backgrounds, we find that four melanogenesis biosynthesis genes and some lipid-related genes might be candidate genomic factors for the evolution of melanin and carotenoid pigmentation, respectively. In addition, a study among 47 birds shows some candidate genes related to carotenoid colouration in a broad range of birds. The transcriptome data further reveal important regulators of the two colourations, particularly one splicing transcript of the microphthalmia-associated transcription factor (MITF) gene for pheomelanin synthesis.<br>Analysis of the golden pheasant and its sister pheasant genomes, as well as comparison with other avian genomes, are helpful to reveal the underlying regulation of their plumage colouration. The present study provides important genomic information and insights for further studies of avian plumage evolution and diversity.
DOI: 10.5524/100473
title: Supporting data for "SVEngine: an efficient and versatile simulator of genome structural variations with features of cancer clonal evolution"

description: Simulating genome sequence data with features can facilitate the development and benchmarking of structural variant analysis programs. However, there are a limited number of data simulators that provide structural variants in silico. Moreover, there are a paucity of programs that generate structural variants with different allelic fraction and haplotypes. We developed SVEngine, an open source tool to address this need. SVEngine simulates next generation sequencing data with embedded structural variations. As input, SVEngine takes template haploid sequences (FASTA) and an external variant file, a variant distribution file and/or a clonal phylogeny tree file (NEWICK) as input. Subsequently, it simulates and outputs sequence contigs (FASTAs), sequence reads (FASTQs) and/or post-alignment files (BAMs). All of the files contain the desired variants, along with BED files containing the ground truth. SVEngine's flexible design process enables one to specify size, position, and allelic fraction for deletion, insertion, duplication, inversion and translocation variants. Finally, SVEngine simulates sequence data that replicates the characteristics of a sequencing library with mixed sizes of DNA insert molecules. To improve the compute speed, SVEngine is highly parallelized to reduce the simulation time. We demonstrated the versatile features of SVEngine and its improved runtime comparisons with other available simulators. SVEngine's features include the simulation of locus-specific variant frequency designed to mimic the phylogeny of cancer clonal evolution. We validated the accuracy of the simulations. Our evaluation included checking various sequencing mapping features such as coverage change, read clipping, insert size shift and neighbouring hanging read pairs for representative variant types. SVEngine is implemented as a standard Python package and is freely available for academic use at: https://bitbucket.org/charade/svengine.
DOI: 10.5524/100446
title: Supporting data for "Independent assessment and improvement of wheat genome sequence assemblies using Fosill jumping libraries."

description: The accurate sequencing and assembly of very large, often polyploid, genomes remain a challenging task, limiting long-range sequence information and phased sequence variation for applications such as plant breeding. The 15 Gb hexaploid bread wheat genome has been particularly challenging to sequence, and several different approaches have recently generated long-range assemblies. Mapping and understanding the types of assembly errors is important for optimising future sequencing and assembly approaches and for comparative genomics. <br>Here we use a Fosill 38 Kb jumping library to assess medium and longerrange order of different publicly available wheat genome assemblies. Modifications to the Fosill protocol generated longer Illumina sequences and enabled comprehensive genome coverage. Analyses of two independent BAC-based chromosome-scale assemblies, two independent Illumina whole genome shotgun assemblies, and a hybrid Single Molecule Real Time (SMRT-PacBio) and short read (Illumina) assembly were carried out. We revealed a surprising scale and variety of discrepancies using Fosill mate-pair mapping and validated several of each class. In addition, Fosill mate-pairs were used to scaffold a whole genome Illumina assembly, leading to a three-fold increase in N50 values.<br>Our analyses, using an independent means to validate different wheat genome assemblies, show that whole genome shotgun assemblies based solely on Illumina sequences are significantly more accurate by all measures compared to BAC-based chromosome-scale assemblies and hybrid SMRT-Illumina approaches. Although current whole genome assemblies are reasonably accurate and useful, additional improvements will be needed to generate complete assemblies of wheat genomes using open-source, computationally efficient and cost-effective methods.
DOI: 10.5524/100655
title: Supporting data for "Assembly of the 373K gene space of the polyploid sugarcane genome reveals reservoirs of functional diversity in the world’s leading biomass crop"

description: Sugarcane cultivars are polyploid interspecific hybrids of giant genomes, typically with 10-13 sets of chromosomes from two Saccharum species. The ploidy, hybridity and size of the genome, estimated to have in excess of 10 Gb, pose a great challenge for sequencing.<br> Here we present a gene space assembly of SP80-3280, including 373,869 putative genes and their potential regulatory regions. The alignment of single-copy genes in diploid grasses to the putative genes, indicates that we could resolve 2-6 (up to 15) putative homo(eo)logs that are 99.1% identical within their coding sequences. Dissimilarities increase in their regulatory regions and gene promoter analysis shows differences in regulatory elements within gene families and are species-specific expressed. We exemplify these differences for sucrose synthase (SuSy) and phenylalanine ammonia-lyase (PAL), two gene families central to carbon partitioning. SP80-3280 have particular regulatory elements involved in sucrose synthesis not found in the ancestor <i>S. spontaneum</i>. PAL regulatory elements are found in co-expressed genes related to fiber synthesis within gene networks defined during plant growth and maturation. Comparison to sorghum reveals predominantly biallelic variations in sugarcane, consistent with the formation of two subgenomes after their divergence ca. 3.8~4.6 MYA and reveals SNVs that may underlie their differences. <br> This assembly represents a large step towards a whole genome assembly of a commercial sugarcane cultivar. It includes a rich diversity of genes and homo(eo)logous resolution for a representative fraction of the gene space, relevant to improve biomass and food production.
DOI: 10.5524/100414
title: Supporting data for "Genome-scale metabolic modelling of responses to polymyxins in <i>Pseudomonas aeruginosa</i>."

