548 results
Search Results
2. Cell wall peptidoglycan mutants of Escherichia coli K-12: existence of two clusters of genes, mra and mrb, for cell wall peptidoglycan biosynthesis.
- Author
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Miyakawa T, Matsuzawa H, Matsuhashi M, and Sugino Y
- Subjects
- Alanine metabolism, Carbon Isotopes, Carboxypeptidases metabolism, Cell-Free System, Chromatography, Paper, Escherichia coli enzymology, Escherichia coli isolation & purification, Glucosamine metabolism, Ligases metabolism, Oxidoreductases metabolism, Peptide Synthases metabolism, Phosphoenolpyruvate, Stereoisomerism, Temperature, Transduction, Genetic, Transferases metabolism, Uridine metabolism, Cell Wall metabolism, Chromosome Mapping, Chromosomes, Bacterial, Escherichia coli metabolism, Mutation, Peptidoglycan biosynthesis
- Abstract
Temperature-sensitive mutants of Escherichia coli K-12 which cannot form cell wall peptidoglycan at 42 C were isolated. The thermosensitive steps were characterized biochemically, and the genes coding the enzymes of peptidoglycan synthesis were mapped. These genes were in two clusters: one group, located at about 1.5 min between leu and azi, was designated as mra (murein a); the second group, located at about 77.5 min close to argH and metB, was designated as mrb (murein b, with the order metB-argH-mrb). No simple relations were found between the gene location and the order or localization of enzymes involved in the sequence of reactions of cell wall peptidoglycan biosynthesis.
- Published
- 1972
- Full Text
- View/download PDF
3. Mapping of the tryptophan genes of Acinetobacter calcoaceticus by transformation.
- Author
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Sawula RV and Crawford IP
- Subjects
- Alcaligenes classification, Alcaligenes enzymology, Cell-Free System, Chromatography, Paper, Culture Media, Cyclohexanecarboxylic Acids, Glutamates metabolism, Glycerophosphates, Hydro-Lyases metabolism, Isomerases metabolism, Mutagens, Mutation, Nitrosoguanidines, Terminology as Topic, Transaminases metabolism, Tryptophan metabolism, Tryptophan Synthase metabolism, ortho-Aminobenzoates, Bacteria, Chromosome Mapping, Chromosomes, Bacterial, Transformation, Genetic, Tryptophan biosynthesis
- Abstract
Auxotrophs of Acinetobacter calcoaceticus blocked in each reaction of the synthetic pathway from chorismic acid to tryptophan were obtained after N-methyl-N'-nitro-N-nitrosoguanidine mutagenesis. One novel class was found to be blocked in both anthranilate and p-aminobenzoate synthesis; these mutants (trpG) require p-aminobenzoate or folate as well as tryptophan (or anthranilate) for growth. The loci of six other auxotrophic classes requiring only tryptophan were defined by growth, accumulation, and enzymatic analysis where appropriate. The trp mutations map in three chromosomal locations. One group contains trpC and trpD (indoleglycerol phosphate synthetase and phosphoribosyl transferase) in addition to trpG mutations; this group is closely linked to a locus conferring a glutamate requirement. Another cluster contains trpA and trpB, coding for the two tryptophan synthetase (EC 4.2.1.20) subunits, along with trpF (phosphoribosylanthranilate isomerase); this group is weakly linked to a his marker. The trpE gene, coding for the large subunit of anthranilate synthetase, is unlinked to any of the above. This chromosomal distribution of the trp genes has not been observed in other organisms.
- Published
- 1972
- Full Text
- View/download PDF
4. Genetic analysis of diaminopimelic acid- and lysine-requiring mutants of Escherichia coli.
- Author
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Bukhari AI and Taylor AL
- Subjects
- Carboxy-Lyases biosynthesis, Carboxy-Lyases metabolism, Cell-Free System, Chromatography, Paper, Colorimetry, Conjugation, Genetic, Culture Media, Escherichia coli enzymology, Escherichia coli growth & development, Escherichia coli isolation & purification, Genes, Isomerases metabolism, Lysine biosynthesis, Pimelic Acids biosynthesis, Transduction, Genetic, Chromosome Mapping, Escherichia coli metabolism, Genetics, Microbial, Lysine metabolism, Mutation, Pimelic Acids metabolism
- Abstract
Several diaminopimelic acid (DAP)- and lysine-requiring mutants of Escherichia coli were isolated and studied by genetic, physiological, and biochemical means. The genes concerned with DAP-lysine synthesis map at several different sites on the E. coli chromosome and, therefore, do not constitute a single operon. Three separate loci affecting DAP synthesis are located in the 0 to 2.5 min region of the genetic map. The order of the loci in this region is thr-dapB-pyrA-ara-leu-pan-dapC-tonA-dapD. Two additional DAP genes map in the region between min 47 and 48, with the gene order being gua-dapA-dapE-ctr. The lys locus at min 55 determines the synthesis of the enzyme DAP decarboxylase, which catalyzes the conversion of DAP into lysine. The order of the genes in this region is serA-lysA-thyA.
- Published
- 1971
- Full Text
- View/download PDF
5. Identification and application of a candidate gene AhAftr1 for aflatoxin production resistance in peanut seed (Arachis hypogaea L.).
- Author
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Yu B, Liu N, Huang L, Luo H, Zhou X, Lei Y, Yan L, Wang X, Chen W, Kang Y, Ding Y, Jin G, Pandey MK, Janila P, Kishan Sudini H, Varshney RK, Jiang H, Liu S, and Liao B
- Subjects
- Plant Proteins genetics, Plant Proteins metabolism, Genetic Linkage, Genes, Plant, Plants, Genetically Modified genetics, Aspergillus genetics, Genotype, Arachis genetics, Arachis microbiology, Arachis immunology, Aflatoxins genetics, Disease Resistance genetics, Quantitative Trait Loci, Plant Diseases microbiology, Plant Diseases genetics, Chromosome Mapping methods, Plant Breeding methods, Seeds genetics
- Abstract
Introduction: Peanut is susceptible to infection of Aspergillus fungi and conducive to aflatoxin contamination, hence developing aflatoxin-resistant variety is highly meaningful. Identifying functional genes or loci conferring aflatoxin resistance and molecular diagnostic marker are crucial for peanut breeding., Objectives: This work aims to (1) identify candidate gene for aflatoxin production resistance, (2) reveal the related resistance mechanism, and (3) develop diagnostic marker for resistance breeding program., Methods: Resistance to aflatoxin production in a recombined inbred line (RIL) population derived from a high-yielding variety Xuhua13 crossed with an aflatoxin-resistant genotype Zhonghua 6 was evaluated under artificial inoculation for three consecutive years. Both genetic linkage analysis and QTL-seq were conducted for QTL mapping. The candidate gene was further fine-mapped using a secondary segregation mapping population and validated by transgenic experiments. RNA-Seq analysis among resistant and susceptible RILs was used to reveal the resistance pathway for the candidate genes., Results: The major effect QTL qAFTRA07.1 for aflatoxin production resistance was mapped to a 1.98 Mbp interval. A gene, AhAftr1 (Arachis hypogaea Aflatoxin resistance 1), was detected structure variation (SV) in leucine rich repeat (LRR) domain of its production, and involved in disease resistance response through the effector-triggered immunity (ETI) pathway. Transgenic plants with overexpression of AhAftr1
(ZH6) exhibited 57.3% aflatoxin reduction compared to that of AhAftr1(XH13) . A molecular diagnostic marker AFTR.Del.A07 was developed based on the SV. Thirty-six lines, with aflatoxin content decrease by over 77.67% compared to the susceptible control Zhonghua12 (ZH12), were identified from a panel of peanut germplasm accessions and breeding lines through using AFTR.Del.A07., Conclusion: Our findings would provide insights of aflatoxin production resistance mechanisms and laid meaningful foundation for further breeding programs., Competing Interests: Declaration of Competing Interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024. Production and hosting by Elsevier B.V.)- Published
- 2024
- Full Text
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6. REPORT on the Fifth International Workshop on Chromosome 9 held at Eynsham, Oxfordshire, UK, September 4–6, 1996
- Author
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POVEY, S, ATTWOOD, J, CHADWICK, B, FREZAL, J, HAINES, JL, KNOWLES, M, KWIATKOWSKI, DJ, OLOPADE, OI, SLAUGENHAUPT, S, SPURR, NK, SMITH, M, STEEL, K, WHITE, JA, and PERICAK‐VANCE, MA
- Subjects
Genetics ,Animals ,Chromosome Aberrations ,Chromosome Disorders ,Chromosome Mapping ,Chromosomes ,Human ,Pair 9 ,Computational Biology ,Humans ,Mice ,Rats ,Species Specificity ,algorithm ,animal cell ,basal cell carcinoma ,bladder cancer ,cancer genetics ,cardiomyopathy ,chromosome 9 ,chromosome analysis ,chromosome map ,conference paper ,consensus sequence ,data analysis ,ehlers danlos syndrome ,friedreich ataxia ,gene location ,gene locus ,gene mapping ,hearing loss ,human ,human cell ,hypoplasia ,lymphatic leukemia ,marker gene ,meiosis ,mouse ,muscular dystrophy ,neuropathy ,nomenclature ,nonhuman ,priority journal ,sex determination ,tuberous sclerosis ,tumor suppressor gene ,workshop ,Clinical Sciences ,Genetics & Heredity - Abstract
The Fifth International workshop on chromosome 9 comprised a gathering of 36 scientists from seven countries and included a fairly even distribution of interests along chromosome 9 as well as a strong input from more global activities and from comparative mapping. At least eight groups had participated in the goal set at the previous workshop which was to improve the fine genetic mapping in different regions of chromosome 9 by meiotic breakpoint mapping in allocated regions and this has resulted in some greatly improved order information. Excellent computing facilities were available and all contributed maps were entered not only into SIGMA (and thence submitted to GDB) but also into a dedicated version of ACEDB which can be accessed on the Web in the form of one of 28 slices into which the chromosome has been arbitrarily divided. It was generally agreed that the amount of data is now overwhelming and that the integration and validation of all data is not only unrealistic in a short meeting but probably impossible until the whole chromosome has been sequenced and fully annotated. Sequence-ready contigs presented at the meeting totalled about 3 MB which is about one fiftieth of the estimated length. The single biggest barrier to integration of maps is the problem of non-standard nomenclature of loci. In the past 2 workshops efforts have been made to compare traditional 'consensus' maps made by human insight (still probably best for small specific regions) with those generated with some computer assistance (such as SIGMA) and those generated objectively by defined computer algorithms such as ldb. Since no single form of map or representation is entirely satisfactory for all purposes the maps reproduced in the published version of the report are confined to one of the genetic maps, in which Genethon and older markers have been incorporated, a Sigma map of the genes as symbols together with a listing of known 'disease' genes on chromosome 9, and a revised assessment of the mouse map together with a list of mouse loci predicted to be on human chromosome 9. One of the 25 ACEDB slices is also shown to illustrate strengths and weaknesses of this approach. Workshop files include not only all maps available at the time but also details of loci and details of the meiotic breakpoints in the CEPH families.
