cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5524/100100
title: Software and supporting material for: "SmileFinder: a resampling-based platform to evaluate signatures of selection from genome-wide sets of matching allele frequency data between populations".

description: <em>SmileFinder</em> is a simple program that looks for the sweep patterns left by historic selection in genome-wide allele frequency datasets by evaluating the diversity and difference between two or more populations of diploid species against the neutral expectation. The program calculates the mean of heterozygosity and of variance in fixation index (F<sub>ST</sub>) in a set of sliding windows of incrementally increasing sizes, and then builds a resampled distribution (the baseline) of random multi-locus sets matched to the sizes of sliding windows, using an unrestricted sampling. Percentiles of the values in the sliding windows are derived from the superimposed resampled distribution. The resampling can easily be scaled from 1K to 100M times; the higher the number the more precise the percentiles ascribed to the extreme observed values. <br>The output from <em>SmileFinder</em> can be used to plot percentile values to look for signatures of selection along chromosome maps, or to compare lists of candidate genes to random gene sets to test for the over-representation of sweeps. Both uses of the algorithms have already been implemented in published studies. This publicly available, open source program should become a useful tool for preliminary scans of selection using worldwide databases of human genetic variation as well as population datasets for many non-human species from which such data is rapidly emerging with the advent of the new genotyping and sequencing technologies.<br><br>A Galaxy workflow showing how Smilefinder can be used is available from GigaGalaxy (http://galaxy.cbiit.cuhk.edu.hk/u/gigascience/g/wguiblet2014).
DOI: 10.5524/100101
title: A comprehensive resource of genomic, epigenomic and transcriptomic sequencing data of black truffle, <em>Tuber melanosporum</em>.

description: <em>Tuber melanosporum</em>, a plant-symbiotic macrofungus and a highly appreciated gastronomic delicacy (truffle), features one of the largest fungal genomes (125 Mb) with an exceptionally high transposable element (TE) and repetitive DNA content (&gt;58%). The main purpose of DNA methylation in fungi is TE silencing. As obligate outcrossing organisms, truffles are bound to a sexual mode of propagation, which together with TEs is thought to represent a major force driving the evolution of DNA methylation. It was thus of interest to examine if and how <em>T. melanosporum</em> exploits DNA methylation to maintain genome integrity.<br>
We performed whole-genome DNA bisulfite sequencing (BS-seq) and mRNA sequencing (RNA-seq) on different developmental stages of <em>T. melanosporum</em>; namely, fruitbody (truffle), free-living mycelium and ectomycorrhiza. The data revealed a high rate of cytosine methylation (&gt;44%), selectively targeting TEs rather than genes with a strong preference for CpG sites. Whole genome DNA sequencing (WG-seq) uncovered multiple TE-enriched, copy number variant regions bearing a significant fraction of hypomethylated and expressed TEs, almost exclusively in <em>in-vitro</em> propagated free-living mycelium. Treatment of mycelia with 5-azacytidine partially reduced DNA methylation and increased TE transcription. Our transcriptome assembly also resulted in the identification of a set of novel transcripts from 614 genes.
The present datasets provide valuable and comprehensive (epi)genomic information that can be of interest for evolutionary genomics studies of multicellular (filamentous) fungi, in particular Ascomycetes belonging to the Pezizomycotina.
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DOI: 10.5524/100104
title: Genome sequence of a Mongolian individual

description: We present the genome sequence of a Mongolian male individual. The genome is assembled using short reads produced from the massive parallel sequencing method, resulting in 130.8-fold genome coverage. We identify high-confidence variation sets validated by chip genotyping and PCR-Sanger sequencing, including 3.7 million single nucleotide polymorphisms and 756,234 short insertions and deletions. We assign the paternal inheritance of the individual to the lineage D3a through Y haplogroup analysis and infer Genghis Khan had a common paternal ancestor with Tibeto-Burman populations. We investigate the gene flow between Mongolians and other ethnic groups and demonstrate that the genetic influences on them most likely resulted from the expansion of the Mongol Empire. The Mongolian genome lays a foundation to further understand human evolution and explore population specific genetic causes of diseases/traits in Mongolians and closely related groups.
DOI: 10.5524/100107
title: Supporting software and material for: "mirnaTA: a bioinformatics tool for identifying differentially expressed microRNAs in temporal studies using Normal Quantile Transformation (NQT)".

