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SNP and indel discovery and genotyping in next-generation sequencing data

Code, logs and data for discovery and genotyping of SNPs and indels, in the the D.melanogaster genome, using GATK HaplotypeCaller. Code is in the zipped folder named code.zip. Run logs for this code as in the zipped folder named logs.zip. The unfiltered vcf genotypes file is named lhm_rg_HC_2015-09-15.vcf.gz. The filtered vcf genotypes file is named f1.lhm_rg_HC_raw.vcf.gz. The vcf submitted to NCBI dbSNP (filtered, and with indels >50bp and variants with null alternate alleles both removed) is named dbSNP.lhm_rg_HC_raw.vcf.gz. The folder local_reference.zip contains the reference assembly files against which genotypes were called against, and includes the code used to format the data prior to use. Also included is genotypes data from the two in-house reference line samples sequenced (BDGP6+ISO1 mito/dm6, Bloomington Drosophila Stock Center no. 2057) Samples are 220 Sussex-LHM hemiclones, and 2 RG. The first run did not include chromosome 4 and the mitochondrial genome, so these were genotyped separately, and then added to the rest of the results. The link for the NCBI dbSNP record is currently https://www.ncbi.nlm.nih.gov/projects/SNP/snp_viewBatch.cgi?sbid=1062461and the submitter handle is MORROW_EBE_SUSSEX. At the time of writting, the NCBI D.melanogaster build is still being updated, and therefore ss identifiers, but not rs identifers are available. The pre-print manuscript for this data is available on biorxiv: "Whole genome resequencing of a laboratory-adapted Drosophila melanogaster population sample" http://biorxiv.org/content/early/2016/10/17/081554 doi: http://dx.doi.org/10.1101/081554

Structural variant discovery and genotyping in next-generation sequencing data

Code, logs, data, and summaries for detection and genotyping of genomic structural variants in the D.melanogaster Sussex LHM hemiclones (and one in-house reference line individual), using Genomestrip/2.0 The unfiltered CNV pipleline results are lhm_gs.cnvs.raw.vcf.gz Filtered CNV results (including removal of bad samples) are filtered.goodS.lhm_gs.cnvs.raw.vcf.gz The file uploaded to NCBI dbVAR (which comprises of the filtered CNVs and indels >50bp from the HaplotypeCaller method) is lhm_sx16.dbVAR.vcf.gz The NCBI dbVAR accession number is nstd134. Code, logs and summary data are in the zipped archives, named accordingly. The archive reference_data.zip contains additional input files required for Genomestrip, including a shell script for making some of them. The file gstrip_lhm_RG_bams.list is also an input for Genomestrip, indicating bam file names and paths. The pre-print manuscript for this data is available on biorxiv: "Whole genome resequencing of a laboratory-adapted Drosophila melanogaster population sample" http://biorxiv.org/content/early/2016/10/17/081554 doi: http://dx.doi.org/10.1101/081554

opencc-by-4.0Apr 2022View details →

Whole-genome genotype data for French Large White pigs from two distinct sampling times

Genotype data at plink binary format for 36 pigs from the french Large White breed: 13 animals from the female line born in 2014 and 2015, 13 animals from the male line born between 2012 and 2016, and 10 animals from a common ancestral line, born in 1977. These genotypes were obtained from individual whole genome sequencing (WGS) data, whiwh are available at https://www.ebi.ac.uk/ena under the accession number PRJEB51909. Two different genotype datasets were obtained from the raw WGS: 1) snp20_auto_cr (.bed/bim/fam): High quality autosomal SNPs, called by 3 different software, with a call rate of at least 90% 2) all10_auto (.bed/bim/fam): All SNPs or indels called by at least one of 3 different software. More details about these datasets and their use can be found in the following study: Boitard et al (under revision): Whole-genome sequencing of cryo-preserved resources from French Large White pigs at two distinct sampling times reveals strong signatures of convergent and divergent selection between the dam and sire lines.

opencc-by-4.0Jul 2022View details →

Mass mortality among colony-breeding seabirds in the German Wadden Sea in 2022 due to distinct genotypes of HPAIV H5N1 clade 2.3.4.4b: data sets on phylogeographic analyses