- Published
- 1997
7. Identification of QTLs associated with yield-related traits and superior genotype prediction using recombinant inbred line population in tobacco.
- Author
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Tong Z, Kamran M, Zhang Q, Lin F, Fang D, Chen X, Zhu T, Xu H, and Xiao B
- Subjects
- Epistasis, Genetic, Plant Breeding methods, Genetic Linkage, Phenotype, Quantitative Trait Loci, Nicotiana genetics, Genotype, Chromosome Mapping methods
- Abstract
Tobacco is an economically significant industrial crop and model plant for genetic research, yet little is known about its genetic architecture. Quantitative trait loci (QTL) analysis was performed for six agronomic traits on an F_7 population of 341 genotypes, parents, and F
1 plants using 1974 SSR markers across two environments. 31 QTLs contributing single-locus additive effects on 13 linkage groups (LGs) and 6 QTL pairs contributing epistatic effects on 6 LGs, were detected by the QTLNetwork 2.0 which was developed for the mixed-linear-model-based composite interval mapping (MCIM). Notably, 5 QTLs and 1 epistatic QTL pair were found to have pleiotropic effects on some genetically related traits. Moreover, the Broad sense heritability of the detected QTLs ranged from 1.05% to 43.33%, while genotype-by-environment interaction heritability spanned from 27.09% to 56.25%. Based on the results of QTL mapping, the potential superior lines for all or specific environments were designed and evaluated. Five major QTLs were finely dissected based on the tobacco reference genome of K326, and 31 candidate genes were predicted. This study offered new insights into the complicated genetic architecture and QTL resources for efficient breeding design for genetic improvement of agronomic traits in tobacco., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024 Elsevier B.V. All rights reserved.)- Published
- 2024
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8. Report and abstracts of the First International Workshop on Chromosome 9. Held at Girton College Cambridge, UK, 22-24 March, 1992.
- Author
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Povey, S, Smith, M, Haines, J, Kwiatkowski, D, Fountain, J, Bale, A, Abbott, C, Jackson, I, Lawrie, M, and Hultén, M
- Subjects
DNA ,Single Stranded ,single stranded DNA ,animal ,chromosome 9 ,chromosome map ,comparative study ,conference paper ,genetic linkage ,genetics ,human ,molecular genetics ,mouse ,nucleotide sequence ,tuberous sclerosis ,Animal ,Base Sequence ,Chromosome Mapping ,Chromosomes ,Human ,Pair 9 ,Comparative Study ,DNA ,Single-Stranded ,Human ,Linkage ,Mice ,Molecular Sequence Data ,Support ,Non-U.S. Gov't ,Support ,U.S. Gov't ,Non-P.H.S. ,Support ,U.S. Gov't ,P.H.S. ,Tuberous Sclerosis ,Clinical Sciences ,Genetics & Heredity ,Genetics - Published
- 1992
9. REPORT on the First International Workshop on Chromosome 9 held at Girton College Cambridge, UK, 22–24 March, 1992
- Author
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POVEY, S, SMITH, M, HAINES, J, KWIATKOWSKI, D, FOUNTAIN, J, BALE, A, ABBOTT, C, JACKSON, I, LAWRIE, M, and HULTÉN, M
- Subjects
Biological Sciences ,Genetics ,Animals ,Base Sequence ,Chromosome Mapping ,Chromosomes ,Human ,Pair 9 ,DNA ,Single-Stranded ,Genetic Linkage ,Humans ,Mice ,Molecular Sequence Data ,Tuberous Sclerosis ,chromosomal localization ,chromosome 9 ,chromosome 9p ,chromosome 9q ,chromosome analysis ,chromosome map ,conference paper ,friedreich ataxia ,gene ,gene mapping ,genetic linkage ,genetic polymorphism ,human ,major clinical study ,normal human ,priority journal ,pulsed field gel electrophoresis ,telomere ,torsion dystonia ,tuberous sclerosis ,Clinical Sciences ,Genetics & Heredity - Published
- 1992
10. Genetic Heterogeneity in Tuberous Sclerosis
- Author
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SMITH, MOYRA, YOSHIYAMA, K, WAGNER, C, FLODMAN, P, and SMITH, B
- Subjects
Ataxia Telangiectasia ,Cell Movement ,Chromosome Mapping ,Chromosomes ,Human ,Pair 9 ,Forecasting ,Genetic Linkage ,Humans ,Likelihood Functions ,Neurons ,Polymorphism ,Restriction Fragment Length ,Tuberous Sclerosis ,chromosome 11q ,conference paper ,family study ,female ,gene mapping ,genetic heterogeneity ,genetic linkage ,human ,major clinical study ,male ,marker gene ,priority journal ,tuberous sclerosis ,Human ,Linkage ,Support ,Non-U.S. Gov't ,Support ,U.S. Gov't ,P.H.S. ,General Science & Technology - Published
- 1991
11. An Attempt to Map Two Genes for Tuberous Sclerosis Using Novel Two‐Point Methodsa
- Author
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POVEY, S, ATTWOOD, J, JANSSEN, LAJ, BURLEY, M, SMITH, M, FLODMAN, P, MORTON, NE, EDWARDS, JH, SAMPSON, JR, YATES, JRW, HAINES, JL, AMOS, J, SHORT, MP, SANDKUYL, LA, HALLEY, DJJ, FRYER, AE, BECH‐HANSEN, T, MUELLER, R, AL‐GHAZALI, L, SUPER, M, and OSBORNE, J
- Subjects
Adult ,Chromosome Mapping ,Chromosomes ,Human ,Pair 11 ,Chromosomes ,Human ,Pair 9 ,Genetic Linkage ,Humans ,Likelihood Functions ,Polymorphism ,Restriction Fragment Length ,Tuberous Sclerosis ,conference paper ,family study ,female ,gene mapping ,human ,major clinical study ,male ,marker gene ,priority journal ,tuberous sclerosis ,Human ,Linkage ,Support ,Non-U.S. Gov't ,General Science & Technology - Published
- 1991
12. A Comparative Study on Genetic Heterogeneity in Tuberous Sclerosis: Evidence for One Gene on 9q34 and a Second Gene on 11q22–23a
- Author
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JANSSEN, LAJ, POVEY, S, ATTWOOD, J, SANDKUYL, LA, LINDHOUT, D, FLODMAN, P, SMITH, M, SAMPSON, JR, HAINES, JL, MERKENS, EC, FLEURY, P, SHORT, P, AMOS, J, and HALLEY, DJJ
- Subjects
Biological Sciences ,Genetics ,Chromosome Mapping ,Chromosomes ,Human ,Pair 11 ,Chromosomes ,Human ,Pair 9 ,Genes ,Genetic Linkage ,Humans ,Likelihood Functions ,Tuberous Sclerosis ,chromosome 11q ,chromosome 9q ,conference paper ,female ,genetic heterogeneity ,genetic linkage ,human ,male ,priority journal ,tuberous sclerosis ,Genes ,Structural ,Human ,Linkage ,Support ,Non-U.S. Gov't ,General Science & Technology - Published
- 1991
13. Reconstructing and counting genomic fragments through tagmentation-based haploid phasing.
- Author
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Leong PPT, Mihajlović A, Bogdanović N, Breberina L, and Xi L
- Subjects
- Genome, Fungal, Genome, Human, Genomic Library, Haploidy, Humans, Neoplasms genetics, Saccharomyces cerevisiae genetics, Chromosome Mapping methods, DNA Copy Number Variations, Sequence Analysis, DNA methods, Single-Cell Analysis methods
- Abstract
Single-cell sequencing provides a new level of granularity in studying the heterogeneous nature of cancer cells. For some cancers, this heterogeneity is the result of copy number changes of genes within the cellular genomes. The ability to accurately determine such copy number changes is critical in tracing and understanding tumorigenesis. Current single-cell genome sequencing methodologies infer copy numbers based on statistical approaches followed by rounding decimal numbers to integer values. Such methodologies are sample dependent, have varying calling sensitivities which heavily depend on the sample's ploidy and are sensitive to noise in sequencing data. In this paper we have demonstrated the concept of integer-counting by using a novel bioinformatic algorithm built on our library construction chemistry in order to detect the discrete nature of the genome., (© 2021. The Author(s).)
- Published
- 2021
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14. Identification of Novel Choroidal Neovascularization-Related Genes Using Laplacian Heat Diffusion Algorithm.
- Author
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Sheng M, Cai H, Cheng M, Li J, Zhang J, and Liu L
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- Algorithms, China, Choroid pathology, Choroidal Neovascularization metabolism, Databases, Genetic, Gene Regulatory Networks genetics, Genetic Association Studies methods, Humans, Protein Interaction Mapping methods, Protein Interaction Maps, Choroidal Neovascularization genetics, Choroidal Neovascularization pathology, Chromosome Mapping methods
- Abstract
Choroidal neovascularization (CNV) is a type of eye disease that can cause vision loss. In recent years, many studies have attempted to investigate the major pathological processes and molecular pathogenic mechanisms of CNV. Because many diseases are related to genes, the genes associated with CNV need to be identified. In this study, we proposed a network-based approach for identifying novel CNV-associated genes. To execute such method, we first employed a protein-protein interaction network reported in STRING. Then, we applied a network diffusion algorithm, Laplacian heat diffusion, on this network by selecting validated CNV-related genes as the seed nodes. As a result, some novel genes that had unknown but strong relationships with validated genes were identified. Furthermore, we used a screening procedure to extract the most essential genes. Eleven latent CNV-related genes were finally obtained. Extensive analyses were performed to confirm that these genes are novel CNV-related genes., Competing Interests: The authors declare that there is no conflict of interest regarding the publication of this paper., (Copyright © 2021 Minjie Sheng et al.)
- Published
- 2021
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15. Efficient algorithms for Longest Common Subsequence of two bucket orders to speed up pairwise genetic map comparison.
