cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5524/100451
title: Supporting data for "ASaiM: a Galaxy-based framework to analyze microbiota data"

description: New generation of sequencing platforms coupled to numerous bioinformatics tools has led to rapid technological progress in metagenomics and metatranscriptomics to investigate complex microorganism communities. Nevertheless, a combination of different bioinformatic tools remains necessary to draw conclusions out of microbiota studies. Modular and user-friendly tools would greatly improve such studies. <br>We therefore developed ASaiM, an Open-Source Galaxy-based framework dedicated to microbiota data analyses. ASaiM provides an extensive collection of tools to assemble, extract, explore and visualize microbiota information from raw metataxonomic, metagenomic or metatranscriptomic sequences. To guide the analyses, several customizable workflows are included and are supported by tutorials and Galaxy interactive tours, which guide users through the analyses step by step. ASaiM is implemented as Galaxy Docker flavour. It is scalable to thousands of datasets, but also can be used on a normal PC. The associated source code is available under Apache 2 license at https://github.com/ASaiM/framework and documentation can be found online (http://asaim.readthedocs.io). <br> Based on the Galaxy framework, ASaiM offers a sophisticated environment with a variety of tools, workflows, documentation and training to scientists working on complex microorganism communities. It makes analysis and exploration analyses of microbiota data easy, quick, transparent, reproducible and shareable.
DOI: 10.5524/100453
title: Supporting data for "Genome of an allotetraploid wild peanut <i>Arachis monticola</i>: a de novo assembly"

description: <i>Arachis monticola</i> (2n = 4x = 40) is the only allotetraploid wild peanut within section Arachis, with an AABB-type genome of about ~2.7 Gb. The AA-type subgenome is derived from diploid wild peanut <i>Arachis duranensis</i>, and the BB-type subgenome is derived from diploid wild peanut <i>Arachis ipaensis</i>. <i>A. monticola</i> is regarded either as the direct progenitor of the cultivated peanut or as an introgressive derivative between the cultivated peanut and wild species. The large polyploidy genome structure and enormous nearly identical regions of the genome make the assembly of chromosomal pseudomolecules very challenging. Here we report the first reference quality assembly of the <i>A. monticola</i> genome, using a series of advanced technologies. The final whole genome of <i>A. monticola</i> is ~2.62 Gb, and has a contig N50 and scaffold N50 of 106.66 Kb and 124.92 Mb, respectively. The vast majority (91.83%) of the assembled sequence was anchored onto the 20 pseudo-chromosomes and 96.07% of assemblies were accurately separated into AA- and BB- subgenomes. We demonstrated efficiency of the current state of the strategy for de novo assembly of the highly complex allotetraploid species, wild peanut (A. monticola), based on whole-genome shotgun sequencing, single molecule real-time (SMRT) sequencing, high-throughput chromosome conformation capture (Hi-C) technology and BioNano optical genome map. These combined technologies produced reference-quality genome of the allotetraploid wild peanut, which is valuable for understanding the peanut domestication and evolution within Arachis genus and among legume crops.
DOI: 10.5524/100454
title: Supporting data for "AMBER: Assessment of Metagenome BinnERs"

description: Reconstructing the genomes of microbial community members is key to the interpretation of shotgun metagenome samples. Genome binning programs deconvolute reads or assembled contigs of such samples into individual bins, but assessing their quality is difficult due to the lack of evaluation software and standardized metrics. We present AMBER, an evaluation package for the comparative assessment of genome reconstructions from metagenome benchmark data sets. It calculates the performance metrics and comparative visualizations used in the first benchmarking challenge of the Initiative for the Critical Assessment of Metagenome Interpretation (CAMI). As an application, we show the outputs of AMBER for eleven different binning programs on two CAMI benchmark data sets. AMBER is implemented in Python and available under the Apache 2.0 license on GitHub.
DOI: 10.5524/100459
title: Supporting data for "YAMP: a containerised workflow enabling reproducibility in metagenomics research"

description: YAMP is a user-friendly workflow that enables the analysis of whole shotgun metagenomics data while using containerisation to ensure computational reproducibility and facilitate collaborative research. YAMP can be executed on any UNIX-like system, and offers seamless support for multiple job schedulers as well as for Amazon AWS cloud. Although YAMP has been developed to be ready-to-use by non-experts, bioinformaticians will appreciate its flexibility, modularisation, and simple customisation. The YAMP script, parameters, and documentation are available via the github repo.
DOI: 10.5524/100461
title: Supporting data for "A reference genome of the European Beech (Fagus sylvatica L.)"

