601
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Wang X, Li S. Chromatin immunoprecipitation-sequencing predicts p300 binding sites in the MCF7 human breast cancer cell line. Int J Mol Med 2015; 35:973-8. [PMID: 25625638 DOI: 10.3892/ijmm.2015.2081] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2014] [Accepted: 12/02/2014] [Indexed: 11/06/2022] Open
Abstract
The aim of the present study was to identify the distribution characters of p300 binding sites in estradiol (E2) stimulated MCF7 cell lines and controls, and to study the roles of transcriptional coactivator p300 in the tumorigenesis and progression of various human cancers following E2 stimulation. The chromatin immunoprecipitation followed by sequencing data of GSES9623 was downloaded from the Gene Expression Omnibus database, including breast cancer data of GSM986085 and control data of GSM986087. MACS peak‑calling software was employed to identify the p300‑bound sites in the two groups. The differential target genes of p300‑bound sites were further analyzed and the concordant factors were predicted. The Gene Ontology (GO) was used to conduct functional enrichment analysis. There were 32,249 p300 binding sites identified in the E2 stimulation group and 43,156 in the control group. GO enrichment analysis of the target genes showed that p300‑regulated target genes mainly participated in the neural cell differentiation‑associated biology process; while in the E2 stimulation group, partial functions of the target genes had changed. A total of 24,899 differential p300‑bound sites of the two groups were identified and GO enrichment analysis demonstrated that E2 stimulation changed p300 binding sites, but did not influence the regulatory function of p300. The effect of E2 in the MCF7 cells suggested that E2 affected the binding affinity of DNA and transcription factors in a large scale. By analyzing the concordant factors, several important factors were discovered, such as BRCA1 and ESR1. Overall, the results of the present study suggested an association between p300 and carcinogenic genes. This may provide theoretical guidance for cancer therapy.
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Affiliation(s)
- Xiemei Wang
- Department of Radiation Medicine and Tumor Research, Chongqing Medical University, Chongqing 400016, P.R. China
| | - Shaolin Li
- Department of Radiation Medicine and Tumor Research, Chongqing Medical University, Chongqing 400016, P.R. China
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602
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Rahn-Lee L, Byrne ME, Zhang M, Le Sage D, Glenn DR, Milbourne T, Walsworth RL, Vali H, Komeili A. A genetic strategy for probing the functional diversity of magnetosome formation. PLoS Genet 2015; 11:e1004811. [PMID: 25569806 PMCID: PMC4287615 DOI: 10.1371/journal.pgen.1004811] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2014] [Accepted: 10/07/2014] [Indexed: 11/18/2022] Open
Abstract
Model genetic systems are invaluable, but limit us to understanding only a few organisms in detail, missing the variations in biological processes that are performed by related organisms. One such diverse process is the formation of magnetosome organelles by magnetotactic bacteria. Studies of model magnetotactic α-proteobacteria have demonstrated that magnetosomes are cubo-octahedral magnetite crystals that are synthesized within pre-existing membrane compartments derived from the inner membrane and orchestrated by a specific set of genes encoded within a genomic island. However, this model cannot explain all magnetosome formation, which is phenotypically and genetically diverse. For example, Desulfovibrio magneticus RS-1, a δ-proteobacterium for which we lack genetic tools, produces tooth-shaped magnetite crystals that may or may not be encased by a membrane with a magnetosome gene island that diverges significantly from those of the α-proteobacteria. To probe the functional diversity of magnetosome formation, we used modern sequencing technology to identify hits in RS-1 mutated with UV or chemical mutagens. We isolated and characterized mutant alleles of 10 magnetosome genes in RS-1, 7 of which are not found in the α-proteobacterial models. These findings have implications for our understanding of magnetosome formation in general and demonstrate the feasibility of applying a modern genetic approach to an organism for which classic genetic tools are not available.
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Affiliation(s)
- Lilah Rahn-Lee
- Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, California, United States of America
| | - Meghan E. Byrne
- Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, California, United States of America
| | - Manjing Zhang
- Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, California, United States of America
| | - David Le Sage
- Department of Physics, Harvard University, Cambridge, Massachusetts, United States of America
- Harvard-Smithsonian Center for Astrophysics, Cambridge, Massachusetts, United States of America
| | - David R. Glenn
- Department of Physics, Harvard University, Cambridge, Massachusetts, United States of America
- Harvard-Smithsonian Center for Astrophysics, Cambridge, Massachusetts, United States of America
- Center for Brain Science, Harvard University, Cambridge, Massachusetts, United States of America
| | - Timothy Milbourne
- Department of Physics, Harvard University, Cambridge, Massachusetts, United States of America
| | - Ronald L. Walsworth
- Department of Physics, Harvard University, Cambridge, Massachusetts, United States of America
- Harvard-Smithsonian Center for Astrophysics, Cambridge, Massachusetts, United States of America
- Center for Brain Science, Harvard University, Cambridge, Massachusetts, United States of America
| | - Hojatollah Vali
- Facility for Electron Microscopy Research, McGill University, Montreal, Quebec, Canada
- Department of Anatomy and Cell Biology, McGill University, Montreal, Quebec, Canada
- Department of Earth and Planetary Sciences, McGill University, Montreal, Quebec, Canada
| | - Arash Komeili
- Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, California, United States of America
- * E-mail:
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603
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Fontaine MC, Pease JB, Steele A, Waterhouse RM, Neafsey DE, Sharakhov IV, Jiang X, Hall AB, Catteruccia F, Kakani E, Mitchell SN, Wu YC, Smith HA, Love RR, Lawniczak MK, Slotman MA, Emrich SJ, Hahn MW, Besansky NJ. Mosquito genomics. Extensive introgression in a malaria vector species complex revealed by phylogenomics. Science 2015; 347:1258524. [PMID: 25431491 PMCID: PMC4380269 DOI: 10.1126/science.1258524] [Citation(s) in RCA: 371] [Impact Index Per Article: 41.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Introgressive hybridization is now recognized as a widespread phenomenon, but its role in evolution remains contested. Here, we use newly available reference genome assemblies to investigate phylogenetic relationships and introgression in a medically important group of Afrotropical mosquito sibling species. We have identified the correct species branching order to resolve a contentious phylogeny and show that lineages leading to the principal vectors of human malaria were among the first to split. Pervasive autosomal introgression between these malaria vectors means that only a small fraction of the genome, mainly on the X chromosome, has not crossed species boundaries. Our results suggest that traits enhancing vectorial capacity may be gained through interspecific gene flow, including between nonsister species.