- Author
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De Mattéo, Lisa, Holtz, Yan, Ranwez, Vincent, and Bérard, Sèverine
- Subjects
PLANT breeding ,GENE mapping ,GENETIC markers ,CHROMOSOME segregation ,PLANT populations - Abstract
Genetic maps order genetic markers along chromosomes. They are, for instance, extensively used in marker-assisted selection to accelerate breeding programs. Even for the same species, people often have to deal with several alternative maps obtained using different ordering methods or different datasets, e.g. resulting from different segregating populations. Having efficient tools to identify the consistency and discrepancy of alternative maps is thus essential to facilitate genetic map comparisons. We propose to encode genetic maps by bucket order, a kind of order, which takes into account the blurred parts of the marker order while being an efficient data structure to achieve low complexity algorithms. The main result of this paper is an O(n log(n)) procedure to identify the largest agreements between two bucket orders of n elements, their Longest Common Subsequence (LCS), providing an efficient solution to highlight discrepancies between two genetic maps. The LCS of two maps, being the largest set of their collinear markers, is used as a building block to compute pairwise map congruence, to visually emphasize maker collinearity and in some scaffolding methods relying on genetic maps to improve genome assembly. As the LCS computation is a key subroutine of all these genetic map related tools, replacing the current LCS subroutine of those methods by ours –to do the exact same work but faster– could significantly speed up those methods without changing their accuracy. To ease such transition we provide all required algorithmic details in this self contained paper as well as an R package implementing them, named LCSLCIS, which is freely available at: . [ABSTRACT FROM AUTHOR]
- Published
- 2018
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16. Genome-wide mapping using new AFLP markers to explore intraspecific variation among pathogenic Sporothrix species.
- Author
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de Carvalho JA, Hagen F, Fisher MC, de Camargo ZP, and Rodrigues AM
- Subjects
- Amplified Fragment Length Polymorphism Analysis, Animals, Brazil epidemiology, Cat Diseases microbiology, Cats, Disease Outbreaks, Genotype, Molecular Epidemiology, Sporothrix isolation & purification, Sporotrichosis microbiology, Cat Diseases epidemiology, Chromosome Mapping, Sporothrix classification, Sporotrichosis epidemiology, Sporotrichosis veterinary
- Abstract
Sporotrichosis is a chronic subcutaneous mycosis caused by Sporothrix species, of which the main aetiological agents are S. brasiliensis, S. schenckii, and S. globosa. Infection occurs after a traumatic inoculation of Sporothrix propagules in mammals' skin and can follow either a classic route through traumatic inoculation by plant debris (e.g., S. schenckii and S. globosa) or an alternative route through zoonotic transmission from animals (e.g., S. brasiliensis). Epizootics followed by a zoonotic route occur in Brazil, with Rio de Janeiro as the epicenter of a recent cat-transmitted epidemic. DNA-based markers are needed to explore the epidemiology of these Sporothrix expansions using molecular methods. This paper reports the use of amplified-fragment-length polymorphisms (AFLP) to assess the degree of intraspecific variability among Sporothrix species. We used whole-genome sequences from Sporothrix species to generate 2,304 virtual AFLP fingerprints. In silico screening highlighted 6 primer pair combinations to be tested in vitro. The protocol was used to genotype 27 medically relevant Sporothrix. Based on the overall scored AFLP markers (97-137 fragments), the values of polymorphism information content (PIC = 0.2552-0.3113), marker index (MI = 0.002-0.0039), effective multiplex ratio (E = 17.8519-35.2222), resolving power (Rp = 33.6296-63.1852), discriminating power (D = 0.9291-0.9662), expected heterozygosity (H = 0.3003-0.3857), and mean heterozygosity (Havp = 0.0001) demonstrated the utility of these primer combinations for discriminating Sporothrix. AFLP markers revealed cryptic diversity in species previously thought to be the most prevalent clonal type, such as S. brasiliensis, responsible for cat-transmitted sporotrichosis, and S. globosa responsible for large sapronosis outbreaks in Asia. Three combinations (#3 EcoRI-FAM-GA/MseI-TT, #5 EcoRI-FAM-GA/MseI-AG, and #6 EcoRI-FAM-TA/MseI-AA) provide the best diversity indices and lowest error rates. These methods make it easier to track routes of disease transmission during epizooties and zoonosis, and our DNA fingerprint assay can be further transferred between laboratories to give insights into the ecology and evolution of pathogenic Sporothrix species and to inform management and mitigation strategies to tackle the advance of sporotrichosis., Competing Interests: The authors have declared that no competing interests exist.
- Published
- 2020
- Full Text
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17. Comparative study of population genomic approaches for mapping colony-level traits.
- Author
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Inbar S, Cohen P, Yahav T, and Privman E
- Subjects
- Alleles, Animals, Ants, Behavior, Animal physiology, Gene Frequency genetics, Genotype, Phenotype, Polymorphism, Single Nucleotide genetics, Quantitative Trait Loci, Social Behavior, Whole Genome Sequencing methods, Chromosome Mapping methods, Genome-Wide Association Study methods, Metagenomics methods
- Abstract
Social insect colonies exhibit colony-level phenotypes such as social immunity and task coordination, which are produced by the individual phenotypes. Mapping the genetic basis of such phenotypes requires associating the colony-level phenotype with the genotypes in the colony. In this paper, we examine alternative approaches to DNA extraction, library construction, and sequencing for genome wide association studies (GWAS) of colony-level traits using a population sample of Cataglyphis niger ants. We evaluate the accuracy of allele frequency estimation from sequencing a pool of individuals (pool-seq) from each colony using either whole-genome sequencing or reduced representation genomic sequencing. Based on empirical measurement of the experimental noise in sequenced DNA pools, we show that reduced representation pool-seq is drastically less accurate than whole-genome pool-seq. Surprisingly, normalized pooling of samples did not result in greater accuracy than un-normalized pooling. Subsequently, we evaluate the power of the alternative approaches for detecting quantitative trait loci (QTL) of colony-level traits by using simulations that account for an environmental effect on the phenotype. Our results can inform experimental designs and enable optimizing the power of GWAS depending on budget, availability of samples and research goals. We conclude that for a given budget, sequencing un-normalized pools of individuals from each colony provides optimal QTL detection power., Competing Interests: The authors have declared that no competing interests exist.
- Published
- 2020
- Full Text
- View/download PDF
18. normGAM: an R package to remove systematic biases in genome architecture mapping data.
- Author
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Liu T and Wang Z
- Subjects
- Bias, Chromatin chemistry, Chromatin genetics, Contig Mapping, Genome genetics, Reproducibility of Results, Chromosome Mapping methods, Software
- Abstract
Background: The genome architecture mapping (GAM) technique can capture genome-wide chromatin interactions. However, besides the known systematic biases in the raw GAM data, we have found a new type of systematic bias. It is necessary to develop and evaluate effective normalization methods to remove all systematic biases in the raw GAM data., Results: We have detected a new type of systematic bias, the fragment length bias, in the genome architecture mapping (GAM) data, which is significantly different from the bias of window detection frequency previously mentioned in the paper introducing the GAM method but is similar to the bias of distances between restriction sites existing in raw Hi-C data. We have found that the normalization method (a normalized variant of the linkage disequilibrium) used in the GAM paper is not able to effectively eliminate the new fragment length bias at 1 Mb resolution (slightly better at 30 kb resolution). We have developed an R package named normGAM for eliminating the new fragment length bias together with the other three biases existing in raw GAM data, which are the biases related to window detection frequency, mappability, and GC content. Five normalization methods have been implemented and included in the R package including Knight-Ruiz 2-norm (KR2, newly designed by us), normalized linkage disequilibrium (NLD), vanilla coverage (VC), sequential component normalization (SCN), and iterative correction and eigenvector decomposition (ICE)., Conclusions: Based on our evaluations, the five normalization methods can eliminate the four biases existing in raw GAM data, with VC and KR2 performing better than the others. We have observed that the KR2-normalized GAM data have a higher correlation with the KR-normalized Hi-C data on the same cell samples indicating that the KR-related methods are better than the others for keeping the consistency between the GAM and Hi-C experiments. Compared with the raw GAM data, the normalized GAM data are more consistent with the normalized distances from the fluorescence in situ hybridization (FISH) experiments. The source code of normGAM can be freely downloaded from http://dna.cs.miami.edu/normGAM/.
- Published
- 2019
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19. Construction of Genetic Linkage Maps in Multiparental Populations.
- Author
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Zheng C, Boer MP, and van Eeuwijk FA
- Subjects
- Algorithms, Animals, Arabidopsis genetics, Breeding, Diploidy, Genetic Markers, Genotyping Techniques methods, Chromosome Mapping methods, Genetics, Population, Software
- Abstract
Construction of genetic linkage maps has become a routine step for mapping quantitative trait loci (QTL), particularly in animal and plant breeding populations. Many multiparental populations have recently been produced to increase genetic diversity and QTL mapping resolution. However, few software packages are available for map construction in these populations. In this paper, we build a general framework for the construction of genetic linkage maps from genotypic data in diploid populations, including bi- and multiparental populations, cross-pollinated (CP) populations, and breeding pedigrees. The framework is implemented as an automatic pipeline called magicMap, where the maximum multilocus likelihood approach utilizes genotypic information efficiently. We evaluate magicMap by extensive simulations and eight real datasets: one biparental, one CP, four multiparent advanced generation intercross (MAGIC), and two nested association mapping (NAM) populations, the number of markers ranging from a few hundred to tens of thousands. Not only is magicMap the only software capable of accommodating all of these designs, it is more accurate and robust to missing genotypes and genotyping errors than commonly used packages., (Copyright © 2019 by the Genetics Society of America.)
- Published
- 2019
- Full Text
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20. DSab-origin: a novel IGHD sensitive VDJ mapping method and its application on antibody response after influenza vaccination.