Highly pathogenic avian influenza viruses (HPAIV) of clade 2.3.4.4b of the H5 goose/Guangdong (gs/GD) lineage have repeatedly emerged in Germany since 2016. Both poultry holdings and wild birds have been heavily hit but the 2020-2021 and 2021-2022 HPAI winter seasons exceeded all previously recorded epizootics in Germany in terms of number of wild bird cases recorded, genetic diversity of viruses, and duration of virus activity. In past seasons regional massing of wild bird cases were seen at the German coasts of the Baltic and North Sea, but species mainly affected varied from season to season. In 2022 a new and, in Europe, unprecedented aspect was observed when several cormorant and seabird breeding colonies became affected since May at the Baltic Sea coast and in the Wadden Sea, respectively by HPAI H5N1 viruses.

opencc-by-4.0Nov 2022View details →

Genotype Data for "A genomic snapshot of demographic and cultural dynamism in Upper Mesopotamia during the Neolithic Transition"

This repository contains genotype data from the article "<a href="https://www.science.org/doi/10.1126/sciadv.abo3609">A genomic snapshot of demographic and cultural dynamism in Upper Mesopotamia during the Neolithic Transition</a>". Dataset preparation protocols are described in the article. Here, we only include the genotype files of 13 newly published Çayönü samples in eigenstrat format. The 1KGYoruba suffix refers to the dataset prepared using variable positions in the Yoruba population (see the paper for details). Others are well known Human Origins and 1240K panels.  Code and processed data related to the paper has been deposited <a href="http://doi.org/10.5281/zenodo.7086441">here</a>. * The first version has missing individuals.

opencc-by-4.0Apr 2023View details →

Microsatellite genotype data and leaf morphological data of the publication "Bidirectional gene flow between Fagus sylvatica L. and F. orientalis Lipsky despite strong genetic divergence"

These data sets were used for analyses in the publication "Bidirectional gene flow between Fagus sylvatica L. and F. orientalis Lipsky despite strong genetic divergence" accepted in Forest Ecology and Management <a href="https://www.sciencedirect.com/journal/forest-ecology-and-management/vol/537/suppl/C">Volume 537</a>, 1 June 2023, 120947, <a href="https://doi.org/10.1016/j.foreco.2023.120947">https://doi.org/10.1016/j.foreco.2023.120947</a> For details about the data, please read the corresponding ReadMe files.

opencc-zeroJan 2016View details →

Supporting raw data for: The key role of the largest extant neotropical frugivore (Tapirus terrestris) in promoting admixture of plant genotypes across the landscape

These files contain the supporting raw data of the journal article The key role of the largest extant neotropical frugivore (Tapirus terrestris) in promoting admixture of plant genotypes across the landscape. They include the geographical coordinates and genotypes (microsatellites) of 259 palm (Syagrus romanzoffiana) individuals analyzed in the mentioned study, as well as an example of one input file for conducting data analysis with the software COLONY 2.0. A text file (´Readme') describing this archived supporting data in further detail is also provided.

Graphing and tabulating next-generation sequencing and genotyping data

Making figures and tables for publication. Each zip archive contains input data, shell script to initiate and log R script, one R script for generating several graphs and tables, and the output graphs and tables themselves. Data was generated by whole-genome resequencing of 22 individual D.melanogaster from Sussex-LHM population and 2 from the Sussex RG line, followed by read-mapping, then genotyping with Haplotype Caller and Genomestrip. Locations for raw data, code, logs, extended QC data: Sequence reads NCBI SRA268956 NCBI dbSNP https://www.ncbi.nlm.nih.gov/projects/SNP/snp_viewBatch.cgi?sbid=1062461 NCBI dbVar accession number pre-release nstd134 The pre-print manuscript for this data is available on biorxiv: "Whole genome resequencing of a laboratory-adapted Drosophila melanogaster population sample" http://biorxiv.org/content/early/2016/10/17/081554 doi: http://dx.doi.org/10.1101/081554