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Affiliation(s)
- Michael C Fontaine
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN 46556, USA. Eck Institute for Global Health, University of Notre Dame, Notre Dame, IN 46556, USA
| | - James B Pease
- Department of Biology, Indiana University, Bloomington, IN 47405, USA
| | - Aaron Steele
- Department of Computer Science and Engineering, University of Notre Dame, Notre Dame, IN 46556, USA
| | - Robert M Waterhouse
- Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, 32 Vassar Street, Cambridge, MA 02139, USA. The Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, MA 02142, USA. Department of Genetic Medicine and Development, University of Geneva Medical School, rue Michel-Servet 1, 1211 Geneva, Switzerland. Swiss Institute of Bioinformatics, rue Michel-Servet 1, 1211 Geneva, Switzerland
| | - Daniel E Neafsey
- The Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, MA 02142, USA
| | - Igor V Sharakhov
- Department of Entomology, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061, USA. The Interdisciplinary PhD Program in Genetics, Bioinformatics, and Computational Biology, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061, USA
| | - Xiaofang Jiang
- The Interdisciplinary PhD Program in Genetics, Bioinformatics, and Computational Biology, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061, USA
| | - Andrew B Hall
- The Interdisciplinary PhD Program in Genetics, Bioinformatics, and Computational Biology, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061, USA
| | - Flaminia Catteruccia
- Department of Immunology and Infectious Diseases, Harvard School of Public Health, Boston, MA 02115, USA. Dipartimento di Medicina Sperimentale e Scienze Biochimiche, Università degli Studi di Perugia, Perugia, Italy
| | - Evdoxia Kakani
- Department of Immunology and Infectious Diseases, Harvard School of Public Health, Boston, MA 02115, USA. Dipartimento di Medicina Sperimentale e Scienze Biochimiche, Università degli Studi di Perugia, Perugia, Italy
| | - Sara N Mitchell
- Department of Immunology and Infectious Diseases, Harvard School of Public Health, Boston, MA 02115, USA
| | - Yi-Chieh Wu
- Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, 32 Vassar Street, Cambridge, MA 02139, USA
| | - Hilary A Smith
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN 46556, USA. Eck Institute for Global Health, University of Notre Dame, Notre Dame, IN 46556, USA
| | - R Rebecca Love
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN 46556, USA. Eck Institute for Global Health, University of Notre Dame, Notre Dame, IN 46556, USA
| | - Mara K Lawniczak
- Department of Life Sciences, Imperial College London, South Kensington Campus, London SW7 2AZ, UK
| | - Michel A Slotman
- Department of Entomology, Texas A&M University, College Station, TX 77843, USA
| | - Scott J Emrich
- Eck Institute for Global Health, University of Notre Dame, Notre Dame, IN 46556, USA. Department of Computer Science and Engineering, University of Notre Dame, Notre Dame, IN 46556, USA
| | - Matthew W Hahn
- Department of Biology, Indiana University, Bloomington, IN 47405, USA. School of Informatics and Computing, Indiana University, Bloomington, IN 47405, USA.
| | - Nora J Besansky
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN 46556, USA. Eck Institute for Global Health, University of Notre Dame, Notre Dame, IN 46556, USA.