- Author
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Zhang Q, Zhang L, Zhou C, Yang Y, Yin Z, Wu D, Tang K, and Cao Z
- Subjects
- Animals, Computational Biology methods, Humans, Mice, Antibodies, Viral genetics, Antibodies, Viral immunology, Chromosome Mapping methods, Influenza Vaccines immunology, Influenza, Human immunology, Influenza, Human prevention & control, V(D)J Recombination genetics, V(D)J Recombination immunology
- Abstract
Background: Functional antibody genes are often assembled by VDJ recombination and then diversified by somatic hypermutation. Identifying the combination of sourcing germline genes is critical to understand the process of antibody maturation, which may facilitate the diagnostics and rapid generation of human monoclonal antibodies in therapeutics. Despite of successful efforts in V and J fragment assignment, method in D segment tracing remains weak for immunoglobulin heavy diversity (IGHD)., Results: In this paper, we presented a D-sensitive mapping method called DSab-origin with accuracies around 90% in human monoclonal antibody data and average 95.8% in mouse data. Besides, DSab-origin achieved the best performance in holistic prediction of VDJ segments assignment comparing with other methods commonly used in simulation data. After that, an application example was explored on the antibody response based on a time-series antibody sequencing data after influenza vaccination. The result indicated that, despite the personal response among different donors, IGHV3-7 and IGHD4-17 were likely to be dominated gene segments in these three donors., Conclusions: This work filled in a computational gap in D segment assignment for VDJ germline gene identification in antibody research. And it offered an application example of DSab-origin for studying the antibody maturation process after influenza vaccination.
- Published
- 2019
- Full Text
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21. GRSR: a tool for deriving genome rearrangement scenarios from multiple unichromosomal genome sequences.
- Author
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Wang D and Wang L
- Subjects
- Translocation, Genetic, Algorithms, Chromosome Mapping methods, Gene Rearrangement, Genome, Bacterial, Mycobacterium tuberculosis genetics, Shewanella genetics
- Abstract
Background: Genome rearrangements describe changes in the genetic linkage relationship of large chromosomal regions, involving reversals, transpositions, block interchanges, deletions, insertions, fissions, fusions and translocations etc. Many algorithms for calculating rearrangement scenarios between two genomes have been proposed. Very often, the calculated rearrangement scenario is not unique for the same pair of permutations. Hence, how to decide which calculated rearrangement scenario is more biologically meaningful becomes an essential task. Up to now, several mechanisms for genome rearrangements have been studied. One important theory is that genome rearrangement may be mediated by repeats, especially for reversal events. Many reversal regions are found to be flanked by a pair of inverted repeats. As a result, whether there are repeats at the breakpoints of the calculated rearrangement events can shed a light on deciding whether the calculated rearrangement events is biologically meaningful. To our knowledge, there is no tool which can automatically identify rearrangement events and check whether there exist repeats at the breakpoints of each calculated rearrangement event., Results: In this paper, we describe a new tool named GRSR which allows us to compare multiple unichromosomal genomes to identify "independent" (obvious) rearrangement events such as reversals, (inverted) block interchanges and (inverted) transpositions and automatically searches for repeats at the breakpoints of each rearrangement event. We apply our tool on the complete genomes of 28 Mycobacterium tuberculosis strains and 24 Shewanella strains respectively. In both Mycobacterium tuberculosis and Shewanella strains, our tool finds many reversal regions flanked by a pair of inverted repeats. In particular, the GRSR tool also finds an inverted transposition and an inverted block interchange in Shewanella, where the repeats at the ends of rearrangement regions remain unchanged after the rearrangement event. To our knowledge, this is the first time such a phenomenon for inverted transposition and inverted block interchange is reported in Shewanella., Conclusions: From the calculated results, there are many examples supporting the theory that the existence of repeats at the breakpoints of a rearrangement event can make the sequences at the breakpoints remain unchanged before and after the rearrangement events, suggesting that the conservation of ends could possibly be a popular phenomenon in many types of genome rearrangement events.
- Published
- 2018
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22. Estimation of QTL heritability based on pooled sequencing data.
- Author
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Tang W, Huang L, Bu S, Zhang X, and Wu W
- Subjects
- Genetics, Population methods, Oryza genetics, Quantitative Trait, Heritable, Sequence Analysis, DNA methods, Yeasts genetics, Algorithms, Chromosome Mapping methods, High-Throughput Nucleotide Sequencing methods, Quantitative Trait Loci
- Abstract
Motivation: Bulked segregant analysis combined with next generation sequencing has proven to be a simple and efficient approach for fast mapping of quantitative trait loci (QTLs). However, how to estimate the proportion of phenotypic variance explained by a QTL (or termed QTL heritability) in such pooled QTL mapping is an unsolved problem., Results: In this paper, we propose a method called PQHE to estimate QTL heritability using pooled sequencing data obtained under different experimental designs. Simulation studies indicated that our method is correct and feasible. Four practical examples from rice and yeast are demonstrated, each representing a different situation., Availability and Implementation: The R scripts of our method are open source under GPLv3 license at http://genetics.fafu.edu.cn/PQHE or https://github.com/biotangweiqi/PQHE. The R scripts require the R package rootSolve., Contact: wuwr@fafu.edu.cn., Supplementary Information: Supplementary data are available at Bioinformatics online.
- Published
- 2018
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23. Simultaneous estimation of QTL parameters for mapping multiple traits.
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Tong L, Sun X, and Zhou Y
- Subjects
- Animals, Computer Simulation, Genotype, Inheritance Patterns genetics, Mice, Probability, Recombination, Genetic genetics, Chromosome Mapping methods, Quantitative Trait Loci genetics, Quantitative Trait, Heritable
- Abstract
The analysis of quantitative trait loci (QTLs) aims at mapping and estimating the positions and effects of the genes that may affect the quantitative trait, and evaluating the relationship between the gene variation and the phenotype. In existing studies, most methods mainly focus on the association/linkage between multiple gene loci and one trait, in which some useful joint information of multiple traits may be ignored. In this paper, we proposed a method of simultaneously estimating all QTL parameters in the framework of multiple-trait multiple-interval mapping. Simulation results show that in accuracy aspect, the proposed method outperforms an existing method for mapping multiple traits. A real example is also provided to validate the performance of the new method.
- Published
- 2018
24. Novel read density distribution score shows possible aligner artefacts, when mapping a single chromosome.
- Author
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Naumenko FM, Abnizova II, Beka N, Genaev MA, and Orlov YL
- Subjects
- Genomics, Artifacts, Chromosome Mapping methods
- Abstract
Background: The use of artificial data to evaluate the performance of aligners and peak callers not only improves its accuracy and reliability, but also makes it possible to reduce the computational time. One of the natural ways to achieve such time reduction is by mapping a single chromosome., Results: We investigated whether a single chromosome mapping causes any artefacts in the alignments' performances. In this paper, we compared the accuracy of the performance of seven aligners on well-controlled simulated benchmark data which was sampled from a single chromosome and also from a whole genome. We found that commonly used statistical methods are insufficient to evaluate an aligner performance, and applied a novel measure of a read density distribution similarity, which allowed to reveal artefacts in aligners' performances. We also calculated some interesting mismatch statistics, and constructed mismatch frequency distributions along the read., Conclusions: The generation of artificial data by mapping of reads generated from a single chromosome to a reference chromosome is justified from the point of view of reducing the benchmarking time. The proposed quality assessment method allows to identify the inherent shortcoming of aligners that are not detected by conventional statistical methods, and can affect the quality of alignment of real data.
- Published
- 2018
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25. Joint Analysis of Strain and Parent-of-Origin Effects for Recombinant Inbred Intercrosses Generated from Multiparent Populations with the Collaborative Cross as an Example.
- Author
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Liu Y, Xiong S, Sun W, and Zou F
- Subjects
- Alleles, Animals, Bayes Theorem, Computer Simulation, Crosses, Genetic, Haplotypes, Inbreeding, Mice, Phenotype, Polymorphism, Single Nucleotide, Algorithms, Chromosome Mapping methods, Models, Genetic, Quantitative Trait Loci genetics
- Abstract
Multiparent populations (MPP) have become popular resources for complex trait mapping because of their wider allelic diversity and larger population size compared with traditional two-way recombinant inbred (RI) strains. In mice, the collaborative cross (CC) is one of the most popular MPP and is derived from eight genetically diverse inbred founder strains. The strategy of generating RI intercrosses (RIX) from MPP in general and from the CC in particular can produce a large number of completely reproducible heterozygote genomes that better represent the (outbred) human population. Since both maternal and paternal haplotypes of each RIX are readily available, RIX is a powerful resource for studying both standing genetic and epigenetic variations of complex traits, in particular, the parent-of-origin (PoO) effects, which are important contributors to many complex traits. Furthermore, most complex traits are affected by >1 genes, where multiple quantitative trait locus mapping could be more advantageous. In this paper, for MPP-RIX data but taking CC-RIX as a working example, we propose a general Bayesian variable selection procedure to simultaneously search for multiple genes with founder allelic effects and PoO effects. The proposed model respects the complex relationship among RIX samples, and the performance of the proposed method is examined by extensive simulations., (Copyright © 2018 Liu et al.)
- Published
- 2018
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26. An atlas of Caenorhabditis elegans chemoreceptor expression.
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Vidal B, Aghayeva U, Sun H, Wang C, Glenwinkel L, Bayer EA, and Hobert O
- Subjects
- Animals, Body Patterning genetics, Body Patterning physiology, Caenorhabditis elegans genetics, Gene Expression Regulation, Developmental genetics, Genes, Reporter, Phenotype, Sensory Receptor Cells physiology, Transcriptome genetics, Caenorhabditis elegans Proteins genetics, Chemoreceptor Cells physiology, Chromosome Mapping methods
- Abstract
One goal of modern day neuroscience is the establishment of molecular maps that assign unique features to individual neuron types. Such maps provide important starting points for neuron classification, for functional analysis, and for developmental studies aimed at defining the molecular mechanisms of neuron identity acquisition and neuron identity diversification. In this resource paper, we describe a nervous system-wide map of the potential expression sites of 244 members of the largest gene family in the C. elegans genome, rhodopsin-like (class A) G-protein-coupled receptor (GPCR) chemoreceptors, using classic gfp reporter gene technology. We cover representatives of all sequence families of chemoreceptor GPCRs, some of which were previously entirely uncharacterized. Most reporters are expressed in a very restricted number of cells, often just in single cells. We assign GPCR reporter expression to all but two of the 37 sensory neuron classes of the sex-shared, core nervous system. Some sensory neurons express a very small number of receptors, while others, particularly nociceptive neurons, coexpress several dozen GPCR reporter genes. GPCR reporters are also expressed in a wide range of inter- and motorneurons, as well as non-neuronal cells, suggesting that GPCRs may constitute receptors not just for environmental signals, but also for internal cues. We observe only one notable, frequent association of coexpression patterns, namely in one nociceptive amphid (ASH) and two nociceptive phasmid sensory neurons (PHA, PHB). We identified GPCRs with sexually dimorphic expression and several GPCR reporters that are expressed in a left/right asymmetric manner. We identified a substantial degree of GPCR expression plasticity; particularly in the context of the environmentally-induced dauer diapause stage when one third of all tested GPCRs alter the cellular specificity of their expression within and outside the nervous system. Intriguingly, in a number of cases, the dauer-specific alterations of GPCR reporter expression in specific neuron classes are maintained during postdauer life and in some case new patterns are induced post-dauer, demonstrating that GPCR gene expression may serve as traits of life history. Taken together, our resource provides an entry point for functional studies and also offers a host of molecular markers for studying molecular patterning and plasticity of the nervous system.
