| 1. |
- Alexeyenko, Andrey, et al.
(författare)
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Efficient de novo assembly of large and complex genomes by massively parallel sequencing of Fosmid pools
- 2014
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Ingår i: BMC Genomics. - : Springer Science and Business Media LLC. - 1471-2164. ; 15, s. 439-
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Tidskriftsartikel (refereegranskat)abstract
- Background: Sampling genomes with Fosmid vectors and sequencing of pooled Fosmid libraries on the Illumina platform for massive parallel sequencing is a novel and promising approach to optimizing the trade-off between sequencing costs and assembly quality. Results: In order to sequence the genome of Norway spruce, which is of great size and complexity, we developed and applied a new technology based on the massive production, sequencing, and assembly of Fosmid pools (FP). The spruce chromosomes were sampled with similar to 40,000 bp Fosmid inserts to obtain around two-fold genome coverage, in parallel with traditional whole genome shotgun sequencing (WGS) of haploid and diploid genomes. Compared to the WGS results, the contiguity and quality of the FP assemblies were high, and they allowed us to fill WGS gaps resulting from repeats, low coverage, and allelic differences. The FP contig sets were further merged with WGS data using a novel software package GAM-NGS. Conclusions: By exploiting FP technology, the first published assembly of a conifer genome was sequenced entirely with massively parallel sequencing. Here we provide a comprehensive report on the different features of the approach and the optimization of the process. We have made public the input data (FASTQ format) for the set of pools used in this study: ftp://congenie.org/congenie/Nystedt_2013/Assembly/ProcessedData/FosmidPools/.(alternatively accessible via http://congenie.org/downloads).The software used for running the assembly process is available at http://research.scilifelab.se/andrej_alexeyenko/downloads/fpools/.
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| 2. |
- Barcala, Maximiliano Estravis, et al.
(författare)
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Whole-genome resequencing facilitates the development of a 50K single nucleotide polymorphism genotyping array for Scots pine (Pinus sylvestris L.) and its transferability to other pine species
- 2024
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Ingår i: The Plant Journal. - 0960-7412 .- 1365-313X. ; 117:3, s. 944-955
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Tidskriftsartikel (refereegranskat)abstract
- Scots pine (Pinus sylvestris L.) is one of the most widespread and economically important conifer species in the world. Applications like genomic selection and association studies, which could help accelerate breeding cycles, are challenging in Scots pine because of its large and repetitive genome. For this reason, genotyping tools for conifer species, and in particular for Scots pine, are commonly based on transcribed regions of the genome. In this article, we present the Axiom Psyl50K array, the first single nucleotide polymorphism (SNP) genotyping array for Scots pine based on whole-genome resequencing, that represents both genic and intergenic regions. This array was designed following a two-step procedure: first, 192 trees were sequenced, and a 430K SNP screening array was constructed. Then, 480 samples, including haploid megagametophytes, full-sib family trios, breeding population, and range-wide individuals from across Eurasia were genotyped with the screening array. The best 50K SNPs were selected based on quality, replicability, distribution across the draft genome assembly, balance between genic and intergenic regions, and genotype–environment and genotype–phenotype associations. Of the final 49 877 probes tiled in the array, 20 372 (40.84%) occur inside gene models, while the rest lie in intergenic regions. We also show that the Psyl50K array can yield enough high-confidence SNPs for genetic studies in pine species from North America and Eurasia. This new genotyping tool will be a valuable resource for high-throughput fundamental and applied research of Scots pine and other pine species.
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| 3. |
- Brodin, Johanna, et al.
(författare)
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PCR-Induced Transitions Are the Major Source of Error in Cleaned Ultra-Deep Pyrosequencing Data
- 2013
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Ingår i: PLOS ONE. - : Public Library of Science (PLoS). - 1932-6203. ; 8:7
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Tidskriftsartikel (refereegranskat)abstract
- Background: Ultra-deep pyrosequencing (UDPS) is used to identify rare sequence variants. The sequence depth is influenced by several factors including the error frequency of PCR and UDPS. This study investigated the characteristics and source of errors in raw and cleaned UDPS data. Results: UDPS of a 167-nucleotide fragment of the HIV-1 SG3Denv plasmid was performed on the Roche/454 platform. The plasmid was diluted to one copy, PCR amplified and subjected to bidirectional UDPS on three occasions. The dataset consisted of 47,693 UDPS reads. Raw UDPS data had an average error frequency of 0.30% per nucleotide site. Most errors were insertions and deletions in homopolymeric regions. We used a cleaning strategy that removed almost all indel errors, but had little effect on substitution errors, which reduced the error frequency to 0.056% per nucleotide. In cleaned data the error frequency was similar in homopolymeric and non-homopolymeric regions, but varied considerably across sites. These site-specific error frequencies were moderately, but still significantly, correlated between runs (r = 0.15-0.65) and between forward and reverse sequencing directions within runs (r = 0.33-0.65). Furthermore, transition errors were 48-times more common than transversion errors (0.052% vs. 0.001%; p<0.0001). Collectively the results indicate that a considerable proportion of the sequencing errors that remained after data cleaning were generated during the PCR that preceded UDPS. Conclusions: A majority of the sequencing errors that remained after data cleaning were introduced by PCR prior to sequencing, which means that they will be independent of platform used for next-generation sequencing. The transition vs. transversion error bias in cleaned UDPS data will influence the detection limits of rare mutations and sequence variants.