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604
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Sun S, Billmyre RB, Mieczkowski PA, Heitman J. Unisexual reproduction drives meiotic recombination and phenotypic and karyotypic plasticity in Cryptococcus neoformans. PLoS Genet 2014; 10:e1004849. [PMID: 25503976 PMCID: PMC4263396 DOI: 10.1371/journal.pgen.1004849] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2014] [Accepted: 10/24/2014] [Indexed: 12/13/2022] Open
Abstract
In fungi, unisexual reproduction, where sexual development is initiated without the presence of two compatible mating type alleles, has been observed in several species that can also undergo traditional bisexual reproduction, including the important human fungal pathogens Cryptococcus neoformans and Candida albicans. While unisexual reproduction has been well characterized qualitatively, detailed quantifications are still lacking for aspects of this process, such as the frequency of recombination during unisexual reproduction, and how this compares with bisexual reproduction. Here, we analyzed meiotic recombination during α-α unisexual and a-α bisexual reproduction of C. neoformans. We found that meiotic recombination operates in a similar fashion during both modes of sexual reproduction. Specifically, we observed that in α-α unisexual reproduction, the numbers of crossovers along the chromosomes during meiosis, recombination frequencies at specific chromosomal regions, as well as meiotic recombination hot and cold spots, are all similar to those observed during a-α bisexual reproduction. The similarity in meiosis is also reflected by the fact that phenotypic segregation among progeny collected from the two modes of sexual reproduction is also similar, with transgressive segregation being observed in both. Additionally, we found diploid meiotic progeny were also produced at similar frequencies in the two modes of sexual reproduction, and transient chromosomal loss and duplication likely occurs frequently and results in aneuploidy and loss of heterozygosity that can span entire chromosomes. Furthermore, in both α-α unisexual and a-α bisexual reproduction, we observed biased allele inheritance in regions on chromosome 4, suggesting the presence of fragile chromosomal regions that might be vulnerable to mitotic recombination. Interestingly, we also observed a crossover event that occurred within the MAT locus during α-α unisexual reproduction. Our results provide definitive evidence that α-α unisexual reproduction is a meiotic process similar to a-α bisexual reproduction. Unisexual reproduction has been reported in several fungal species that have been traditionally thought to undergo bisexual reproduction, including major human fungal pathogens such as Cryptococcus neoformans and Candida albicans. While it has been well characterized qualitatively, quantitative description of unisexual reproduction, and detailed comparisons between unisexual and bisexual reproduction, are lacking. Here, by analyzing meiotic progeny generated from both α-α unisexual and a-α bisexual reproduction in C. neoformans, we find that the progeny collected from the two modes of sexual reproduction show similar phenotypic segregation, with transgressive segregation of several phenotypes being observed in both. Additionally, the two modes of sexual reproduction are similar in all the aspects of meiotic recombination that we have examined, providing definitive evidence that α-α unisexual reproduction is a meiotic process that operates similarly as in a-α bisexual reproduction. The ability to undergo both unisexual and bisexual reproduction may provide evolutionary advantages in environments where suitable mating partners are scarce, or where sexual reproduction is favored over asexual reproduction by mixing genetic materials and producing spores that are more tolerant of harsh environments. We discuss the implications of these findings in the context of the evolution of pathogenesis, mating types, and mating systems.
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Affiliation(s)
- Sheng Sun
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, North Carolina, United States of America
| | - R. Blake Billmyre
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Piotr A. Mieczkowski
- Department of Biology, High-Throughput Sequencing Facility, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Joseph Heitman
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, North Carolina, United States of America
- * E-mail:
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605
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Morin-Adeline V, Lomas R, O’Meally D, Stack C, Conesa A, Šlapeta J. Comparative transcriptomics reveals striking similarities between the bovine and feline isolates of Tritrichomonas foetus: consequences for in silico drug-target identification. BMC Genomics 2014; 15:955. [PMID: 25374366 PMCID: PMC4247702 DOI: 10.1186/1471-2164-15-955] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2014] [Accepted: 10/22/2014] [Indexed: 11/25/2022] Open
Abstract
BACKGROUND Few, if any, protozoan parasites are reported to exhibit extreme organ tropism like the flagellate Tritrichomonas foetus. In cattle, T. foetus infects the reproductive system causing abortion, whereas the infection in cats results in chronic large bowel diarrhoea. In the absence of a T. foetus genome, we utilized a de novo approach to assemble the transcriptome of the bovine and feline genotype to identify host-specific adaptations and virulence factors specific to each genotype. Furthermore, a subset of orthologs was used to characterize putative druggable targets and expose complications of in silico drug target mining in species with indefinite host-ranges. RESULTS Illumina RNA-seq reads were assembled into two representative bovine and feline transcriptomes containing 42,363 and 36,559 contigs, respectively. Coding and non-coding regions of the genome libraries revealed striking similarities, with 24,620 shared homolog pairs reduced down to 7,547 coding orthologs between the two genotypes. The transcriptomes were near identical in functional category distribution; with no indication of selective pressure acting on orthologs despite differences in parasite origins/host. Orthologs formed a large proportion of highly expressed transcripts in both genotypes (bovine genotype: 76%, feline genotype: 56%). Mining the libraries for protease virulence factors revealed the cysteine proteases (CP) to be the most common. In total, 483 and 445 bovine and feline T. foetus transcripts were identified as putative proteases based on MEROPS database, with 9 hits to putative protease inhibitors. In bovine T. foetus, CP8 is the preferentially transcribed CP while in the feline genotype, transcription of CP7 showed higher abundance. In silico druggability analysis of the two genotypes revealed that when host sequences are taken into account, drug targets are genotype-specific. CONCLUSION Gene discovery analysis based on RNA-seq data analysis revealed prominent similarities between the bovine and feline T. foetus, suggesting recent adaptation to their respective host/niche. T. foetus represents a unique case of a mammalian protozoan expanding its parasitic grasp across distantly related host lineages. Consequences of the host-range for in silico drug targeting are exposed here, demonstrating that targets of the parasite in one host are not necessarily ideal for the same parasite in another host.