description: The European Beech is arguably the most important climax broad-leaved tree species in Central Europe, widely planted for its valuable wood. Here we report the 542 Mb draft genome sequence of an up to 300-year-old individual (Bhaga) from an undisturbed stand in the Kellerwald-Edersee National Park in central Germany.<br>Using a hybrid assembly approach with Illumina reads with short- and long-insert libraries, coupled with long PacBio reads, we obtained an assembled genome size of 542 Mb, in line with flow cytometric genome size estimation. The largest scaffold was of 1.15 Mb, the N50 length was 145 kb, and the L50 count was 983. The assembly contained 0.12 % of Ns. A BUSCO (Benchmarking with Universal Single-Copy Orthologs) analysis retrieved 94% complete BUSCO genes, well in the range of other high-quality draft genomes of trees. A total of 62,012 protein-coding genes were predicted, assisted by transcriptome sequencing. In addition, we are reporting an efficient method for extracting high molecular weight DNA from dormant buds, by which contamination by environmental bacteria and fungi was kept at a minimum.<br>The assembled genome is a valuable resource and reference for future population genomics studies on the evolution and past climate change adaptation of beech and will be helpful for identifying genes, e.g. involved in drought tolerance, in order to select and breed individuals to adapt forestry to climate change in Europe. A continuously updated genome browser and download page can be accessed from beechgenome.net, which will include future genome versions of the reference individual Bhaga, as new sequencing approaches develop.
DOI: 10.5524/100416
title: Supporting data for "Differential protein expression and post-translational modifications in Metronidazole-resistant Giardia duodenalis"

description: Metronidazole (Mtz) is the frontline drug treatment for multiple anaerobic pathogens, including the gastrointestinal protist, <em>Giardia duodenalis</em>. However, treatment failure is common and linked to <em>in vivo </em>drug resistance. In <em>Giardia</em>, <em>in vitro</em> drug-resistant lines allow controlled experimental interrogation of resistance mechanisms in isogenic cultures. However, resistance-associated changes are inconsistent between lines, phenotypic data are incomplete, and resistance is rarely genetically fixed, highlighted by reversion to sensitivity after drug selection ceases, or via passage through the life cycle. Comprehensive quantitative approaches are required to resolve isolate variability, fully define Mtz resistance phenotypes, and explore the role of post-translational modifications (PTMs) therein. We performed quantitative proteomics to describe differentially expressed proteins (DEPs) in three seminal Mtz resistant (MtzR) lines compared to their isogenic, Mtz-susceptible, parental line. We also probed changes in PTMs including protein acetylation, methylation, ubiquitination and phosphorylation via immunoblotting. We quantified over 1000 proteins in each genotype, recording substantial genotypic variation in DEPs between isotypes. Our data confirms substantial changes in the antioxidant network, glycolysis and electron transport, and indicates links between protein acetylation and Mtz resistance, including cross-resistance to deacetylase inhibitor Trichostatin A (TSA) in Mtz resistant lines. Finally, we performed the first controlled, longitudinal study of Mtz resistance stability, monitoring lines after cessation of drug selection, revealing isolate-dependent phenotypic plasticity. Our data demonstrate understanding of Mtz resistance must be broadened to post-transcriptional and post-translational responses, and that Mtz resistance is polygenic, driven by isolate-dependent variation, and is correlated with changes in protein acetylation networks.
DOI: 10.5524/100417
title: Supporting data for "Whole-genome resequencing reveals signatures of selection and timing of duck domestication"