description: <i>Pseudomonas aeruginosa</i> often causes multidrug-resistant infections in immunocompromised patients and polymyxins are often used as the last-line therapy. Alarmingly, resistance to polymyxins has been increasingly reported worldwide recently. To rescue this last-resort class of antibiotics, it is necessary to systematically understand how <i>P. aeruginosa</i> alters its metabolism in response to polymyxin treatment, thereby facilitating the development of effective therapies. To this end, a genome-scale metabolic model (GSMM) was employed to analyse bacterial metabolic changes at the systems level.<br>
A high-quality GSMM iPAO1 was constructed for <i>P. aeruginosa</i> PAO1 for antimicrobial pharmacological research. Model iPAO1 encompasses an additional periplasmic compartment and contains 3,022 metabolites, 4,265 reactions and 1,458 genes in total. Growth prediction on 190 carbon and 95 nitrogen sources achieved an accuracy of 89.1%, outperforming all reported <i>P. aeruginosa</i> models. Notably, prediction of the essential genes for growth achieved a high accuracy of 87.9%. Metabolic simulation showed that lipid A modifications associated with polymyxin resistance exerted a limited impact on bacterial growth and metabolism, but remarkably changed the physiochemical properties of the outer membrane. Modelling with transcriptomic constraints revealed a broad range of metabolic responses to polymyxin treatment, including reduced biomass synthesis, upregulated amino acids catabolism, induced flux through the tricarboxylic acid cycle, and increased redox turnover. <br>Overall, iPAO1 represents the most comprehensive GSMM constructed to date for <i>Pseudomonas</i>. It provides a powerful systems pharmacology platform for the elucidation of complex killing mechanisms of antibiotics.
DOI: 10.5524/100428
title: Supporting data for “m6ASNP: a tool for annotating genetic variants by m6A function”

description: Large-scale genome sequencing projects have identified many genetic variants for diverse diseases. A major goal of these projects is to characterize these genetic variants to provide insight into their function and roles in diseases. N6-methyladenosine (m6A) is one of the most abundant RNA modifications in eukaryotes. Recent studies have revealed that aberrant m6A modifications are involved in many diseases. In this study, we present a user-friendly web server called m6ASNP that is dedicated to the identification of genetic variants targeting m6A modification sites. A random forest model was implemented in m6ASNP to predict whether the methylation status of an m6A site is altered by the variants surrounding the site. In m6ASNP, genetic variants in a standard VCF format are accepted as the input data, and the output includes an interactive table containing the genetic variants annotated by m6A function. In addition, statistical diagrams and a genome browser are provided to visualize the characteristics and annotate the genetic variants. Altogether, we believe that m6ASNP is a highly convenient tool that can be used to boost further functional studies investigating genetic variants. The web server m6ASNP is implemented in JAVA and PHP and is freely available at http://m6asnp.renlab.org.
DOI: 10.5524/100429
title: Supporting data for "Evidence of Evolutionary History and Selective Sweeps in the Genome of Meishan Pig Reveals Its Genetic and Phenotypic Characteristics"

description: Meishan is a pig breed indigenous to China and famous for its high fecundity. The traits of Meishan strongly associated with its distinct evolutionary history and domestication. However, the genomic evidence linking the domestication of Meishan pigs with the unique features are still poorly understood. The goal of this study is to investigate the genomic signatures an d evolutionary evidence related to phenotypic traits of Meishan by large-scale sequencing.<br>We found the unique domestication of Meishan pigs happened at Taihu Basin area between the Majiabang and the Liangzhu culture, during which 300 protein-coding genes have undergone positive selection. Notably, the FoxO signaling pathway with significant enrichment signal and the harbored gene IGF1R were likely associated with high fertility of Meishan pig. Moreover, NFKB1 exhibited strong selective sweep signals and positively participated in hyaluronan biosynthesis as the key gene of KF-kB signaling, which might have resulted in the wrinkled skin and face of Meishan pig. Particularly, three population-specific synonymous single nucleotide variants (SNVs) occurred in PYROXD1, MC1R, and FAM83G genes, of which T305C substitution in the MCIR gene explained the black coat in Meishan pig well. In addition, the shared haplotypes between Meishan and Duroc breeds confirmed the previous Asian-derived introgression and demonstrated the specific contribution of Meishan pigs.<br>
The findings will help us explain the unique genetic and phenotypic characteristics of Meishan pigs, and offer a plausible method for the utilization of Meishan pigs as valuable genetic resources in pig breeding, and as the model animal for human wrinkled skin disease research.