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Affiliation(s)
| | - Rodrigo Lomas
- />Genomics of Gene Expression Lab, Prince Felipe Research Centre, Valencia, Spain
| | - Denis O’Meally
- />Faculty of Veterinary Science, University of Sydney, New South Wales, 2006 Australia
| | - Colin Stack
- />School of Science and Health, University of Western Sydney, Penrith, New South Wales 2751 Australia
| | - Ana Conesa
- />Genomics of Gene Expression Lab, Prince Felipe Research Centre, Valencia, Spain
| | - Jan Šlapeta
- />Faculty of Veterinary Science, University of Sydney, New South Wales, 2006 Australia
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606
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Fang H, Wu Y, Narzisi G, O'Rawe JA, Barrón LTJ, Rosenbaum J, Ronemus M, Iossifov I, Schatz MC, Lyon GJ. Reducing INDEL calling errors in whole genome and exome sequencing data. Genome Med 2014; 6:89. [PMID: 25426171 PMCID: PMC4240813 DOI: 10.1186/s13073-014-0089-z] [Citation(s) in RCA: 120] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2014] [Accepted: 10/16/2014] [Indexed: 12/30/2022] Open
Abstract
Background INDELs, especially those disrupting protein-coding regions of the genome, have been strongly associated with human diseases. However, there are still many errors with INDEL variant calling, driven by library preparation, sequencing biases, and algorithm artifacts. Methods We characterized whole genome sequencing (WGS), whole exome sequencing (WES), and PCR-free sequencing data from the same samples to investigate the sources of INDEL errors. We also developed a classification scheme based on the coverage and composition to rank high and low quality INDEL calls. We performed a large-scale validation experiment on 600 loci, and find high-quality INDELs to have a substantially lower error rate than low-quality INDELs (7% vs. 51%). Results Simulation and experimental data show that assembly based callers are significantly more sensitive and robust for detecting large INDELs (>5 bp) than alignment based callers, consistent with published data. The concordance of INDEL detection between WGS and WES is low (53%), and WGS data uniquely identifies 10.8-fold more high-quality INDELs. The validation rate for WGS-specific INDELs is also much higher than that for WES-specific INDELs (84% vs. 57%), and WES misses many large INDELs. In addition, the concordance for INDEL detection between standard WGS and PCR-free sequencing is 71%, and standard WGS data uniquely identifies 6.3-fold more low-quality INDELs. Furthermore, accurate detection with Scalpel of heterozygous INDELs requires 1.2-fold higher coverage than that for homozygous INDELs. Lastly, homopolymer A/T INDELs are a major source of low-quality INDEL calls, and they are highly enriched in the WES data. Conclusions Overall, we show that accuracy of INDEL detection with WGS is much greater than WES even in the targeted region. We calculated that 60X WGS depth of coverage from the HiSeq platform is needed to recover 95% of INDELs detected by Scalpel. While this is higher than current sequencing practice, the deeper coverage may save total project costs because of the greater accuracy and sensitivity. Finally, we investigate sources of INDEL errors (for example, capture deficiency, PCR amplification, homopolymers) with various data that will serve as a guideline to effectively reduce INDEL errors in genome sequencing. Electronic supplementary material The online version of this article (doi:10.1186/s13073-014-0089-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Han Fang
- Stanley Institute for Cognitive Genomics, Cold Spring Harbor Laboratory, One Bungtown Road, Cold Spring Harbor, NY USA ; Stony Brook University, 100 Nicolls Rd, Stony Brook, NY USA ; Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, One Bungtown Road, Cold Spring Harbor, NY USA
| | - Yiyang Wu
- Stanley Institute for Cognitive Genomics, Cold Spring Harbor Laboratory, One Bungtown Road, Cold Spring Harbor, NY USA ; Stony Brook University, 100 Nicolls Rd, Stony Brook, NY USA
| | - Giuseppe Narzisi
- Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, One Bungtown Road, Cold Spring Harbor, NY USA ; New York Genome Center, New York, NY USA
| | - Jason A O'Rawe
- Stanley Institute for Cognitive Genomics, Cold Spring Harbor Laboratory, One Bungtown Road, Cold Spring Harbor, NY USA ; Stony Brook University, 100 Nicolls Rd, Stony Brook, NY USA
| | - Laura T Jimenez Barrón
- Stanley Institute for Cognitive Genomics, Cold Spring Harbor Laboratory, One Bungtown Road, Cold Spring Harbor, NY USA ; Centro de Ciencias Genomicas, Universidad Nacional Autonoma de Mexico, Cuernavaca, Morelos Mexico
| | - Julie Rosenbaum
- Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, One Bungtown Road, Cold Spring Harbor, NY USA
| | - Michael Ronemus
- Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, One Bungtown Road, Cold Spring Harbor, NY USA
| | - Ivan Iossifov
- Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, One Bungtown Road, Cold Spring Harbor, NY USA
| | - Michael C Schatz
- Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, One Bungtown Road, Cold Spring Harbor, NY USA
| | - Gholson J Lyon
- Stanley Institute for Cognitive Genomics, Cold Spring Harbor Laboratory, One Bungtown Road, Cold Spring Harbor, NY USA ; Stony Brook University, 100 Nicolls Rd, Stony Brook, NY USA
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607
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Mangado A, Tronchoni J, Morales P, Novo M, Quirós M, Gonzalez R. An impaired ubiquitin ligase complex favors initial growth of auxotrophic yeast strains in synthetic grape must. Appl Microbiol Biotechnol 2014; 99:1273-86. [PMID: 25620600 DOI: 10.1007/s00253-014-6126-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2014] [Revised: 09/28/2014] [Accepted: 09/30/2014] [Indexed: 10/24/2022]
Abstract