- Published
- 2018
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27. Genome contact map explorer: a platform for the comparison, interactive visualization and analysis of genome contact maps.
- Author
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Kumar R, Sobhy H, Stenberg P, and Lizana L
- Subjects
- Cell Line, Tumor, Chromosome Mapping statistics & numerical data, Computer Graphics, Humans, Information Storage and Retrieval, K562 Cells, Lymphocytes metabolism, Lymphocytes pathology, Chromosome Mapping methods, Genetic Markers, Genome, Human, Software
- Abstract
Hi-C experiments generate data in form of large genome contact maps (Hi-C maps). These show that chromosomes are arranged in a hierarchy of three-dimensional compartments. But to understand how these compartments form and by how much they affect genetic processes such as gene regulation, biologists and bioinformaticians need efficient tools to visualize and analyze Hi-C data. However, this is technically challenging because these maps are big. In this paper, we remedied this problem, partly by implementing an efficient file format and developed the genome contact map explorer platform. Apart from tools to process Hi-C data, such as normalization methods and a programmable interface, we made a graphical interface that let users browse, scroll and zoom Hi-C maps to visually search for patterns in the Hi-C data. In the software, it is also possible to browse several maps simultaneously and plot related genomic data. The software is openly accessible to the scientific community., (© The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.)
- Published
- 2017
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28. Transient crosslinking kinetics optimize gene cluster interactions.
- Author
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Walker, Benjamin, Taylor, Dane, Lawrimore, Josh, Hult, Caitlin, Adalsteinsson, David, Bloom, Kerry, and Forest, M. Gregory
- Subjects
GENE clusters ,CHROMOSOME structure ,COMPUTATIONAL biology ,RIBOSOMAL DNA - Abstract
Our understanding of how chromosomes structurally organize and dynamically interact has been revolutionized through the lens of long-chain polymer physics. Major protein contributors to chromosome structure and dynamics are condensin and cohesin that stochastically generate loops within and between chains, and entrap proximal strands of sister chromatids. In this paper, we explore the ability of transient, protein-mediated, gene-gene crosslinks to induce clusters of genes, thereby dynamic architecture, within the highly repeated ribosomal DNA that comprises the nucleolus of budding yeast. We implement three approaches: live cell microscopy; computational modeling of the full genome during G1 in budding yeast, exploring four decades of timescales for transient crosslinks between 5kbp domains (genes) in the nucleolus on Chromosome XII; and, temporal network models with automated community (cluster) detection algorithms applied to the full range of 4D modeling datasets. The data analysis tools detect and track gene clusters, their size, number, persistence time, and their plasticity (deformation). Of biological significance, our analysis reveals an optimal mean crosslink lifetime that promotes pairwise and cluster gene interactions through “flexible” clustering. In this state, large gene clusters self-assemble yet frequently interact (merge and separate), marked by gene exchanges between clusters, which in turn maximizes global gene interactions in the nucleolus. This regime stands between two limiting cases each with far less global gene interactions: with shorter crosslink lifetimes, “rigid” clustering emerges with clusters that interact infrequently; with longer crosslink lifetimes, there is a dissolution of clusters. These observations are compared with imaging experiments on a normal yeast strain and two condensin-modified mutant cell strains. We apply the same image analysis pipeline to the experimental and simulated datasets, providing support for the modeling predictions. [ABSTRACT FROM AUTHOR]
- Published
- 2019
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29. PhyloToL: A Taxon/Gene-Rich Phylogenomic Pipeline to Explore Genome Evolution of Diverse Eukaryotes.
- Author
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Cerón-Romero, Mario A, Maurer-Alcalá, Xyrus X, Grattepanche, Jean-David, Yan, Ying, Fonseca, Miguel M, and Katz, L A
- Abstract
Estimating multiple sequence alignments (MSAs) and inferring phylogenies are essential for many aspects of comparative biology. Yet, many bioinformatics tools for such analyses have focused on specific clades, with greatest attention paid to plants, animals, and fungi. The rapid increase in high-throughput sequencing (HTS) data from diverse lineages now provides opportunities to estimate evolutionary relationships and gene family evolution across the eukaryotic tree of life. At the same time, these types of data are known to be error-prone (e.g. substitutions, contamination). To address these opportunities and challenges, we have refined a phylogenomic pipeline, now named PhyloToL, to allow easy incorporation of data from HTS studies, to automate production of both MSAs and gene trees, and to identify and remove contaminants. PhyloToL is designed for phylogenomic analyses of diverse lineages across the tree of life (i.e. at scales of >100 My). We demonstrate the power of PhyloToL by assessing stop codon usage in Ciliophora, identifying contamination in a taxon- and gene-rich database and exploring the evolutionary history of chromosomes in the kinetoplastid parasite Trypanosoma brucei , the causative agent of African sleeping sickness. Benchmarking PhyloToL's homology assessment against that of OrthoMCL and a published paper on superfamilies of bacterial and eukaryotic organellar outer membrane pore-forming proteins demonstrates the power of our approach for determining gene family membership and inferring gene trees. PhyloToL is highly flexible and allows users to easily explore HTS data, test hypotheses about phylogeny and gene family evolution and combine outputs with third-party tools (e.g. PhyloChromoMap, iGTP). [ABSTRACT FROM AUTHOR]
- Published
- 2019
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30. Leveraging functional annotations in genetic risk prediction for human complex diseases.
- Author
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Hu Y, Lu Q, Powles R, Yao X, Yang C, Fang F, Xu X, and Zhao H
- Subjects
- Data Interpretation, Statistical, Data Mining methods, Databases, Genetic, Epigenomics methods, Genetic Variation genetics, Humans, Linkage Disequilibrium genetics, Polymorphism, Single Nucleotide genetics, Proportional Hazards Models, Quantitative Trait Loci genetics, Chromosome Mapping methods, Genetic Association Studies methods, Genetic Predisposition to Disease epidemiology, Genetic Predisposition to Disease genetics, Genome, Human genetics, Risk Assessment methods
- Abstract
Genetic risk prediction is an important goal in human genetics research and precision medicine. Accurate prediction models will have great impacts on both disease prevention and early treatment strategies. Despite the identification of thousands of disease-associated genetic variants through genome wide association studies (GWAS), genetic risk prediction accuracy remains moderate for most diseases, which is largely due to the challenges in both identifying all the functionally relevant variants and accurately estimating their effect sizes in the presence of linkage disequilibrium. In this paper, we introduce AnnoPred, a principled framework that leverages diverse types of genomic and epigenomic functional annotations in genetic risk prediction for complex diseases. AnnoPred is trained using GWAS summary statistics in a Bayesian framework in which we explicitly model various functional annotations and allow for linkage disequilibrium estimated from reference genotype data. Compared with state-of-the-art risk prediction methods, AnnoPred achieves consistently improved prediction accuracy in both extensive simulations and real data.
- Published
- 2017
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31. Approaches in Characterizing Genetic Structure and Mapping in a Rice Multiparental Population.
- Author
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Raghavan C, Mauleon R, Lacorte V, Jubay M, Zaw H, Bonifacio J, Singh RK, Huang BE, and Leung H
- Subjects
- Breeding, Computational Biology methods, Founder Effect, Genetics, Population, Genome-Wide Association Study, Genotype, Haplotypes, Phenotype, Quantitative Trait, Heritable, Recombination, Genetic, Chromosome Mapping, Genome, Plant, Genomics methods, Oryza genetics, Quantitative Trait Loci
- Abstract
Multi-parent Advanced Generation Intercross (MAGIC) populations are fast becoming mainstream tools for research and breeding, along with the technology and tools for analysis. This paper demonstrates the analysis of a rice MAGIC population from data filtering to imputation and processing of genetic data to characterizing genomic structure, and finally quantitative trait loci (QTL) mapping. In this study, 1316 S6:8 indica MAGIC (MI) lines and the eight founders were sequenced using Genotyping by Sequencing (GBS). As the GBS approach often includes missing data, the first step was to impute the missing SNPs. The observable number of recombinations in the population was then explored. Based on this case study, a general outline of procedures for a MAGIC analysis workflow is provided, as well as for QTL mapping of agronomic traits and biotic and abiotic stress, using the results from both association and interval mapping approaches. QTL for agronomic traits (yield, flowering time, and plant height), physical (grain length and grain width) and cooking properties (amylose content) of the rice grain, abiotic stress (submergence tolerance), and biotic stress (brown spot disease) were mapped. Through presenting this extensive analysis in the MI population in rice, we highlight important considerations when choosing analytical approaches. The methods and results reported in this paper will provide a guide to future genetic analysis methods applied to multi-parent populations., (Copyright © 2017 Raghavan et al.)
- Published
- 2017
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32. Fast and general tests of genetic interaction for genome-wide association studies.
- Author
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Frånberg M, Strawbridge RJ, Hamsten A, de Faire U, Lagergren J, and Sennblad B
- Subjects
- Algorithms, Animals, Humans, Models, Theoretical, Chromosome Mapping methods, Epistasis, Genetic genetics, Genetic Association Studies methods, Genome-Wide Association Study methods, Linear Models, Models, Genetic
- Abstract
A complex disease has, by definition, multiple genetic causes. In theory, these causes could be identified individually, but their identification will likely benefit from informed use of anticipated interactions between causes. In addition, characterizing and understanding interactions must be considered key to revealing the etiology of any complex disease. Large-scale collaborative efforts are now paving the way for comprehensive studies of interaction. As a consequence, there is a need for methods with a computational efficiency sufficient for modern data sets as well as for improvements of statistical accuracy and power. Another issue is that, currently, the relation between different methods for interaction inference is in many cases not transparent, complicating the comparison and interpretation of results between different interaction studies. In this paper we present computationally efficient tests of interaction for the complete family of generalized linear models (GLMs). The tests can be applied for inference of single or multiple interaction parameters, but we show, by simulation, that jointly testing the full set of interaction parameters yields superior power and control of false positive rate. Based on these tests we also describe how to combine results from multiple independent studies of interaction in a meta-analysis. We investigate the impact of several assumptions commonly made when modeling interactions. We also show that, across the important class of models with a full set of interaction parameters, jointly testing the interaction parameters yields identical results. Further, we apply our method to genetic data for cardiovascular disease. This allowed us to identify a putative interaction involved in Lp(a) plasma levels between two 'tag' variants in the LPA locus (p = 2.42 ⋅ 10-09) as well as replicate the interaction (p = 6.97 ⋅ 10-07). Finally, our meta-analysis method is used in a small (N = 16,181) study of interactions in myocardial infarction.