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| 4. |
- Franzen, Oscar, et al.
(författare)
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Draft genome sequencing of Giardia intestinalis assemblage B isolate GS : is human giardiasis caused by two different species?
- 2009
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Ingår i: PLoS Pathogens. - : Public Library of Science (PLoS). - 1553-7366 .- 1553-7374. ; 5:8, s. e1000560-
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Tidskriftsartikel (refereegranskat)abstract
- Giardia intestinalis is a major cause of diarrheal disease worldwide and two major Giardia genotypes, assemblages A and B, infect humans. The genome of assemblage A parasite WB was recently sequenced, and the structurally compact 11.7 Mbp genome contains simplified basic cellular machineries and metabolism. We here performed 454 sequencing to 16 x coverage of the assemblage B isolate GS, the only Giardia isolate successfully used to experimentally infect animals and humans. The two genomes show 77% nucleotide and 78% amino-acid identity in protein coding regions. Comparative analysis identified 28 unique GS and 3 unique WB protein coding genes, and the variable surface protein (VSP) repertoires of the two isolates are completely different. The promoters of several enzymes involved in the synthesis of the cyst-wall lack binding sites for encystation-specific transcription factors in GS. Several synteny-breaks were detected and verified. The tetraploid GS genome shows higher levels of overall allelic sequence polymorphism (0.5 versus <0.01% in WB). The genomic differences between WB and GS may explain some of the observed biological and clinical differences between the two isolates, and it suggests that assemblage A and B Giardia can be two different species.
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| 5. |
- Hedskog, Charlotte, et al.
(författare)
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Dynamics of HIV-1 Quasispecies during Antiviral Treatment Dissected Using Ultra-Deep Pyrosequencing
- 2010
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Ingår i: PLOS ONE. - : Public Library of Science (PLoS). - 1932-6203. ; 5:7, s. e11345-
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Tidskriftsartikel (refereegranskat)abstract
- Background: Ultra-deep pyrosequencing (UDPS) allows identification of rare HIV-1 variants and minority drug resistance mutations, which are not detectable by standard sequencing. Principal Findings: Here, UDPS was used to analyze the dynamics of HIV-1 genetic variation in reverse transcriptase (RT) (amino acids 180-220) in six individuals consecutively sampled before, during and after failing 3TC and AZT containing antiretroviral treatment. Optimized UDPS protocols and bioinformatic software were developed to generate, clean and analyze the data. The data cleaning strategy reduced the error rate of UDPS to an average of 0.05%, which is lower than previously reported. Consequently, the cut-off for detection of resistance mutations was very low. A median of 16,016 (range 2,406-35,401) sequence reads were obtained per sample, which allowed detection and quantification of minority resistance mutations at amino acid position 181, 184, 188, 190, 210, 215 and 219 in RT. In four of five pre-treatment samples low levels (0.07-0.09%) of the M184I mutation were observed. Other resistance mutations, except T215A and T215I were below the detection limit. During treatment failure, M184V replaced M184I and dominated the population in combination with T215Y, while wild-type variants were rarely detected. Resistant virus disappeared rapidly after treatment interruption and was undetectable as early as after 3 months. In most patients, drug resistant variants were replaced by wild-type variants identical to those present before treatment, suggesting rebound from latent reservoirs. Conclusions: With this highly sensitive UDPS protocol preexisting drug resistance was infrequently observed; only M184I, T215A and T215I were detected at very low levels. Similarly, drug resistant variants in plasma quickly decreased to undetectable levels after treatment interruption. The study gives important insights into the dynamics of the HIV-1 quasispecies and is of relevance for future research and clinical use of the UDPS technology.
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| 6. |
- Nehme, Ralda, et al.