We used experimental evolution in order to identify genes involved in the adaptation of Saccharomyces cerevisiae to the early stages of alcoholic fermentation. Evolution experiments were run for about 200 generations, in continuous culture conditions emulating the initial stages of wine fermentation. We performed whole-genome sequencing of four adapted strains from three independent evolution experiments. Mutations identified in these strains pointed to the Rsp5p-Bul1/2p ubiquitin ligase complex as the preferred evolutionary target under these experimental conditions. Rsp5p is a multifunctional enzyme able to ubiquitinate target proteins participating in different cellular processes, while Bul1p is an Rsp5p substrate adaptor specifically involved in the ubiquitin-dependent internalization of Gap1p and other plasma membrane permeases. While a loss-of-function mutation in BUL1 seems to be enough to confer a selective advantage under these assay conditions, this did not seem to be the case for RSP5 mutated strains, which required additional mutations, probably compensating for the detrimental effect of altered Rsp5p activity on essential cellular functions. The power of this experimental approach is illustrated by the identification of four independent mutants, each with a limited number of SNPs, affected within the same pathway. However, in order to obtain information relevant for a specific biotechnological process, caution must be taken in the choice of the background yeast genotype (as shown in this case for auxotrophies). In addition, the use of very stable continuous fermentation conditions might lead to the selection of a rather limited number of adaptive responses that would mask other possible targets for genetic improvement.
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Affiliation(s)
- Ana Mangado
- Instituto de Ciencias de la Vid y del Vino, ICVV, (CSIC-Universidad de La Rioja-Gobierno de La Rioja), Madre de Dios 51, 26006, Logroño, La Rioja, Spain
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608
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Kamada M, Hase S, Sato K, Toyoda A, Fujiyama A, Sakakibara Y. Whole genome complete resequencing of Bacillus subtilis natto by combining long reads with high-quality short reads. PLoS One 2014; 9:e109999. [PMID: 25329997 PMCID: PMC4199626 DOI: 10.1371/journal.pone.0109999] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2014] [Accepted: 09/04/2014] [Indexed: 01/24/2023] Open
Abstract
De novo microbial genome sequencing reached a turning point with third-generation sequencing (TGS) platforms, and several microbial genomes have been improved by TGS long reads. Bacillus subtilis natto is closely related to the laboratory standard strain B. subtilis Marburg 168, and it has a function in the production of the traditional Japanese fermented food "natto." The B. subtilis natto BEST195 genome was previously sequenced with short reads, but it included some incomplete regions. We resequenced the BEST195 genome using a PacBio RS sequencer, and we successfully obtained a complete genome sequence from one scaffold without any gaps, and we also applied Illumina MiSeq short reads to enhance quality. Compared with the previous BEST195 draft genome and Marburg 168 genome, we found that incomplete regions in the previous genome sequence were attributed to GC-bias and repetitive sequences, and we also identified some novel genes that are found only in the new genome.
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Affiliation(s)
- Mayumi Kamada
- Department of Biosciences and Informatics, Keio University, Kohoku-ku, Yokohama, Japan
| | - Sumitaka Hase
- Department of Biosciences and Informatics, Keio University, Kohoku-ku, Yokohama, Japan
| | - Kengo Sato
- Department of Biosciences and Informatics, Keio University, Kohoku-ku, Yokohama, Japan
| | - Atsushi Toyoda
- Center for Information Biology, National Institute of Genetics, Mishima, Shizuoka, Japan
| | - Asao Fujiyama
- Center for Information Biology, National Institute of Genetics, Mishima, Shizuoka, Japan
- Principles of Informatics Research Division, National Institute of Informatics, Chiyoda-ku, Tokyo, Japan
| | - Yasubumi Sakakibara
- Department of Biosciences and Informatics, Keio University, Kohoku-ku, Yokohama, Japan
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609
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Panova M, Johansson T, Canbäck B, Bentzer J, Rosenblad MA, Johannesson K, Tunlid A, André C. Species and gene divergence in Littorina snails detected by array comparative genomic hybridization. BMC Genomics 2014; 15:687. [PMID: 25135785 PMCID: PMC4148934 DOI: 10.1186/1471-2164-15-687] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2014] [Accepted: 08/11/2014] [Indexed: 12/11/2022] Open
Abstract
Background Array comparative genomic hybridization (aCGH) is commonly used to screen different types of genetic variation in humans and model species. Here, we performed aCGH using an oligonucleotide gene-expression array for a non-model species, the intertidal snail Littorina saxatilis. First, we tested what types of genetic variation can be detected by this method using direct re-sequencing and comparison to the Littorina genome draft. Secondly, we performed a genome-wide comparison of four closely related Littorina species: L. fabalis, L. compressa, L. arcana and L. saxatilis and of populations of L. saxatilis found in Spain, Britain and Sweden. Finally, we tested whether we could identify genetic variation underlying “Crab” and “Wave” ecotypes of L. saxatilis. Results We could reliably detect copy number variations, deletions and high sequence divergence (i.e. above 3%), but not single nucleotide polymorphisms. The overall hybridization pattern and number of significantly diverged genes were in close agreement with earlier phylogenetic reconstructions based on single genes. The trichotomy of L. arcana, L. compressa and L. saxatilis could not be resolved and we argue that these divergence events have occurred recently and very close in time. We found evidence for high levels of segmental duplication in the Littorina genome (10% of the transcripts represented on the array and up to 23% of the analyzed genomic fragments); duplicated genes and regions were mostly the same in all analyzed species. Finally, this method discriminated geographically distant populations of L. saxatilis, but we did not detect any significant genome divergence associated with ecotypes of L. saxatilis. Conclusions The present study provides new information on the sensitivity and the potential use of oligonucleotide arrays for genotyping of non-model organisms. Applying this method to Littorina species yields insights into genome evolution following the recent species radiation and supports earlier single-gene based phylogenies. Genetic differentiation of L. saxatilis ecotypes was not detected in this study, despite pronounced innate phenotypic differences. The reason may be that these differences are due to single-nucleotide polymorphisms. Electronic supplementary material The online version of this article (doi:10.1186/1471-2164-15-687) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Marina Panova
- Department of Biological and Environmental Sciences - Tjärnö, Gothenburg University, Gothenburg, Sweden.