description: The genetic basis of animal domestication remains poorly understood, and systems with substantial phenotypic differences between wild and domestic populations are useful for elucidating the genetic basis of adaptation to new environments as well as the genetic basis of rapid phenotypic change. <br>Here, we sequenced the whole genome of 78 individual ducks, from two wild and seven domesticated populations, with an average sequencing depth of 6.42X per individual. <br>Our population and demographic analyses indicate a complex history of domestication, with early selection for separate meat and egg lineages. Genomic comparison of wild to domesticated populations suggest that genes affecting brain and neuronal development have undergone strong positive selection during domestication. Our FST analysis also indicates that the duck white plumage is the result of selection at the melanogenesis associated transcription factor locus. <br> Our results advance the understanding of animal domestication and selection for complex phenotypic traits.
DOI: 10.5524/100418
title: Supporting data for "The first whole transcriptomic exploration of pre-oviposited early chicken embryos using single and bulked embryonic RNA-sequencing".

description: The chicken is a valuable model organism, especially in evolutionary and embryology research because its embryonic development occurs in the egg. However, despite its scientific importance, no transcriptome data have been generated for deciphering the early developmental stages of the chicken because of practical and technical constraints accessing pre-oviposited embryos.<br>Here, we determine the entire transcriptome of pre-oviposited avian embryos, including oocyte, zygote, and intrauterine embryos from Eyal-giladi and Kochav stage I (EGK.I) to EGK.X collected using a non-invasive approach for the first time. We also compare RNA sequencing data obtained using bulked embryo sequencing and single embryo/cell sequencing technique. The raw sequencing data were pre-processed with two different genome builds, Galgal4 and Galgal5, and the expression of 17,108 and 26,102 genes was quantified in the respective builds. There were some differences between the two techniques,as well as between the two genome builds, and these were affected by the emergence of long intergenic non-coding RNA annotations.<br>The first transcriptome datasets of pre-oviposited early chicken embryos based on bulked and single embryo sequencing techniques will serve as a valuable resource for investigating early avian embryogenesis, for comparative studies among vertebrates, and for novel gene annotation in the chicken genome.
DOI: 10.5524/100424
title: Supporting data for "Comparative whole genome DNA methylation profiling of cattle sperm and somatic tissues reveals striking hypomethylated patterns in sperm"

description: Compared to somatic cells, sperm cells undergo nearly complete reprogramming of DNA methylation and exchange histones by protamine. Although sperm DNA methylation has been studied in humans and other model species, as the most beneficiary species of artificial insemination, its status in cattle is largely unknown. Using whole-genome bisulfite sequencing (WGBS), we profiled the DNA methylome of cattle sperm through comparison with somatic cells from three bovine tissues (mammary gland, brain, and blood). Large differences between cattle sperm and somatic cells were observed in the methylation patterns of global CpGs, pericentromeric satellites, partially methylated domains (PMDs), hypomethylated regions (HMRs), and common repeats. As expected and like other species, we observed low methylation in the promoter regions and high methylation in the bodies of active genes. We detected selective hypomethylation of megabase domains of centromeric satellite clusters, which may be related to chromosome segregation during meiosis and their rapid transcriptional activation upon fertilization. We found more PMDs in sperm cells than in the somatic cells and identified meiosis-related genes like KIF2B and REPIN1, which are hypomethylated in sperm but hypermethylated in somatic cells. Besides the common HMRs around gene promoters which showed substantial differences between sperm and somatic cells, the sperm-specific HMRs also targeted to distinct spermatogenesis-related genes, including BOLL, MAEL, ASZ1, SYCP3, CTCFL, MND1, SPATA22, PLD6, DDX4, RBBP8, FKBP6, and SYCE1. Although common repeats were heavily methylated in both sperm and somatic cells, some hypomethylated repeats were enriched in gene promoters with large variations among tissues. For example, some young Bov-A2 repeats, which belong to the SINE family, were hypomethylated and could affect the promoter structures by introducing new regulatory elements. Our study provides a comprehensive resource for bovine sperm epigenomic research and enables new discoveries about DNA methylation and its role in male fertility.
DOI: 10.5524/100432
title: Supporting data for "SILAC-based phosphoproteomics reveals new PP2A-Cdc55-regulated processes in budding yeast."