Genotype reproducibility testing in next-generation sequencing data

Code, log and results summary for testing the reproducibility of genotypes with three pairs of hemiclones in the Sussex LHM D.melanogaster population sample. Discovery and genotyping of genomic sequence variants was done using GATK HaplotypeCaller, and Genomestrip. Numerical comparison of genotype calls within each pairs of hemiclone individuals was performed using GATK GenotypeConcordance. The pre-print manuscript for this data is available on biorxiv: "Whole genome resequencing of a laboratory-adapted Drosophila melanogaster population sample" http://biorxiv.org/content/early/2016/10/17/081554 doi: http://dx.doi.org/10.1101/081554

opencc-by-4.0Apr 2017View details →

Physiological trait and genotype data for 1,038 outbred CFW mice

R data set containing physiological trait data and genotype data for 1,038 mice from the Carworth Farms White (CFW) outbred mouse stock. These data were collected as part of a large study to assess the viability of using Carworth Farms White (CFW) mice for mapping genes and genetic loci underlying complex traits relevant to the study of human disease and psychology. The data accompany the following publication: Parker CC, Gopalakrishnan G, Carbonetto P, Gonzales NM, Leung E, Park YJ, Aryee E, Davis J, Blizard DA, Ackert-Bicknell CL, Lionikas A, Pritchard JK, Palmer AA. Genome-wide association study of behavioral, physiological and gene expression traits in commercially available outbred CFW mice. Nature Genetics 48: 919–926. To use these data for your research, please cite this Zenodo resource, as well as the paper published in Nature Genetics. After loading these data into the R environment, e.g., by running "load(cfw.RData)", you will find R objects including: "pheno"—a 1,038 x 7 matrix containing the quantitative trait, or "phenotype", data. Traits include body weight, tibia length, muscle weights (EDL and soleus), and a binary indicator for abnormal bone health. "map"—a data frame containing information for 79,748 single nucleotide polymorphisms (SNPs) on chromosomes 1–19 genotyped in the CFW mice. All genomic positions are based on Mouse Genome Assembly 38 from the NCBI database (mm10, December 2011). "geno"—a 1,038 x 79,748 matrix containing genotype data for 1,038 mice at 79,748 SNPs. For more information on these data, please refer to the Data Dryad repository: http://dx.doi.org/10.5061/dryad.2rs41 For code implementing QTL mapping of physiological, behavioral and gene expression phenotypes, and other analyses of these data, see: http://github.com/pcarbo/cfw

opencc-by-nc-4.0Feb 2017View details →

Raw Genotyping data from: Variation in recombination rate and its genetic determinism in sheep populations from combining multiple genomewide datasets

Data supporting : Variation in recombination rate and its genetic determinism in sheep populations from combining multiple genomewide datasets Morgane Petit, Jean-Michel Astruc, Julien Sarry, Laurence Drouilhet, Stephane Fabre, Carole Moreno, Bertrand Servin http://doi.org/10.1534/genetics.117.300123 Abstract Recombination is a complex biological process that results from a cascade of multiple events during meiosis. Understanding the genetic determinism of recombination can help to understand if and how these events are interacting. To tackle this question, we studied the patterns of recombination in sheep, using multiple approaches and datasets. We constructed male recombination maps in a dairy breed from the south of France (the Lacaune breed) at a fine scale by combining meiotic recombination rates from a large pedigree genotyped with a 50K SNP array and historical recombination rates from a sample of unrelated individuals genotyped with a 600K SNP array. This analysis revealed recombination patterns in sheep similar to other mammals but also genome regions that have likely been affected by directional and diversifying selection. We estimated the average recombination rate of Lacaune sheep at 1.5 cM/Mb, identified about 50,000 crossover hotspots on the genome and found a high correlation between historical and meiotic recombination rate estimates. A genome-wide association study revealed two major loci affecting inter-individual variation in recombination rate in Lacaune, including the RNF212 and HEI10 genes and possibly 2 other loci of smaller effects including  the KCNJ15  and FSHR genes. Finally, we compared our results to those obtained previously in a distantly related population of domestic sheep, the Soay. This comparison revealed that Soay and Lacaune males have a very similar distribution of recombination along the genome and that the two datasets can be combined to create more precise male meiotic recombination maps in sheep. Despite their similar recombination maps, we show that Soay and Lacaune males exhibit different heritabilities and QTL effects for inter-individual variation in genome-wide recombination rates.   Data files are provided in Plink format ( https://www.cog-genomics.org/plink2 ).