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610
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Baker JJ, Johnson BK, Abramovitch RB. Slow growth of Mycobacterium tuberculosis at acidic pH is regulated by phoPR and host-associated carbon sources. Mol Microbiol 2014; 94:56-69. [PMID: 24975990 DOI: 10.1111/mmi.12688] [Citation(s) in RCA: 103] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/21/2014] [Indexed: 01/07/2023]
Abstract
During pathogenesis, Mycobacterium tuberculosis (Mtb) colonizes environments, such as the macrophage or necrotic granuloma, that are acidic and rich in cholesterol and fatty acids. The goal of this study was to examine how acidic pH and available carbon sources interact to regulate Mtb physiology. Here we report that Mtb growth at acidic pH requires host-associated carbon sources that function at the intersection of glycolysis and the TCA cycle, such as pyruvate, acetate, oxaloacetate and cholesterol. In contrast, in other tested carbon sources, Mtb fully arrests its growth at acidic pH and establishes a state of non-replicating persistence. Growth-arrested Mtb is resuscitated by the addition of pyruvate suggesting that growth arrest is due to a pH-dependent checkpoint on metabolism. Additionally, we demonstrate that the phoPR two-component regulatory system is required to slow Mtb growth at acidic pH and functions to maintain redox homeostasis. Transcriptional profiling and functional metabolic studies demonstrate that signals from acidic pH and carbon source are integrated to remodel pathways associated with anaplerotic central metabolism, lipid anabolism and the regeneration of oxidized cofactors. Because phoPR is required for Mtb virulence in animals, we suggest that pH-driven adaptation may be critical to Mtb pathogenesis.
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Affiliation(s)
- Jacob J Baker
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI, 48824, USA
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611
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Puig-Oliveras A, Ramayo-Caldas Y, Corominas J, Estellé J, Pérez-Montarelo D, Hudson NJ, Casellas J, Folch JM, Ballester M. Differences in muscle transcriptome among pigs phenotypically extreme for fatty acid composition. PLoS One 2014; 9:e99720. [PMID: 24926690 PMCID: PMC4057286 DOI: 10.1371/journal.pone.0099720] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2013] [Accepted: 05/19/2014] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND Besides having an impact on human health, the porcine muscle fatty acid profile determines meat quality and taste. The RNA-Seq technologies allowed us to explore the pig muscle transcriptome with an unprecedented detail. The aim of this study was to identify differentially-expressed genes between two groups of 6 sows belonging to an Iberian × Landrace backcross with extreme phenotypes according to FA profile. RESULTS We sequenced the muscle transcriptome acquiring 787.5 M of 75 bp paired-end reads. About 85.1% of reads were mapped to the reference genome. Of the total reads, 79.1% were located in exons, 6.0% in introns and 14.9% in intergenic regions, indicating expressed regions not annotated in the reference genome. We identified a 34.5% of the intergenic regions as interspersed repetitive regions. We predicted a total of 2,372 putative proteins. Pathway analysis with 131 differentially-expressed genes revealed that the most statistically-significant metabolic pathways were related with lipid metabolism. Moreover, 18 of the differentially-expressed genes were located in genomic regions associated with IMF composition in an independent GWAS study in the same genetic background. Thus, our results indicate that the lipid metabolism of FAs is differently modulated when the FA composition in muscle differs. For instance, a high content of PUFA may reduce FA and glucose uptake resulting in an inhibition of the lipogenesis. These results are consistent with previous studies of our group analysing the liver and the adipose tissue transcriptomes providing a view of each of the main organs involved in lipid metabolism. CONCLUSIONS The results obtained in the muscle transcriptome analysis increase the knowledge of the gene regulation of IMF deposition, FA profile and meat quality, in terms of taste and nutritional value. Besides, our results may be important in terms of human health.