(författare)
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The 22q11.2 region regulates presynaptic gene-products linked to schizophrenia
- 2022
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Ingår i: Nature Communications. - : Nature Publishing Group. - 2041-1723. ; 13:1
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Tidskriftsartikel (refereegranskat)abstract
- It is unclear how the 22q11.2 deletion predisposes to psychiatric disease. To study this, we generated induced pluripotent stem cells from deletion carriers and controls and utilized CRISPR/Cas9 to introduce the heterozygous deletion into a control cell line. Here, we show that upon differentiation into neural progenitor cells, the deletion acted in trans to alter the abundance of transcripts associated with risk for neurodevelopmental disorders including autism. In excitatory neurons, altered transcripts encoded presynaptic factors and were associated with genetic risk for schizophrenia, including common and rare variants. To understand how the deletion contributed to these changes, we defined the minimal protein-protein interaction network that best explains gene expression alterations. We found that many genes in 22q11.2 interact in presynaptic, proteasome, and JUN/FOS transcriptional pathways. Our findings suggest that the 22q11.2 deletion impacts genes that may converge with psychiatric risk loci to influence disease manifestation in each deletion carrier.
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| 7. |
- Nisson, D.M., et al.
(författare)
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Hydrogeochemical and isotopic signatures elucidate deep subsurface hypersaline brine formation through radiolysis driven water-rock interaction
- 2023
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Ingår i: Geochimica et Cosmochimica Acta. - : Elsevier. - 0016-7037 .- 1872-9533. ; 340, s. 65-84
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Tidskriftsartikel (refereegranskat)abstract
- Geochemical and isotopic fluid signatures from a 2.9–3.2 km deep, 45–55 °C temperature, hypersaline brine from Moab Khotsong gold and uranium mine in the Witwatersrand Basin of South Africa were combined with radiolytic and water–rock isotopic exchange models to delineate brine evolution over geologic time, and to explore brine conditions for habitability. The Moab Khotsong brines were hypersaline (Ca-Na-Cl) with 215–246 g/L TDS, and Cl− concentrations up to 4 mol/L suggesting their position as a hypersaline end-member significantly more saline than any previously sampled Witwatersrand Basin fluids. The brines revealed low DIC (∼0.266–∼1.07 mmol/L) with high (∼8.49–∼23.6 mmol/L) DOC pools, and several reduced gaseous species (up to 46 % by volume H2) despite microoxic conditions (Eh = 135–161 mV). Alpha particle radiolysis of water to H2, H2O2, and O2 along with anhydrous-silicate-to-clay alteration reactions predicted 4 mol/L Cl− brine concentration and deuterium enrichment in the fracture waters over a period > 1.00 Ga, consistent with previously reported 40Ar noble gas-derived residence times of 1.20 Ga for this system. In addition, radiolytic production of 7–26 nmol/(L × yr) H2, 3–11 nmol/(L × yr) O2, and 1–8 nmol/(L × yr) H2O2 was predicted for 1–100 g/g 238U dosage scenarios, supporting radiolysis as a significant source of H2 and oxidant species to deep brines over time that are available to a low biomass system (102–103 cells/mL). The host rock lithology was predominately Archaean quartzite, with minerals exposed on fracture surfaces that included calcite, pyrite, and chlorite. Signatures of 18Ocalcite, 13Ccalcite, Δ33Spyrite, 34Spyrite and 87Sr/86Sr obtained from secondary ion mass spectrometry (SIMS) microanalyses suggest several discrete fluid events as the basin cooled from peak greenschist conditions to equilibrium with present-day brine temperatures. The brine physiochemistry, geochemistry, and cellular abundances were significantly different from those of a younger, shallower, low salinity dolomitic fluid in the same mine, and both were different from the mine service water. These results indicate the discovery of one of few long-isolated systems that supports subsurface brine formation via extended water–rock interaction, and an example of a subsurface brine system where abiotic geochemistry may support a low biomass microbial community.
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| 8. |
- Nystedt, Björn, et al.
(författare)
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The Norway spruce genome sequence and conifer genome evolution
- 2013
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Ingår i: Nature. - : Nature Publishing Group. - 0028-0836 .- 1476-4687. ; 497:7451, s. 579-584
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Tidskriftsartikel (refereegranskat)abstract
- Conifers have dominated forests for more than 200 million years and are of huge ecological and economic importance. Here we present the draft assembly of the 20-gigabase genome of Norway spruce (Picea abies), the first available for any gymnosperm. The number of well-supported genes (28,354) is similar to the >100 times smaller genome of Arabidopsis thaliana, and there is no evidence of a recent whole-genome duplication in the gymnosperm lineage. Instead, the large genome size seems to result from the slow and steady accumulation of a diverse set of long-terminal repeat transposable elements, possibly owing to the lack of an efficient elimination mechanism. Comparative sequencing of Pinus sylvestris, Abies sibirica, Juniperus communis, Taxus baccata and Gnetum gnemon reveals that the transposable element diversity is shared among extant conifers. Expression of 24-nucleotide small RNAs, previously implicated in transposable element silencing, is tissue-specific and much lower than in other plants. We further identify numerous long (>10,000 base pairs) introns, gene-like fragments, uncharacterized long non-coding RNAs and short RNAs. This opens up new genomic avenues for conifer forestry and breeding.