dryad40/100

Data for: Microbe-induced plant resistance alters aphid inter-genotypic competition leading to rapid evolution with consequences for plant growth and aphid abundance

Plants and insect herbivores are two of the most diverse multicellular groups in the world, and both are strongly influenced by interactions with the belowground soil microbiome. Effects of reciprocal rapid evolution on ecological interactions between herbivores and plants have been repeatedly demonstrated, but it is unknown if (and how) the soil microbiome could mediate these eco-evolutionary processes on a shared host plant. We tested the role of a plant-beneficial soil bacterium (Acidovorax radicis) in altering eco-evolutionary interactions between different aphid genotypes (Sitobion avenae; genotypes Sickte and Fescue) feeding on barley (Hordeum vulgare). We measured fecundity, longevity and population growth of two aphid genotypes reared separately or together (population mixture) on three different barley varieties that were inoculated with or without A. radicis. Results showed that across all plant varieties A. radicis increased plant growth and suppressed aphid populations via reduced longevity and fecundity. The strength of effect was dependent on aphid genotype and barley variety, while the direction of effect was altered by aphid population mixture. Using Lotka-Volterra modelling, we demonstrated that while A. radicis inoculation decreased growth rates for both aphid genotypes it increased the competitiveness of one genotype against the other. In general, in the presence of A. radicis, the Fescue aphid genotype became more inhibitory of Sickte aphids, while Sickte aphids facilitated the growth of Fescue aphids. Our work demonstrates that plant rhizosphere microbiomes exert community-level influences by mediating eco-evolutionary interactions between herbivores and host plants. By altering competitive interaction outcomes among aphids and thus impacting processes such as rapid evolution, soil microbes contribute to the short- and long-term structure and functioning of terrestrial habitats.

opencc-zeroJan 2024View details →

opencc-by-4.0Nov 2021View details →

Genotyping and phenotyping data for Genome-wide analyses of body fat reserves in ewes

Among the adaptive capacities of animals, the management of energetic body reserves (BR) through the BR mobilization and accretion processes (BR dynamics, BRD) has become an increasingly valuable attribute for livestock sustainability, allowing animals to cope with more variable environments. BRD has previously been reported to be heritable in ruminants. In the present study, we conducted genome-wide studies (GWAS) in sheep to determine genetic variants associated with BRD. BR levels and BR changes over time were obtained through body condition score measurements at eight physiological stages throughout each productive cycle in Romane ewes (n=1034) and were used as phenotypes for GWAS. After quality controls and imputation, 48,513 single nucleotide polymorphisms (SNP) were included in the GWAS. Among the QTLs identified, a major QTL associated with BR levels during pregnancy and lactation was identified on chromosome 1. In this region, several significant SNPs mapped to the leptin receptor gene (LEPR), among which one SNP mapped to the coding sequence. The point mutation induces the p.P1019S substitution in the cytoplasmic domain, close to tyrosine phosphorylation sites. The frequency of the SNP associated with increased BR levels was 32%, and the LEPR genotype explained up to 5% of the variance of the trait. These results provide strong evidence for involvement of LEPR in the regulation of BRD in sheep and highlight it as a major candidate for improving adaptive capacities.

opencc-by-4.0Dec 2021View details →

Combining genotypes and T cell receptor distributions to infer genetic loci determining V(D)J recombination probabilities: discovery cohort meta data and parsed TCR repertoire data