description: The microRNA Temporal Analyzer (mirnaTA) is a bioinformatics tool which can be used to identify differentially expressed miRNAs in temporal studies. It is implemented in Perl and R package (&gt;= 2.13.0) and can be run across multiple platforms such as Linux, Mac and Windows. The mirnaTA requires that users provide data from a minimum of two time point series and analyze up to 20 time points. To normalize data and remove technical variability, Normal Quantile Transformation (NQT) was used, and the normalized data is analyzed using linear regression model to locate any miRNAs which are differentially expressed in a linear manner. Any miRNAs with P-value&lt;0.05 are considered statistically significant. The remaining miRNAs which did not fit in linear model are further analyzed in two different methods: (1) if the number of time points &lt;=3, cumulative density function (CDF) of the normal distribution, and (2) if the number of time points is &gt; 3, an analysis of variances (ANOVA) is utilized.<br>
Here the software and scripts are all archived together in a TAR file taken from SourceForge at time of publication, it represents a snapshot in time of the package. <br>For the most recent up to date version please visit the mirnaTA SourceForge page.
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DOI: 10.5524/100108
title: Nontargeted metabolomics and lipidomics HPLC-MS data from maternal plasma of 180 healthy pregnant women.

description: Metabolic variations occur during normal pregnancy to provide the growing fetus with a supply of nutrients required for its development and to ensure the health of the woman during gestation. Mass spectrometry-based metabolomics was employed to study the metabolic phenotype variations in the maternal plasma that are induced by pregnancy in each of its three trimesters.<br>
Here we provide the LC-MS data from 180 healthy pregnant women, each individual was followed up to term to make sure that women had normal term pregnancy and healthy babies. All volunteers gave written consent and filled out individual questionnaire at the time of sample collection.<br>
The samples were divided into six sub-groups according to the gestational week of their pregnancy at the time of sampling, T1 (<em>n</em>= 30, 9-12 weeks), T2 (<em>n</em>=30, 13-16 weeks), T3 (<em>n</em>=30, 17-20 weeks), T4 (<em>n</em>=30, 21-24 weeks), T5 (<em>n</em>=30, 25-28 weeks), and T6 (<em>n</em>=30, 29-40 weeks). Body mass index (BMI), age, and gestational week were recorded for each individual.<br>
The repository contains data in 3 modalities: positive and negative ion 'global' non-targeted LC-MS and shotgun lipidomics (including carnitine profiling) LC-MS.
DOI: 10.5524/100148
title: Supporting materials for "SOAPdenovo2 Case Study".

description: The SOAPdenovo2 case study is a reproducibility study aimed at exploring how existing research objects and workflow enactment engines can help assess, record and preserve scientific workflows and associated findings by reviewing a comparison between sequence assembly algorithm performance in the light of development of the SOAPdenovo2 de novo genome assembler. The case study was a joint effort by the GigaScience journal, the Investigation/Study/Assay (ISA) infrastructure, Nanopublication (Nanopub) and Research Object (RO) communities and SOAPdenovo2 de novo genome assembler developers. Included here are the relevant ISA-TAB, linkedISA, nanopubs and Research Object files. For more see the paper and GitHub page.
DOI: 10.5524/100350
title: Supporting data for "LAGOS-NE: A multi-scaled geospatial and temporal database of lake ecological context and water quality for thousands of U.S. lakes"

description: Understanding the factors that affect water quality and the ecological services provided by freshwater ecosystems is an urgent global environmental issue. Predicting how water quality will respond to global changes not only requires water quality data, but also information about the ecological context of individual water bodies across broad spatial extents. Because lake water quality is usually sampled in limited geographic regions, often for limited time periods, assessing the environmental controls of water quality requires compilation of many datasets across broad regions and across time into an integrated database. LAGOS-NE accomplishes this goal for lakes in the northeastern-most 17 U.S. states. 
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LAGOS-NE contains data for 51,101 lakes and reservoirs larger than 4 ha in 17 lake-rich U.S. states. The database includes three data modules for: lake location and physical characteristics for all lakes; ecological context (i.e., the land use, geologic, climatic, and hydrologic setting of lakes) for all lakes; and in situ measurements of lake water quality for a subset of the lakes from the past three decades for approximately 2,600-12,000 lakes depending on the variable. The database contains over 200,000 measures of chlorophyll concentration and almost 900,000 measures of Secchi depth. The water quality data were compiled from 87 lake water quality datasets from federal, state, tribal, and non-profit agencies, university researchers, and citizen scientists. 