description: Protein phosphatase 2A (PP2A) is a family of conserved serine/threonine phosphatases involved in several essential aspects of cell growth and proliferation. PP2ACdc55 phosphatase has been extensively related to cell cycle events in budding yeast, however few PP2ACdc55 substrates have been identified. Here, we performed a quantitative mass spectrometry approach to reveal new substrates of PP2ACdc55 phosphatase and new PP2A-related processes in mitotic arrested cells. 
We identified 62 statistically significant PP2ACdc55 substrates involved mainly in actincytoskeleton organization. In addition, we validated new PP2ACdc55 substrates such as Slk19 and Lte1, involved in early and late anaphase pathways, and Zeo1, a component of the cell wall integrity pathway. Finally, we constructed docking models of Cdc55 and its substrate Mob1. We found that the predominant interface on Cdc55 is mediated by a protruding loop consisting of residues 84-90, thus highlighting the relevance of these aminoacids for substrate interaction. We used phosphoproteomics of Cdc55 deficient cells to uncover new PP2ACdc55substrates and functions in mitosis. As expected, several hyperphosphorylated proteins corresponded to Cdk1-dependent substrates, although other kinases' consensus motifs were also enriched in our dataset, suggesting that PP2ACdc55 counteracts and regulates other kinases distinct from Cdk1. Indeed, Pkc1 emerged as a novel node of PP2ACdc55 regulation, highlighting a major role of PP2ACdc55 in actin cytoskeleton and cytokinesis, gene ontology terms significantly enriched in the PP2ACdc55- dependent phosphoproteome.
DOI: 10.5524/100440
title: A gene catalogue of the Sprague-Dawley rat gut metagenome

description: Laboratory rats such as the Sprague-Dawley (SD) rats are important model for biomedical studies in relation to human physiological or pathogenic processes. Here we report on the first catalog of microbial genes in fecal samples from Sprague-Dawley rats. The catalog was established using 98 fecal samples from 49 SD rats divided in 7 experimental groups collected at different time points 30 days apart. The established gene catalog comprises 5,130,167 non-redundant genes with an average length of 750 base pairs (BP), among which 64.6% and 26.7% were annotated to phylum and genus levels, respectively. Functionally, 53.1%, 21.8% and 31% of the genes could be annotated to KEGG orthologous groups (KOs), modules and pathways, respectively. A comparison of rat gut metagenome catalogue with human or mouse revealed a higher pairwise overlap between rats and humans (2.47%) than between mice and humans (1.19%) at the gene level. 97% of the functional pathways in the human catalog were present in the rat catalogue underscoring the potential use of rats for biomedical research.
DOI: 10.5524/100445
title: Supporting data for "<em>De novo</em> genome assembly of the red silk cotton tree (<em>Bombax ceiba</em>)".

description: <i>Bombax ceiba</i> L. (the red silk cotton tree) is a large deciduous tree that is distributed in tropical and sub-tropical Asia, and northern Australia. It has great economic and ecological importance, with several applications in industry and traditional medicine in many Asian countries. To facilitate the further utilization of this plant resource, we present here the draft genome sequence for <i>B. ceiba</i>. <br> We assembled a relatively intact genome of <i>B. ceiba</i> by using PacBio single-molecule sequencing and BioNano optical mapping technologies. The final draft genome is approximately 895 Mb long, with contig and scaffold N50 sizes of 1.0 Mb and 2.06 Mb, respectively.<br>The high-quality draft genome assembly of <i>B. ceiba</i> will be a valuable resource enabling further genetic improvement and more effective use of this tree species.
DOI: 10.5524/100413
title: Supporting data for "Homoeolog-specific activation of genes for heat acclimation in the allopolyploid grass Brachypodium hybridum"