- Published
- 2017
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33. graph-GPA: A graphical model for prioritizing GWAS results and investigating pleiotropic architecture.
- Author
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Chung D, Kim HJ, and Zhao H
- Subjects
- Algorithms, Computer Simulation, Genetic Pleiotropy, Models, Statistical, Programming Languages, Chromosome Mapping methods, Computer Graphics, Genetic Association Studies methods, Models, Genetic, Polymorphism, Single Nucleotide genetics, User-Computer Interface
- Abstract
Genome-wide association studies (GWAS) have identified tens of thousands of genetic variants associated with hundreds of phenotypes and diseases, which have provided clinical and medical benefits to patients with novel biomarkers and therapeutic targets. However, identification of risk variants associated with complex diseases remains challenging as they are often affected by many genetic variants with small or moderate effects. There has been accumulating evidence suggesting that different complex traits share common risk basis, namely pleiotropy. Recently, several statistical methods have been developed to improve statistical power to identify risk variants for complex traits through a joint analysis of multiple GWAS datasets by leveraging pleiotropy. While these methods were shown to improve statistical power for association mapping compared to separate analyses, they are still limited in the number of phenotypes that can be integrated. In order to address this challenge, in this paper, we propose a novel statistical framework, graph-GPA, to integrate a large number of GWAS datasets for multiple phenotypes using a hidden Markov random field approach. Application of graph-GPA to a joint analysis of GWAS datasets for 12 phenotypes shows that graph-GPA improves statistical power to identify risk variants compared to statistical methods based on smaller number of GWAS datasets. In addition, graph-GPA also promotes better understanding of genetic mechanisms shared among phenotypes, which can potentially be useful for the development of improved diagnosis and therapeutics. The R implementation of graph-GPA is currently available at https://dongjunchung.github.io/GGPA/.
- Published
- 2017
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34. Sparse regression models for unraveling group and individual associations in eQTL mapping
- Author
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Cheng, Wei, Shi, Yu, Zhang, Xiang, and Wang, Wei
- Subjects
Biological Sciences ,Genetics ,Human Genome ,Generic health relevance ,Algorithms ,Chromosome Mapping ,Phenotype ,Polymorphism ,Single Nucleotide ,Quantitative Trait Loci ,Regression Analysis ,Saccharomyces cerevisiae ,eQTL mapping ,Group-wise association ,Computation efficiency ,Mathematical Sciences ,Information and Computing Sciences ,Bioinformatics ,Biological sciences ,Information and computing sciences ,Mathematical sciences - Abstract
BackgroundAs a promising tool for dissecting the genetic basis of common diseases, expression quantitative trait loci (eQTL) study has attracted increasing research interest. Traditional eQTL methods focus on testing the associations between individual single-nucleotide polymorphisms (SNPs) and gene expression traits. A major drawback of this approach is that it cannot model the joint effect of a set of SNPs on a set of genes, which may correspond to biological pathways.ResultsTo alleviate this limitation, in this paper, we propose geQTL, a sparse regression method that can detect both group-wise and individual associations between SNPs and expression traits. geQTL can also correct the effects of potential confounders. Our method employs computationally efficient technique, thus it is able to fulfill large scale studies. Moreover, our method can automatically infer the proper number of group-wise associations. We perform extensive experiments on both simulated datasets and yeast datasets to demonstrate the effectiveness and efficiency of the proposed method. The results show that geQTL can effectively detect both individual and group-wise signals and outperforms the state-of-the-arts by a large margin.ConclusionsThis paper well illustrates that decoupling individual and group-wise associations for association mapping is able to improve eQTL mapping accuracy, and inferring individual and group-wise associations.
- Published
- 2016
35. Genetics and molecular mapping of resistance to Plasmodiophora brassicae pathotypes 2, 3, 5, 6, and 8 in rutabaga (Brassica napus var. napobrassica).
- Author
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Hasan MJ and Rahman H
- Subjects
- Crosses, Genetic, Genetic Association Studies, Genetic Linkage, Genetic Markers, Haploidy, Microsatellite Repeats, Quantitative Trait Loci, Brassica napus genetics, Brassica napus parasitology, Chromosome Mapping, Disease Resistance genetics, Genes, Plant, Plant Diseases genetics, Plant Diseases parasitology, Plasmodiophorida genetics, Plasmodiophorida isolation & purification
- Abstract
Clubroot disease, caused by Plasmodiophora brassicae, is a threat to the production of Brassica crops including oilseed B. napus. In Canada, several pathotypes of this pathogen, such as pathotypes 2, 3, 5, 6, and 8, were identified, and resistance to these pathotypes was found in a rutabaga (B. napus var. napobrassica) genotype. In this paper, we report the genetic basis and molecular mapping of this resistance by use of F
2 , backcross (BC1 ), and doubled haploid (DH) populations generated from crossing of this rutabaga line to a susceptible spring B. napus canola line. The F1 , F2 , and BC1 populations were evaluated for resistance to pathotype 3, and the DH population was evaluated for resistance to pathotypes 2, 3, 5, 6, and 8. A 3:1 segregation in F2 and a 1:1 segregation in BC1 were found for resistance to pathotype 3, and a 1:1 segregation was found in the DH population for resistance to all pathotypes. Molecular mapping by using the DH population identified a genomic region on chromosome A8 carrying resistance to all five pathotypes. This suggests that a single gene or a cluster of genes, located in this genomic region, is involved in the control of resistance to these pathotypes.- Published
- 2016
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36. Identification of a novel, dominant dwarfing gene (Ddw4) and its effect on morphological traits of rye.
- Author
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Kantarek, Zuzanna, Masojć, Piotr, Bienias, Anna, and Milczarski, Paweł
- Subjects
RYE ,PLANT stems ,PLANT genes ,PLANT morphology ,CORN breeders - Abstract
Shortening rye stems to improve lodging resistance is among the major tasks awaiting breeders of this cereal. The most straightforward way to achieve this goal is the implementation of a dominant dwarfing gene into high yielding cultivars. The choice of dominant dwarfing genes in rye is limited to Ddw1 and Ddw3 loci, which are well characterized with respect to map position and tightly linked molecular markers on the long arms of chromosomes 5RL and 1RL, respectively. This paper reports on the identification and preliminary characterization of a novel dominant dwarfing gene, Ddw4, from line S44. This was mapped within the centromeric region of chromosome 3R. The Ddw4 gene is sensitive to exogenous gibberellin. Its introduction into the rye populational cultivar Dańkowskie Amber decreased plant height by c. 54% without any negative effects on spike length and number of kernels per spike. Further genetic studies are needed to determine the perspectives for application of the newly detected dwarfing gene into breeding programs for short-stem rye. [ABSTRACT FROM AUTHOR]
- Published
- 2018
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- View/download PDF
37. Autotriploid origin of Carassius auratus as revealed by chromosomal locus analysis.
- Author
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Qin Q, Wang J, Hu M, Huang S, and Liu S
- Subjects
- Animals, In Situ Hybridization, Fluorescence, Carps genetics, Chromosome Mapping, Triploidy
- Abstract
In the Dongting water system, the Carassius auratus (Crucian carp) complex is characterized by the coexistence of diploid forms (2n=100, 2nCC) and polyploid forms. Chromosomal and karyotypic analyses have suggested that the polyploid C. auratus has a triploid (3n=150, 3nCC) and a tetraploid origin (4n=200), respectively. However, there is a lack of direct genetic evidence to support this conclusion. In this paper, analysis of the 5S rDNA chromosomal locus revealed that the 3nCC is of triploid origin. Analysis of the species-specific chromosomal centromere locus revealed that 3nCC individuals possess three sets of C. auratus-derived chromosomes. Our results provide direct cytogenetic evidence suggesting that individuals with 150 chromosomes are of autotriploid origin within the C. auratus complex. It marks an important contribution to the study of polyploidization and the evolution of vertebrates.
- Published
- 2016
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38. META2: Intercellular DNA Methylation Pairwise Annotation and Integrative Analysis.
- Author
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Tang B
- Subjects
- Systems Integration, Algorithms, Chromosome Mapping methods, DNA genetics, DNA Methylation genetics, Sequence Analysis, DNA methods, Software
- Abstract
Genome-wide deciphering intercellular differential DNA methylation as well as its roles in transcriptional regulation remains elusive in cancer epigenetics. Here we developed a toolkit META2 for DNA methylation annotation and analysis, which aims to perform integrative analysis on differentially methylated loci and regions through deep mining and statistical comparison methods. META2 contains multiple versatile functions for investigating and annotating DNA methylation profiles. Benchmarked with T-47D cell, we interrogated the association within differentially methylated CpG (DMC) and region (DMR) candidate count and region length and identified major transition zones as clues for inferring statistically significant DMRs; together we validated those DMRs with the functional annotation. Thus META2 can provide a comprehensive analysis approach for epigenetic research and clinical study., Competing Interests: The author declares that there are no competing interests regarding the publication of this paper.
- Published
- 2016
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39. Identification of a Large SLC25A13 Deletion via Sophisticated Molecular Analyses Using Peripheral Blood Lymphocytes in an Infant with Neonatal Intrahepatic Cholestasis Caused by Citrin Deficiency (NICCD): A Clinical and Molecular Study.