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| 9. |
- Rubin, Carl-Johan, et al.
(författare)
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Whole genome resequencing reveals loci under selection during chicken domestication
- 2010
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Ingår i: Nature. - London : Springer Science and Business Media LLC. - 0028-0836 .- 1476-4687. ; 464:7288, s. 587-591
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Tidskriftsartikel (refereegranskat)abstract
- Domestic animals are excellent models for genetic studies of phenotypic evolution. They have evolved genetic adaptations to a new environment, the farm, and have been subjected to strong human-driven selection leading to remarkable phenotypic changes in morphology, physiology and behaviour. Identifying the genetic changes underlying these developments provides new insight into general mechanisms by which genetic variation shapes phenotypic diversity. Here we describe the use of massively parallel sequencing to identify selective sweeps of favourable alleles and candidate mutations that have had a prominent role in the domestication of chickens (Gallus gallus domesticus) and their subsequent specialization into broiler (meat-producing) and layer (egg-producing) chickens. We have generated 44.5-fold coverage of the chicken genome using pools of genomic DNA representing eight different populations of domestic chickens as well as red jungle fowl (Gallus gallus), the major wild ancestor. We report more than 7,000,000 single nucleotide polymorphisms, almost 1,300 deletions and a number of putative selective sweeps. One of the most striking selective sweeps found in all domestic chickens occurred at the locus for thyroid stimulating hormone receptor (TSHR), which has a pivotal role in metabolic regulation and photoperiod control of reproduction in vertebrates. Several of the selective sweeps detected in broilers overlapped genes associated with growth, appetite and metabolic regulation. We found little evidence that selection for loss-of-function mutations had a prominent role in chicken domestication, but we detected two deletions in coding sequences that we suggest are functionally important. This study has direct application to animal breeding and enhances the importance of the domestic chicken as a model organism for biomedical research.
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| 10. |
- Sherwood, Ellen
(författare)
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Methods and applications in DNA sequence alignments
- 2007
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- DNA sequence alignment is one of the most common bioinformatics tasks. Alignment analysis for eukaryotic genomes is challenging because the datasets are large. Repeat sequences also make the analysis difficult. This thesis describes new methods which we have developed for DNA sequence alignment that address these problems. We have applied these new methods in chicken and Trypanosoma cruzi genome analysis projects, and this publication also describes the result from these projects. Most alignment programs use a seed and extend method, where subsequences (seeds) are used to locate potential alignments that are verified. There is a tradeoff between sensitivity and specificity in the seeding process, as short seeds are inefficient in eliminating spurious matches and long seeds are more likely to omit true alignments in the presence of sequencing errors and polymorphisms. We developed an approximate seed matching algorithm which reduces the impact of this tradeoff by allowing mismatches within the seeds. Approximate seed matching allows the use of long seeds, which results in high specificity in the seeding and a faster alignment program. At the same time, sequencing errors and polymorphisms between the sequences do not reduce sensitivity. The chicken is both an important agricultural source of protein and model organism in biological research. The genome sequencing of the wild ancestor of domestic chickens have offered an opportunity to study genetic factors involved in domestication. Sequences from three domestic chicken breeds were available for comparison to the genome sequence. We used this data to find signs of selective sweeps between wild and domestic chickens by searching for regions with low diversity within domestic breeds. The results showed no evidence of large, domestic-specific sweeps. These findings indicate substantial sequence variation within chicken breeds. Copy number variation is emerging as an important source of genotypic and phenotypic variation in humans. We investigated the presence of such structural variation in the chicken genome through array comparative genome hybridizations of different chicken breeds. The results show extensive copy number variation, in some cases unique to domestic chickens. Trypanosoma cruzi is a protozoan parasite which causes Chagas disease. It has interesting biological features, including a genome structure with many repeated genes. Genes are often repeated in tandem arrays, including surface antigen genes and housekeeping genes. The genome assembly shows numerous gaps and collapsed gene copies. We investigated the copy number of the annotated genes and found the gene content of T. cruzi to be even more repetitive than previously thought. The genome analysis studies described in this thesis validated the DNA sequence alignment methods we have developed, and have provided important information for the chicken and T. cruzi research communities.
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