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Affiliation(s)
- Anna Puig-Oliveras
- Departament de Genètica Animal, Centre de Recerca en Agrigenòmica (CRAG), Bellaterra, Spain
- Departament de Ciència Animal i dels Aliments, Universitat Autònoma de Barcelona (UAB), Bellaterra, Spain
| | - Yuliaxis Ramayo-Caldas
- Génétique Animale et Biologie Intégrative UMR1313 (GABI), Institut National de la Recherche Agronomique (INRA), Jouy-en-Josas, France
| | - Jordi Corominas
- Departament de Genètica Animal, Centre de Recerca en Agrigenòmica (CRAG), Bellaterra, Spain
- Departament de Ciència Animal i dels Aliments, Universitat Autònoma de Barcelona (UAB), Bellaterra, Spain
| | - Jordi Estellé
- Génétique Animale et Biologie Intégrative UMR1313 (GABI), Institut National de la Recherche Agronomique (INRA), Jouy-en-Josas, France
- Génétique Animale et Biologie Intégrative UMR1313 (GABI), AgroParisTech, Jouy-en-Josas, France
- Laboratoire de Radiobiologie et Etude du Génome (LREG), Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Jouy-en-Josas, France
| | - Dafne Pérez-Montarelo
- Departamento de Genética Animal, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Madrid, Spain
| | - Nicholas J. Hudson
- Computational and Systems Biology, Commonwealth Scientific and Industrial Research Organisation (CSIRO) Animal, Food and Health SciencesQLD, Brisbane, Australia
| | - Joaquim Casellas
- Departament de Ciència Animal i dels Aliments, Universitat Autònoma de Barcelona (UAB), Bellaterra, Spain
- Departament de Genètica i Millora Animal, Institut de Recerca i Tecnologies Agroalimentàries (IRTA), Lleida, Spain
| | - Josep M. Folch
- Departament de Genètica Animal, Centre de Recerca en Agrigenòmica (CRAG), Bellaterra, Spain
- Departament de Ciència Animal i dels Aliments, Universitat Autònoma de Barcelona (UAB), Bellaterra, Spain
| | - Maria Ballester
- Departament de Genètica Animal, Centre de Recerca en Agrigenòmica (CRAG), Bellaterra, Spain
- Departament de Ciència Animal i dels Aliments, Universitat Autònoma de Barcelona (UAB), Bellaterra, Spain
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612
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Paszkiewicz KH, Farbos A, O'Neill P, Moore K. Quality control on the frontier. Front Genet 2014; 5:157. [PMID: 24904650 PMCID: PMC4033843 DOI: 10.3389/fgene.2014.00157] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2013] [Accepted: 05/12/2014] [Indexed: 01/17/2023] Open
Abstract
In the world of high-throughput sequencing there are numerous challenges to effective data quality control. There are no single quality metrics which are appropriate in all conditions. Here we detail the different open source software used at the Exeter Sequencing Service to provide generic quality control information, as well as more specific metrics for genomic and transcriptomic libraries run on Illumina platforms.
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Affiliation(s)
- Konrad H Paszkiewicz
- Exeter Sequencing Service, Biosciences, College of Life and Environmental Science, University of Exeter Exeter, UK
| | - Audrey Farbos
- Exeter Sequencing Service, Biosciences, College of Life and Environmental Science, University of Exeter Exeter, UK
| | - Paul O'Neill
- Exeter Sequencing Service, Biosciences, College of Life and Environmental Science, University of Exeter Exeter, UK
| | - Karen Moore
- Exeter Sequencing Service, Biosciences, College of Life and Environmental Science, University of Exeter Exeter, UK
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613
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Chen C, Khaleel SS, Huang H, Wu CH. Software for pre-processing Illumina next-generation sequencing short read sequences. SOURCE CODE FOR BIOLOGY AND MEDICINE 2014; 9:8. [PMID: 24955109 PMCID: PMC4064128 DOI: 10.1186/1751-0473-9-8] [Citation(s) in RCA: 156] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 08/08/2013] [Accepted: 04/22/2014] [Indexed: 01/08/2023]
Abstract
Background When compared to Sanger sequencing technology, next-generation sequencing (NGS) technologies are hindered by shorter sequence read length, higher base-call error rate, non-uniform coverage, and platform-specific sequencing artifacts. These characteristics lower the quality of their downstream analyses, e.g. de novo and reference-based assembly, by introducing sequencing artifacts and errors that may contribute to incorrect interpretation of data. Although many tools have been developed for quality control and pre-processing of NGS data, none of them provide flexible and comprehensive trimming options in conjunction with parallel processing to expedite pre-processing of large NGS datasets. Methods We developed ngsShoRT (next-generation sequencing Short Reads Trimmer), a flexible and comprehensive open-source software package written in Perl that provides a set of algorithms commonly used for pre-processing NGS short read sequences. We compared the features and performance of ngsShoRT with existing tools: CutAdapt, NGS QC Toolkit and Trimmomatic. We also compared the effects of using pre-processed short read sequences generated by different algorithms on de novo and reference-based assembly for three different genomes: Caenorhabditis elegans, Saccharomyces cerevisiae S288c, and Escherichia coli O157 H7. Results Several combinations of ngsShoRT algorithms were tested on publicly available Illumina GA II, HiSeq 2000, and MiSeq eukaryotic and bacteria genomic short read sequences with the focus on removing sequencing artifacts and low-quality reads and/or bases. Our results show that across three organisms and three sequencing platforms, trimming improved the mean quality scores of trimmed sequences. Using trimmed sequences for de novo and reference-based assembly improved assembly quality as well as assembler performance. In general, ngsShoRT outperformed comparable trimming tools in terms of trimming speed and improvement of de novo and reference-based assembly as measured by assembly contiguity and correctness. Conclusions Trimming of short read sequences can improve the quality of de novo and reference-based assembly and assembler performance. The parallel processing capability of ngsShoRT reduces trimming time and improves the memory efficiency when dealing with large datasets. We recommend combining sequencing artifacts removal, and quality score based read filtering and base trimming as the most consistent method for improving sequence quality and downstream assemblies. ngsShoRT source code, user guide and tutorial are available at http://research.bioinformatics.udel.edu/genomics/ngsShoRT/. ngsShoRT can be incorporated as a pre-processing step in genome and transcriptome assembly projects.