- Author
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Zheng QQ, Zhang ZH, Zeng HS, Lin WX, Yang HW, Yin ZN, and Song YZ
- Subjects
- Cholestasis, Intrahepatic diagnosis, Cholestasis, Intrahepatic etiology, Citrullinemia complications, Citrullinemia diagnosis, Gene Deletion, Genetic Markers genetics, Genetic Predisposition to Disease genetics, Humans, Infant, Newborn, Male, Mitochondrial Membrane Transport Proteins blood, Molecular Diagnostic Techniques, Polymorphism, Single Nucleotide genetics, Cholestasis, Intrahepatic genetics, Chromosome Mapping methods, Citrullinemia genetics, DNA Mutational Analysis methods, Leukocytes, Mononuclear metabolism, Mitochondrial Membrane Transport Proteins genetics
- Abstract
Background. Neonatal intrahepatic cholestasis caused by citrin deficiency (NICCD) is a Mendelian disorder arising from biallelic SLC25A13 mutations, and SLC25A13 genetic analysis was indispensable for its definite diagnosis. However, conventional SLC25A13 analysis could not detect all mutations, especially obscure large insertions/deletions. This paper aimed to explore the obscure SLC25A13 mutation in an NICCD infant. Methods. Genomic DNA was extracted to screen for 4 high-frequency SLC25A13 mutations, and then all 18 exons and their flanking sequences were analyzed by Sanger sequencing. Subsequently, cDNA cloning, SNP analyses, and semiquantitative PCR were performed to identify the obscure mutation. Results. A maternally inherited mutation IVS16ins3kb was screened out, and then cDNA cloning unveiled paternally inherited alternative splicing variants (ASVs) featuring exon 5 skipping. Ultimately, a large deletion c.329-1687_c.468+3865del5692bp, which has never been described in any other references, was identified via intensive study on the genomic DNA around exon 5 of SLC25A13 gene. Conclusions. An NICCD patient was definitely diagnosed as a compound heterozygote of IVS16ins3kb and c.329-1687_c.468+3865del5692bp. The large deletion enriched the SLC25A13 mutation spectrum, and its identification supported the concept that cDNA cloning analysis, along with other molecular tools such as semiquantitative PCR, could provide valuable clues, facilitating the identification of obscure SLC25A13 deletions.
- Published
- 2016
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40. An Efficient Genome-Wide Multilocus Epistasis Search.
- Author
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Kärkkäinen HP, Li Z, and Sillanpää MJ
- Subjects
- Animals, Genome, Models, Genetic, Quantitative Trait Loci, Software, Chromosome Mapping, Epistasis, Genetic, Swine genetics
- Abstract
There has been a continuing interest in approaches that analyze pairwise locus-by-locus (epistasis) interactions using multilocus association models in genome-wide data sets. In this paper, we suggest an approach that uses sure independence screening to first lower the dimension of the problem by considering the marginal importance of each interaction term within the huge loop. Subsequent multilocus association steps are executed using an extended Bayesian least absolute shrinkage and selection operator (LASSO) model and fast generalized expectation-maximization estimation algorithms. The potential of this approach is illustrated and compared with PLINK software using data examples where phenotypes have been simulated conditionally on marker data from the Quantitative Trait Loci Mapping and Marker Assisted Selection (QTLMAS) Workshop 2008 and real pig data sets., (Copyright © 2015 by the Genetics Society of America.)
- Published
- 2015
- Full Text
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41. Evolutionary conservation analysis between the essential and nonessential genes in bacterial genomes.
- Author
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Luo H, Gao F, and Lin Y
- Subjects
- Bacterial Proteins genetics, Base Sequence, Molecular Sequence Data, Chromosome Mapping methods, Conserved Sequence genetics, Evolution, Molecular, Genes, Bacterial genetics, Genes, Essential genetics, Genome, Bacterial genetics
- Abstract
Essential genes are thought to be critical for the survival of the organisms under certain circumstances, and the natural selection acting on essential genes is expected to be stricter than on nonessential ones. Up to now, essential genes have been identified in approximately thirty bacterial organisms by experimental methods. In this paper, we performed a comprehensive comparison between the essential and nonessential genes in the genomes of 23 bacterial species based on the Ka/Ks ratio, and found that essential genes are more evolutionarily conserved than nonessential genes in most of the bacteria examined. Furthermore, we also analyzed the conservation by functional clusters with the clusters of orthologous groups (COGs), and found that the essential genes in the functional categories of G (Carbohydrate transport and metabolism), H (Coenzyme transport and metabolism), I (Transcription), J (Translation, ribosomal structure and biogenesis), K (Lipid transport and metabolism) and L (Replication, recombination and repair) tend to be more evolutionarily conserved than the corresponding nonessential genes in bacteria. The results suggest that the essential genes in these subcategories are subject to stronger selective pressure than the nonessential genes, and therefore, provide more insights of the evolutionary conservation for the essential and nonessential genes in complex biological processes.
- Published
- 2015
- Full Text
- View/download PDF
42. GDC 2: Compression of large collections of genomes.
- Author
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Deorowicz S, Danek A, and Niemiec M
- Subjects
- Arabidopsis genetics, Genome, Human genetics, Genome, Plant genetics, Humans, Reproducibility of Results, Sequence Analysis, DNA methods, Algorithms, Chromosome Mapping methods, Data Compression methods, Genomics methods
- Abstract
The fall of prices of the high-throughput genome sequencing changes the landscape of modern genomics. A number of large scale projects aimed at sequencing many human genomes are in progress. Genome sequencing also becomes an important aid in the personalized medicine. One of the significant side effects of this change is a necessity of storage and transfer of huge amounts of genomic data. In this paper we deal with the problem of compression of large collections of complete genomic sequences. We propose an algorithm that is able to compress the collection of 1092 human diploid genomes about 9,500 times. This result is about 4 times better than what is offered by the other existing compressors. Moreover, our algorithm is very fast as it processes the data with speed 200 MB/s on a modern workstation. In a consequence the proposed algorithm allows storing the complete genomic collections at low cost, e.g., the examined collection of 1092 human genomes needs only about 700 MB when compressed, what can be compared to about 6.7 TB of uncompressed FASTA files. The source code is available at http://sun.aei.polsl.pl/REFRESH/index.php?page=projects&project=gdc&subpage=about.
- Published
- 2015
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- View/download PDF
43. Assessment of the impact of using a reference transcriptome in mapping short RNA-Seq reads.
- Author
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Zhao S
- Subjects
- Base Sequence, Gene Expression Profiling, Humans, Kidney metabolism, Liver metabolism, Lung metabolism, Molecular Sequence Data, Myocardium metabolism, RNA chemistry, RNA Splicing, Sequence Analysis, RNA, User-Computer Interface, Chromosome Mapping, RNA metabolism, Transcriptome
- Abstract
RNA-Seq has become increasingly popular in transcriptome profiling. The major challenge in RNA-Seq data analysis is the accurate mapping of junction reads to their genomic origins. To detect splicing sites in short reads, many RNA-Seq aligners use reference transcriptome to inform placement of junction reads. However, no systematic evaluation has been performed to assess or quantify the benefits of incorporating reference transcriptome in mapping RNA-Seq reads. In this paper, we have studied the impact of reference transcriptome on mapping RNA-Seq reads, especially on junction ones. The same dataset were analysed with and without RefGene transcriptome, respectively. Then a Perl script was developed to analyse and compare the mapping results. It was found that about 50-55% junction reads can be mapped to the same genomic regions regardless of the usage of RefGene model. More than one-third of reads fail to be mapped without the help of a reference transcriptome. For "Alternatively" mapped reads, i.e., those reads mapped differently with and without RefGene model, the mappings without RefGene model are usually worse than their corresponding alignments with RefGene model. For junction reads that span more than two exons, it is less likely to align them correctly without the assistance of reference transcriptome. As the sequencing technology evolves, the read length is becoming longer and longer. When reads become longer, they are more likely to span multiple exons, and thus the mapping of long junction reads is actually becoming more and more challenging without the assistance of reference transcriptome. Therefore, the advantages of using reference transcriptome in the mapping demonstrated in this study are becoming more evident for longer reads. In addition, the effect of the completeness of reference transcriptome on mapping of RNA-Seq reads is discussed.
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- 2014
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44. High density SNP and SSR-based genetic maps of two independent oil palm hybrids.
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Ting NC, Jansen J, Mayes S, Massawe F, Sambanthamurthi R, Ooi LC, Chin CW, Arulandoo X, Seng TY, Alwee SS, Ithnin M, and Singh R
- Subjects
- Amplified Fragment Length Polymorphism Analysis, Genetic Linkage, Genome, Plant, Genotype, Polymorphism, Restriction Fragment Length, Quantitative Trait Loci, Arecaceae genetics, Chromosome Mapping, Microsatellite Repeats genetics, Polymorphism, Single Nucleotide genetics
- Abstract
Background: Oil palm is an important perennial oil crop with an extremely long selection cycle of 10 to 12 years. As such, any tool that speeds up its genetic improvement process, such as marker-assisted breeding is invaluable. Previously, genetic linkage maps based on AFLP, RFLP and SSR markers were developed and QTLs for fatty acid composition and yield components identified. High density genetic maps of crosses of different genetic backgrounds are indispensable tools for investigating oil palm genetics. They are also useful for comparative mapping analyses to identify markers closely linked to traits of interest., Results: A 4.5 K customized oil palm SNP array was developed using the Illumina Infinium platform. The SNPs and 252 SSRs were genotyped on two mapping populations, an intraspecific cross with 87 palms and an interspecific cross with 108 palms. Parental maps with 16 linkage groups (LGs), were constructed for the three fruit forms of E. guineensis (dura, pisifera and tenera). Map resolution was further increased by integrating the dura and pisifera maps into an intraspecific integrated map with 1,331 markers spanning 1,867 cM. We also report the first map of a Colombian E. oleifera, comprising 10 LGs with 65 markers spanning 471 cM. Although not very dense due to the high level of homozygosity in E. oleifera, the LGs were successfully integrated with the LGs of the tenera map. Direct comparison between the parental maps identified 603 transferable markers polymorphic in at least two of the parents. Further analysis revealed a high degree of marker transferability covering 1,075 cM, between the intra- and interspecific integrated maps. The interspecific cross displayed higher segregation distortion than the intraspecific cross. However, inclusion of distorted markers in the genetic maps did not disrupt the marker order and no map expansion was observed., Conclusions: The high density SNP and SSR-based genetic maps reported in this paper have greatly improved marker density and genome coverage in comparison with the first reference map based on AFLP and SSR markers. Therefore, it is foreseen that they will be more useful for fine mapping of QTLs and whole genome association mapping studies in oil palm.
- Published
- 2014
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45. Comparison of mapping algorithms used in high-throughput sequencing: application to Ion Torrent data.