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This database is one of the largest and most comprehensive databases of its type because it includes both in situ measurements and ecological context data. Because ecological context can be used to study a variety of other questions about lakes, streams, and wetlands, this database can also be used as the foundation for other studies of freshwaters at broad spatial and ecological scales.
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Please note- all current data is hosted on the Environmental Data Initiative portal (EDI). The copy that is hosted on the GigaDB FTP server was taken at point of publication and will not be updated, please visit the EDI portal for the most recent updates.
DOI: 10.5524/100091
title: Supporting materials from “Joint assembly and genetic mapping of the Atlantic horseshoe crab genome reveals ancient whole genome duplication.”

description: Atlantic horseshoe crabs (<em>Limulus polyphemus</em>) are marine arthropods with a fossil record extending back approximately 450 million years. They exhibit remarkable morphological stability over their long evolutionary history, retaining a number of ancestral arthropod traits, and are often cited as examples of living fossils. <br><br>
We constructed a genetic linkage map of this 2.7 Gbp genome by sequencing the nuclear DNA of 34 wild-collected, full-sibling embryos and their parents at a mean redundancy of 1.1x per sample. The map includes 84,307 sequence markers grouped into 1,876 distinct genetic intervals and 5,775 candidate conserved protein coding genes.
DOI: 10.5524/100055
title: Holobiomic division of labor in fungus-farming termites.

description: Termites, <em>Macrotermes natalensis</em>, rely on gut symbionts to decompose organic matter, but the derived Macrotermitinae domesticated <em>Termitomyces</em> fungi to produce their food. This transition to fungiculture led to a change in the ancestral gut symbionts towards a novel gut microbiome, but the complementary roles of the major components of this obligate symbiosis have remained enigmatic. Here we obtained the genomes of a <em>Macrotermes natalensis</em> termite, its <em>Termitomyces</em> fungus cultivar, as well as community gut microbiomes from young major worker guts, minor soldier guts and the queen gut.<br> The ~1.3Gb genome of <em>M. natalensis</em> (dataset 100057)
makes it one of the largest insect genomes sequenced to date, and the genome was sequenced using HiSeq 2000 Illumina and assembled to a high-quality draft with &gt; 16,000 annotated genes despite massive stretches of repeat sequence.<br>The draft genome of <em>Termitomyces sp. J132</em> (dataset 100056) was of similar high quality, contains &gt; 11,000 annotated genes and has an estimated genome size of 83.7Mb. <br>The three gut microbiomes (dataset 100058)
were assembled to 446Mb (&gt;1,200,000 genes), 337Mb (&gt;900,000 genes), and 33Mb (&gt;50,000 genes) for workers, soldiers and the queen, respectively.<br> 
By sequencing all of the major partners in the symbiosis, unprecedented insight can be attained to the complementary functions that have evolved between the partners since the origin of termite fungiculture more than 30mya.<br>
DOI: 10.5524/100057
title: <em>Macrotermes natalensis</em> genome assembly data.

description: <b>Background:</b><em>Macrotermes natalensis</em> belong to a single monophyletic sub-family, the <em>Macrotermitinae</em>. They realized a major evolutionary transition ca. 30 MYA, when they domesticated the ancestor of the extant fungal genus <em>Termitomyces</em> to form an obligate symbiosis.<br>
<b>Sampling:</b> <em>Macrotermes natalensis</em> colony (Mn117) was collected from a natural population in Mookgophong , South Africa (S24°4030.5 E28°4750.4, elevation 1045 m) in 2011. The DNA of a single <em>Macrotermes natalensis</em> queen was extracted for sequencing.<br>
<b>Finding:</b> The final termite genome assembly yielded a size of 1.17Gb sequence, with a scaffold N50 of about 2Mb. 16,310 genes were annotated with the help of termite transcriptome data.
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DOI: 10.5524/100058
title: <em>Macrotermes natalensis</em> gut metagenome assembly data.

description: <b>Background:</b> Most termites rely on gut microbial symbionts to decompose organic matter. During the process of Macrotermitinae domesticating Termitomyces fungi, it led to the loss of their ancestral gut symbionts and the acquisition a novel gut microbiome, but the complementary roles of the major components of this obligate symbiosis remain enigmatic. Here we provide sequence assemblies for the gut microbiome of 3 distinct castes within the a single colony of termite.<br>
<b>Sampling:</b> The gut DNA were extract from major workers, minor soldiers and the queen from <em>M. natalensis</em> colony Mn117 (S24°4030.5 E28°4750.4, elevation 1045 m). In workers and soldiers, duplicate extractions were performed on 2 x 50 guts pulled out of individuals aseptically, which were pooled after extraction. The queen gut DNA was from a entire queen gut dissected out aseptically.<br>
<b>Finding:</b> The three gut microbiomes were assembled to 446Mb (&gt;1,200,000 genes), 337Mb (&gt;900,000 genes), and 33Mb (&gt;50,000 genes) for workers, soldiers and the queen, respectively.
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DOI: 10.5524/100061
title: CEGMA gene predictions for Assemblathon 2 entries.