Meta data corresponding the the discovery cohort for the paper, "Combining genotypes and T cell receptor distributions to infer genetic loci determining V(D)J recombination probabilities" by Magdalena L Russell, Aisha Souquette, David M Levine, Stefan A Schattgen, E Kaitlynn Allen, Guillermina Kuan, Noah Simon, Angel Balmaseda, Aubree Gordon, Paul G Thomas, Frederick A Matsen IV, and Philip Bradley. These meta data include:  (1) a file mapping the SNP data subject IDs to the TCR repertoire data subject IDs (gwas_id_mapping.tsv) (2) a file including the PCAir PCs, self-reported ancestry, and genomic ancestry for each subject (all_pc_air.txt) (3) a file including the PCAir variance explained by each PC (all_pc_air_variance.txt) (3) a file including the SNP ID, chromosome, hg19 position, allele, rsid, and quality control metrics for each SNP in the SNP array (emerson_snp_rs_data.tsv) (4) a file including IMGT genes and sequences used for parsing TCRB repertoire data (human_vj_allele_cdr3_nucseqs.tsv) (5) a file including predicted TRBD2 allele genotypes for each subject (emerson_trbd2_alleles.tsv) (6) Parsed TCRB repertoire data. These raw data were first published in Emerson et. al, Nature Genetics 2017. (emerson_parsed_tcrb.tgz) Corresponding discovery cohort raw TCR repertoire data is available here: https: //doi.org/10.21417/B7001Z (ImmuneACCESS database) Corresponding discovery cohort SNP data is available here: https: //www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id=phs001918.v1.p1 (The database of Genotypes and Phenotypes, accession number: phs001918) Software tools designed to work with these data are available here: https://github.com/phbradley/tcr-gwas

opencc-by-4.0Mar 2022View details →

CONGA: Copy number variation genotyping in ancient genomes and low-coverage sequencing data

To date, ancient genome analyses have been largely confined to the study of single nucleotide polymorphisms (SNPs). Copy number variants (CNVs) are a major contributor of disease and of evolutionary adaptation, but identifying CNVs in ancient shotgun-sequenced genomes is hampered by (i) most published genomes being <1x coverage, (ii) ancient DNA fragments being typically <80 bps. These characteristics preclude state-of-the-art CNV detection software to be effectively applied to ancient genomes. Here we present CONGA, an algorithm tailored for genotyping deletion and duplication events in genomes with low depths of coverage. Simulations and down-sampling experiments show that CONGA can genotype deletions >1 kbps with F-scores >0.75 at >=1x, and distinguish between heterozygous and homozygous states. Using CONGA, we analyse deletion events at 10,018 loci in 56 ancient human genomes spanning the last 50,000 years, with coverages 0.4x-26x. We show that inter-individual genetic diversity measured using deletions and SNPs are highly correlated, as in modern-day genomes, confirming that deletion frequencies broadly reflect demographic history. We also identify signatures of strong purifying selection on deletions in ancient-genomes, such as an excess of singletons compared to those in SNPs. CONGA paves the way for systematic studies of drift, mutation load, and adaptation in ancient and modern-day gene pools through the lens of CNVs.

dryad40/100

Data for: Range and niche expansion through multiple interspecific hybridization - a genotyping by sequencing analysis of Cherleria (Caryophyllaceae)

Background: Cherleria (Caryophyllaceae) is a circumboreal genus that also occurs in the high mountains of the northern hemisphere. In this study, we focus on a clade that diversified in the European High Mountains, which was identified using nuclear ribosomal (nrDNA) sequence data in a previous study. With the nrDNA data, all but one species was monophyletic, with little sequence variation within most species. Here, we use genotyping by sequencing (GBS) data to determine whether the nrDNA data showed the full picture of the evolution in the genomes of these species. Results: The overall relationships found with the GBS data were congruent with those from the nrDNA study. Most of the species were still monophyletic and many of the same subclades were recovered, including a clade of three narrow endemic species from Greece and a clade of largely calcifuge species. The GBS data provided additional resolution within the two species with the best sampling, C. langii and C. laricifolia, with structure that was congruent with geography. In addition, the GBS data showed significant hybridization between several species, including species whose ranges did not currently overlap. Conclusions: The hybridization led us to hypothesize that lineages came in contact on the Balkan Peninsula after they diverged, even when those lineages are no longer present on the Balkan Peninsula. Hybridization may also have helped lineages expand their niches to colonize new substrates and different areas. Not only do genome-wide data provide increased phylogenetic resolution of difficult nodes, they also give evidence for a more complex evolutionary history than what can be depicted by a simple, branching phylogeny.

opencc-zeroJun 2022View details →