description: Allopolyploid plants often show wider environmental tolerances than their ancestors; this is expected to be due to the merger of multiple distinct genomes with a fixed heterozygosity. The complex homoeologous gene expression could have been evolutionarily advantageous for the adaptation of allopolyploid plants. Despite multiple previous studies reporting homoeolog-specific gene expression in allopolyploid species, there are no clear examples of homoeolog-specific function in acclimation to a long-term stress condition.<br>
We found that the allopolyploid grass Brachypodium hybridum and its ancestor Brachypodium stacei show long-term heat stress tolerance, unlike its other ancestor, Brachypodium distachyon. To understand the physiological traits of B. hybridum, we compared the transcriptome of the three Brachypodium species grown under normal and heat stress conditions. We found that the expression patterns of ~26% and ~38% of the homoeolog groups in B. hybridum changed towards non-additive expression and non-ancestral expression, respectively, under normal condition. Moreover, we found that B. distachyon showed similar expression patterns between normal and heat stress conditions, whereas B. hybridum and B. stacei significantly altered their transcriptome in response to heat after 3 days of stress exposure, and homoeologs that were inherited from B. stacei may have contributed to the transcriptional stress response to heat in B. hybridum. After 15 days of heat exposure, B. hybridum and B. stacei maintained transcriptional states similar to those under normal conditions. These results suggested that an earlier response to heat that was specific to homoeologs originating from B. stacei contributed to cellular homeostasis under long-term heat stress in B. hybridum.<br>
Our results provide insights into different regulatory events of the homoeo-transcriptome that are associated with stress acclimation in allopolyploid plants.
DOI: 10.5524/100419
title: Supporting data for "Draft genome of the Peruvian scallop <em>Argopecten purpuratus</em>"

description: The Peruvian scallop, Argopecten purpuratus, is mainly cultured in southern Chile and was introduced into China in last century. Unlike other Argopecten scallops, the Peruvian scallop normally has a long life span of up to 7-10 years. Therefore, researchers have been employing it to develop hybrid vigor. Here, we performed whole genome sequencing, assembly, and gene annotation of the Peruvian scallop, with an important aim to develop genomic resources for genetic breeding in scallops. A total of 463.19-Gb (Gigabase) raw DNA reads were sequenced. The draft genome assembly of 724.78 Mb was generated (accounting for 81.87% of the estimated genome size of 885.29 Mb), with a contig N50 size of 80.11 kb and a scaffold N50 size of 1.02 Mb. Meanwhile, the repeat sequences were calculated to reach 33.74% of the whole genome, and a total of 26,256 protein-coding genes and 3,057 non-coding RNAs were predicted from the assembly. We generated a high quality draft genome assembly of the Peruvian scallop, which will provide solid resource for further genetic breeding and evolutionary history analysis of this economically important scallop.
DOI: 10.5524/100422
title: Supporting data for "Innovative assembly strategy contributes to understanding the evolution and conservation genetics of the endangered Solenodon paradoxus from the island of Hispaniola"

description: Solenodons are insectivores living in Hispaniola and Cuba that form an isolated branch in the tree of placental mammals highly divergent from other eulipothyplan insectivores The history, unique biology and adaptations of these enigmatic venomous species could be illuminated by the availability of genome data, but a whole genome assembly for solenodons has not been previously performed, partially due to the difficulty in obtaining samples from the field. <br>Island isolation and reduced numbers have likely resulted in high homozygosity within the Hispaniolan solenodon (<i>Solenodon paradoxus</i>), thus we tested the performance of several assembly strategies on the genome of this genetically impoverished species. The string-graph based assembly strategy seemed a better choice compared to the conventional de Bruijn graph approach, due to the high levels of homozygosity, which is often a hallmark of endemic or endangered species. <br>A consensus reference genome was assembled from sequences of five individuals from the southern subspecies (<i>S. p. woodi</i>). In addition, we obtained additional sequence from one sample of the northern subspecies (<i>S. p. paradoxus</i>). The resulting genome assemblies were compared to each other, and annotated for genes, with a specific emphasis on venom genes, repeats, variable microsatellite loci and other genomic variants. Phylogenetic positioning and selection signatures were inferred based on 4,416 single copy orthologs from 10 other mammals. We estimated that solenodons diverged from other extant mammals 73.6 Mya. Patterns of SNP variation allowed us to infer population demography, which supported a subspecies split within the Hispaniolan solenodon at least 300 Kya.