description: Assemblathon 2 genome assemblies were assessed for their genic content. This was done by using published tool (CEGMA) that looks for the presence of nearly full-length genes within a single scaffold sequence. Such genes must match HMMs made from a set of 458 highly conserved genes that are presumed to be conserved in all eukaryotes.
DOI: 10.5524/100062
title: Assembled Fosmid sequences used for assessment of Assemblathon 2 entries.

description: Assemblathon 2 genome assemblies for bird and snake were assessed using high-confidence regions of assembled Fosmid sequences. These validated Fosmid regions (VFRs) were included as an additional file as part of the Assemblathon 2 manuscript. This file contains the complete assembled Fosmid sequences for both species (47 sequences for bird, 29 for snake).
DOI: 10.5524/100063
title: Transcriptomic, DNA barcoding, and micro-CT imaging data from an advanced taxonomic description of a novel centipede species (<em>Eupolybothrus cavernicolus</em> Komerički & Stoev, sp. n.).

description: The species description of a cave-dwelling centipede, <em>Eupolybothrus cavernicolus Komeriki & Stoev sp. n.</em> (Chilopoda: Lithobiomorpha: Lithobiidae), found in a remote karst region in Knin, Croatia. This is the first eukaryotic species for which, in addition to traditional morphological description, a fully sequenced transcriptome, DNA barcode (i.e., mitochondrial Cytochrome C Oxidase Subunit I gene; COI), and detailed anatomical X-ray microtomography (micro-CT) scan has been provided. This project illustrates a workflow of producing, storing, publishing and disseminating large data sets associated with a description of a new taxon. <br>This dataset consist of the transcriptomic and annotation data as well as the Micro-CT scans, photographs, scanning electron micrographs (SEM) and video footage of the species.
DOI: 10.5524/100064
title: Supporting data for the paper: "An integrated catalog of reference genes in the human gut microbiome".

description: Here we sequenced 249 fecal samples from European adults, leading to a total of 760 samples in the Metagenome of the Human Intestinal Tract (MetaHIT) project. All 6.4TB whole-genome shotgun sequencing data from 1267 fecal samples in MetaHIT, the Human Microbiome Project (HMP) and our diabetes study on Chinese adults were processed with the MOCAT pipeline. The resulting gene catalogs were merged using CD-HIT and complemented with genes from 511 sequenced human gut-related prokaryotic genomes that were present in our gut metagenomes. The final high-quality integrated reference catalog of the human gut microbiome contains 9,879,896 non-redundant genes. The genes were phylogenetically annotated according to 3449 bacterial and archaeal genomes and draft genomes from NCBI, and functionally annotated using orthologous groups from the Kyoto Encyclopedia of Genes and Genomes (KEGG) and the evolutionary genealogy of genes: Non-supervised Orthologous Groups (eggNOG) databases. In addition, 11 samples from the Chinese cohort were re-extracted using the MetaHIT DNA extraction protocol and shotgun-sequenced to compare with the original data generated by a slightly different DNA extraction protocol.
DOI: 10.5524/100066
title: Genomic data from the Black Flying Fox (<em>Pteropus alecto</em>).

description: The black flying fox, <em>Pteropus alecto</em>, is a megabat in the family <em>Pteropodidae</em>. Members of the genus <em>Pteropus</em> include the largest bats in the world. The <em>Pteropus</em> genus currently has about 57 recognised species. The genus is primarily an island taxon, with 55 species having some or all of their distribution on islands. <br> We applied a whole genome shotgun strategy and next-generation sequencing 
technologies using an Illumina HiSeq 2000 platform to sequence the genome of an individual 
adult male <em>P. alecto</em>. In order to lower the risk of 
non-randomness, we constructed 26 paired-end libraries sequenced on 26 lanes, with insert sizes of about 250 base pairs (bp), 500 bp, 800 bp, 2 kb, 5 kb, 10 kb and 20 kb. In total, we generated about 219.7 Gb (109.8x coverage) of high quality sequence for the assembly. The genome was de novo assembled by SOAPdenovo. The final total contig size and N50 were 1.99 Gb and 25.7 kb, respectively. The total scaffold size and N50 were 2.03 Gb and 15.8 Mb, respectively.<br>
DOI: 10.5524/100067
title: Genomic data from the Insectivorous bat (<em>Myotis davidii</em>).