- Author
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Caboche S, Audebert C, Lemoine Y, and Hot D
- Subjects
- Databases, Nucleic Acid, Internet, Reproducibility of Results, Sensitivity and Specificity, Algorithms, Chromosome Mapping methods, Computational Biology methods, Genomics methods, High-Throughput Nucleotide Sequencing, Software
- Abstract
Background: The rapid evolution in high-throughput sequencing (HTS) technologies has opened up new perspectives in several research fields and led to the production of large volumes of sequence data. A fundamental step in HTS data analysis is the mapping of reads onto reference sequences. Choosing a suitable mapper for a given technology and a given application is a subtle task because of the difficulty of evaluating mapping algorithms., Results: In this paper, we present a benchmark procedure to compare mapping algorithms used in HTS using both real and simulated datasets and considering four evaluation criteria: computational resource and time requirements, robustness of mapping, ability to report positions for reads in repetitive regions, and ability to retrieve true genetic variation positions. To measure robustness, we introduced a new definition for a correctly mapped read taking into account not only the expected start position of the read but also the end position and the number of indels and substitutions. We developed CuReSim, a new read simulator, that is able to generate customized benchmark data for any kind of HTS technology by adjusting parameters to the error types. CuReSim and CuReSimEval, a tool to evaluate the mapping quality of the CuReSim simulated reads, are freely available. We applied our benchmark procedure to evaluate 14 mappers in the context of whole genome sequencing of small genomes with Ion Torrent data for which such a comparison has not yet been established., Conclusions: A benchmark procedure to compare HTS data mappers is introduced with a new definition for the mapping correctness as well as tools to generate simulated reads and evaluate mapping quality. The application of this procedure to Ion Torrent data from the whole genome sequencing of small genomes has allowed us to validate our benchmark procedure and demonstrate that it is helpful for selecting a mapper based on the intended application, questions to be addressed, and the technology used. This benchmark procedure can be used to evaluate existing or in-development mappers as well as to optimize parameters of a chosen mapper for any application and any sequencing platform.
- Published
- 2014
- Full Text
- View/download PDF
46. Mapping of imprinted quantitative trait loci using immortalized F2 populations.
- Author
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Wen Y and Wu W
- Subjects
- Algorithms, Computer Simulation, Crosses, Genetic, Models, Genetic, Chromosome Mapping, Genomic Imprinting, Quantitative Trait Loci
- Abstract
Mapping of imprinted quantitative trait loci (iQTLs) is helpful for understanding the effects of genomic imprinting on complex traits in animals and plants. At present, the experimental designs and corresponding statistical methods having been proposed for iQTL mapping are all based on temporary populations including F2 and BC1, which can be used only once and suffer some other shortcomings respectively. In this paper, we propose a framework for iQTL mapping, including methods of interval mapping (IM) and composite interval mapping (CIM) based on conventional low-density genetic maps and point mapping (PM) and composite point mapping (CPM) based on ultrahigh-density genetic maps, using an immortalized F2 (imF2) population generated by random crosses between recombinant inbred lines or doubled haploid lines. We demonstrate by simulations that imF2 populations are very desirable and the proposed statistical methods (especially CIM and CPM) are very powerful for iQTL mapping, with which the imprinting effects as well as the additive and dominance effects of iQTLs can be unbiasedly estimated.
- Published
- 2014
- Full Text
- View/download PDF
47. Development and characterization of SSR markers from Pinus massoniana and their transferability to P. elliottii, P. caribaea and P. yunnanensis.
- Author
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Feng YH, Yang ZQ, Wang J, Luo QF, and Li HG
- Subjects
- China, Pinus growth & development, Polymerase Chain Reaction methods, Polymorphism, Genetic, Vietnam, Chromosome Mapping, Microsatellite Repeats genetics, Pinus genetics
- Abstract
Pinus massoniana (Masson's pine) is a widespread tree species in central and southern China and northern Vietnam; it is valued for rosin and paper production. Despite the significant economic value of Masson's pine, little work has been done on its molecular genetics. We developed 318 SSR primers from genome sequences of P. massoniana, and we identified 10 polymorphic markers. The number of alleles in the population of P. massoniana that we examined ranged from two to four, and the Shannon diversity index ranged from 0.150 to 1.133. Cross-species transferability of the 318 SSRs was also analyzed in the slash pine (Pinus elliottii), the Caribbean pine (Pinus caribaea) and the Yunnan pine (Pinus yunnanensis); 15, 10, and 10 primer pairs generated polymorphic amplification, respectively. These sets of polymorphic SSR markers will be useful for population genetics studies of P. massoniana, for genetic identification of interspecific hybridization, and for phylogeographic studies of Pinus spp.
- Published
- 2014
- Full Text
- View/download PDF
48. Combined linkage disequilibrium and linkage mapping: Bayesian multilocus approach.
- Author
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Pikkuhookana P and Sillanpää MJ
- Subjects
- Genotype, Humans, Models, Genetic, Neoplasms genetics, Pedigree, Phenotype, Polymorphism, Single Nucleotide, Quantitative Trait Loci, Bayes Theorem, Chromosome Mapping methods, Linkage Disequilibrium
- Abstract
Quantitative trait loci (QTL) affecting the phenotype of interest can be detected using linkage analysis (LA), linkage disequilibrium (LD) mapping or a combination of both (LDLA). The LA approach uses information from recombination events within the observed pedigree and LD mapping from the historical recombinations within the unobserved pedigree. We propose the Bayesian variable selection approach for combined LDLA analysis for single-nucleotide polymorphism (SNP) data. The novel approach uses both sources of information simultaneously as is commonly done in plant and animal genetics, but it makes fewer assumptions about population demography than previous LDLA methods. This differs from approaches in human genetics, where LDLA methods use LA information conditional on LD information or the other way round. We argue that the multilocus LDLA model is more powerful for the detection of phenotype-genotype associations than single-locus LDLA analysis. To illustrate the performance of the Bayesian multilocus LDLA method, we analyzed simulation replicates based on real SNP genotype data from small three-generational CEPH families and compared the results with commonly used quantitative transmission disequilibrium test (QTDT). This paper is intended to be conceptual in the sense that it is not meant to be a practical method for analyzing high-density SNP data, which is more common. Our aim was to test whether this approach can function in principle.
- Published
- 2014
- Full Text
- View/download PDF
49. Linkage maps of the Atlantic salmon (Salmo salar) genome derived from RAD sequencing.
- Author
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Gonen S, Lowe NR, Cezard T, Gharbi K, Bishop SC, and Houston RD
- Subjects
- Animals, Female, Gene Duplication, Genetic Markers, Genome, Genomics, Genotype, Male, Microsatellite Repeats, Physical Chromosome Mapping, Polymorphism, Single Nucleotide, Quantitative Trait Loci, Recombination, Genetic, Reproducibility of Results, Synteny, Chromosome Mapping, Genetic Linkage, Salmo salar genetics, Sequence Analysis, DNA
- Abstract
Background: Genetic linkage maps are useful tools for mapping quantitative trait loci (QTL) influencing variation in traits of interest in a population. Genotyping-by-sequencing approaches such as Restriction-site Associated DNA sequencing (RAD-Seq) now enable the rapid discovery and genotyping of genome-wide SNP markers suitable for the development of dense SNP linkage maps, including in non-model organisms such as Atlantic salmon (Salmo salar). This paper describes the development and characterisation of a high density SNP linkage map based on SbfI RAD-Seq SNP markers from two Atlantic salmon reference families., Results: Approximately 6,000 SNPs were assigned to 29 linkage groups, utilising markers from known genomic locations as anchors. Linkage maps were then constructed for the four mapping parents separately. Overall map lengths were comparable between male and female parents, but the distribution of the SNPs showed sex-specific patterns with a greater degree of clustering of sire-segregating SNPs to single chromosome regions. The maps were integrated with the Atlantic salmon draft reference genome contigs, allowing the unique assignment of ~4,000 contigs to a linkage group. 112 genome contigs mapped to two or more linkage groups, highlighting regions of putative homeology within the salmon genome. A comparative genomics analysis with the stickleback reference genome identified putative genes closely linked to approximately half of the ordered SNPs and demonstrated blocks of orthology between the Atlantic salmon and stickleback genomes. A subset of 47 RAD-Seq SNPs were successfully validated using a high-throughput genotyping assay, with a correspondence of 97% between the two assays., Conclusions: This Atlantic salmon RAD-Seq linkage map is a resource for salmonid genomics research as genotyping-by-sequencing becomes increasingly common. This is aided by the integration of the SbfI RAD-Seq SNPs with existing reference maps and the draft reference genome, as well as the identification of putative genes proximal to the SNPs. Differences in the distribution of recombination events between the sexes is evident, and regions of homeology have been identified which are reflective of the recent salmonid whole genome duplication.
- Published
- 2014
- Full Text
- View/download PDF
50. Genome-wide mapping of loci explaining variance in scrotal circumference in Nellore cattle.
- Author
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Utsunomiya YT, Carmo AS, Neves HH, Carvalheiro R, Matos MC, Zavarez LB, Ito PK, Pérez O'Brien AM, Sölkner J, Porto-Neto LR, Schenkel FS, McEwan J, Cole JB, da Silva MV, Van Tassell CP, Sonstegard TS, and Garcia JF
- Subjects
- Animals, Cattle, Chromosomes ultrastructure, Fertility, Genome, Genotype, Male, Organ Size, Phenotype, Polymorphism, Single Nucleotide, Quantitative Trait Loci, Chromosome Mapping veterinary, Genome-Wide Association Study, Scrotum anatomy & histology
- Abstract
The reproductive performance of bulls has a high impact on the beef cattle industry. Scrotal circumference (SC) is the most recorded reproductive trait in beef herds, and is used as a major selection criterion to improve precocity and fertility. The characterization of genomic regions affecting SC can contribute to the identification of diagnostic markers for reproductive performance and uncover molecular mechanisms underlying complex aspects of bovine reproductive biology. In this paper, we report a genome-wide scan for chromosome segments explaining differences in SC, using data of 861 Nellore bulls (Bos indicus) genotyped for over 777,000 single nucleotide polymorphisms. Loci that excel from the genome background were identified on chromosomes 4, 6, 7, 10, 14, 18 and 21. The majority of these regions were previously found to be associated with reproductive and body size traits in cattle. The signal on chromosome 14 replicates the pleiotropic quantitative trait locus encompassing PLAG1 that affects male fertility in cattle and stature in several species. Based on intensive literature mining, SP4, MAGEL2, SH3RF2, PDE5A and SNAI2 are proposed as novel candidate genes for SC, as they affect growth and testicular size in other animal models. These findings contribute to linking reproductive phenotypes to gene functions, and may offer new insights on the molecular biology of male fertility.
- Published
- 2014
- Full Text
- View/download PDF
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