description: The microbats constitute the suborder <em>Microchiroptera</em> within the order <em>Chiroptera</em> (bats). They are most often referred to by their scientific name. Other English names are "insectivorous bats", "echolocating bats", "small bats" or "true bats". All these names are somewhat inaccurate, because not all microbats feed on insects, and some of them are larger than small megabats. <br> We applied a whole genome shotgun strategy and next-generation sequencing technologies using an Illumina HiSeq 2000 platform to sequence the genome of an individual adult male <em>M. davidii</em>. In order to lower the risk of non-randomness, we constructed 26 paired-end libraries sequenced on 26 lanes, with insert sizes of about 250 base pairs (bp), 500 bp, 800 bp, 2 kb, 5 kb, 10 kb and 20 kb. In total, we generated about 237.2 Gb (118.6x coverage) of high quality sequence for the assembly. The genome was de novo assembled by SOAPdenovo. The final contig size and N50 were 1.91 Gb and 13.2 kb, 
respectively. The total scaffold size and N50 were 2.09 Gb and 3.39 Mb, respectively.
DOI: 10.5524/100076
title: Genomic data of the chickpea (<em>Cicer arietinum</em>).

description: Chickpea (<em>Cicer arietinum</em>) is one of the world's most consumed pulses. The Chickpea plant has finely divided leaves, giving it a feathery appearance. The pods are oblong (2 to 3 by 1 to 2 cm) and contain one or two beaked seeds which may be white, yellow, red, brown, or nearly black. They do well in a cool, dry climate and are grown in India as a winter crop. <br> The draft of the chickpea genome is based on genotype CDC Frontier, a Canadian kabuli chickpea variety.<br><br> DNA from the chickpea was collected and e sequenced the 0.74 Gb genome to a depth of approximately 207 x with short reads from a series of libraries with various insert sizes ( 170bp, 500bp, 800bp, 2kb, 5kb, 10kb and 20kb) on a HiSeq 2000 sequencer.<br>The assembled scaffolds of high quality sequences total 153 Gb, with the contig and scaffold N50 values of 645 kb and 39.9 Mb respectively. We identified 28,256 protein-coding genes with an mean coding length of 1,166 bp.
DOI: 10.5524/100078
title: Genomic data of the Diamondback moth (<em>Plutella xylostella</em>).

description: How an insect evolves to become a successful herbivore is of profound biological and practical importance. Herbivores are often adapted to feed on a specific group of evolutionarily and biochemically related host plants, but the genetic and molecular bases for adaptation to plant defense compounds remain poorly understood. <br><em>P. xylostella</em> has become the most destructive pest of economically important food crops, including rapeseed, cauliflower and cabbage. This insect is the first species to have evolved resistance to dichlorodiphenyltrichloroethane (DDT) in the 1950s and to Bacillus thuringiensis (Bt) toxins in the 1990s and has developed resistance to all classes of insecticide, making it increasingly difficult to control. <br>A strain of the diamondback moth (DBM) (Fuzhou-S), <em>P. xylostella</em>, was reared on radish seedlings without exposure to insecticides for 5 years, spanning at least 100 generations. An inbred line was developed by successive single-pair sibling matings. Male pupae were used for genome sequencing.<br>DNA from the diamondback moth was collected in Fuzhou, China. We sequenced the 0.34 Gb genome to a depth of approximately 131.2 X with short reads from a series of libraries with various insert sizes ( 250bp and 500bp libraries per fosmid clone) on a HiSeq 2000 sequencer.<br>The assembled scaffolds have an N50 of 0.7 Mb. We identified 18,071 protein-coding genes.
DOI: 10.5524/100081
title: Genomic data of Flax (<em>Linum usitatissimum</em>).

description: Flax (<em>Linum usitatissimum</em>) is also known as linseed. It is an ancient crop that is widely cultivated as a source of ber, oil and medicinally relevant compounds. <br>We sequenced the genome to a depth of approximately 69 X with short reads from a series of libraries with various insert sizes ( 300bp, 500bp, 2kb, 5kb and 10kb) on a HiSeq 2000 sequencer.<br>The assembled scaffolds of high quality sequences total 25.9 Gb, with the contig and scaffold N50 values of 20.1 kb and 0.7 Mb respectively. We identified 43,484 protein-coding genes.