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Affiliation(s)
- Chuming Chen
- Center for Bioinformatics and Computational Biology, University of Delaware, Newark, DE USA
| | - Sari S Khaleel
- Geisel School of Medicine, Dartmouth College, Hanover, NH USA
| | - Hongzhan Huang
- Center for Bioinformatics and Computational Biology, University of Delaware, Newark, DE USA
| | - Cathy H Wu
- Center for Bioinformatics and Computational Biology, University of Delaware, Newark, DE USA
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614
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Characterization of limes (Citrus aurantifolia) grown in Bhutan and Indonesia using high-throughput sequencing. Sci Rep 2014; 4:4853. [PMID: 24781859 PMCID: PMC5381282 DOI: 10.1038/srep04853] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2013] [Accepted: 04/14/2014] [Indexed: 11/15/2022] Open
Abstract
Lime [Citrus aurantifolia (Cristm.) Swingle] is a Citrus species that is a popular ingredient in many cuisines. Some citrus plants are known to originate in the area ranging from northeastern India to southwestern China. In the current study, we characterized and compared limes grown in Bhutan (n = 5 accessions) and Indonesia (n = 3 accessions). The limes were separated into two groups based on their morphology. Restriction site-associated DNA sequencing (RAD-seq) separated the eight accessions into two clusters. One cluster contained four accessions from Bhutan, whereas the other cluster contained one accession from Bhutan and the three accessions from Indonesia. This genetic classification supported the morphological classification of limes. The analysis suggests that the properties associated with asexual reproduction, and somatic homologous recombination, have contributed to the genetic diversification of limes.
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615
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Mach N, Berri M, Esquerré D, Chevaleyre C, Lemonnier G, Billon Y, Lepage P, Oswald IP, Doré J, Rogel-Gaillard C, Estellé J. Extensive expression differences along porcine small intestine evidenced by transcriptome sequencing. PLoS One 2014; 9:e88515. [PMID: 24533095 PMCID: PMC3922923 DOI: 10.1371/journal.pone.0088515] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2013] [Accepted: 01/07/2014] [Indexed: 11/22/2022] Open
Abstract
The aim of this study was to analyse gene expression along the small intestine (duodenum, jejunum, ileum) and in the ileal Peyer's patches in four young pigs with no clinical signs of disease by transcriptome sequencing. Multidimensional scaling evidenced that samples clustered by tissue type rather than by individual, thus prefiguring a relevant scenario to draw tissue-specific gene expression profiles. Accordingly, 1,349 genes were found differentially expressed between duodenum and jejunum, and up to 3,455 genes between duodenum and ileum. Additionally, a considerable number of differentially expressed genes were found by comparing duodenum (7,027 genes), jejunum (6,122 genes), and ileum (6,991 genes) with ileal Peyer's patches tissue. Functional analyses revealed that most of the significant differentially expressed genes along small intestinal tissues were involved in the regulation of general biological processes such as cell development, signalling, growth and proliferation, death and survival or cell function and maintenance. These results suggest that the intrinsic large turnover of intestinal tissues would have local specificities at duodenum, ileum and jejunum. In addition, in concordance with their biological function, enteric innate immune pathways were overrepresented in ileal Peyer's patches. The reported data provide an expression map of the cell pathway variation in the different small intestinal tissues. Furthermore, expression levels measured in healthy individuals could help to understand changes in gene expression that occur in dysbiosis or pathological states.
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Affiliation(s)
- Núria Mach
- UMR1313 Génétique Animale et Biologie Intégrative, INRA, Jouy-en-Josas, France
- UMR1313 Génétique Animale et Biologie Intégrative, AgroParisTech, Jouy-en-Josas, France
- DSV/iRCM/SREIT/LREG, CEA, Jouy-en-Josas, France
- UMR1319 MICALIS, INRA, Jouy-en-Josas, France
- UMR1319 MICALIS, AgroParisTech, Jouy-en-Josas, France
- * E-mail:
| | - Mustapha Berri
- UMR1282 ISP, INRA, Nouzilly, France
- UMR1282 ISP, Université de Tours, Tours, France
| | - Diane Esquerré
- UMR444 LGC-Plateforme GET, INRA, Castanet-Tolosan, France
| | - Claire Chevaleyre
- UMR1282 ISP, INRA, Nouzilly, France
- UMR1282 ISP, Université de Tours, Tours, France
| | - Gaëtan Lemonnier
- UMR1313 Génétique Animale et Biologie Intégrative, INRA, Jouy-en-Josas, France
- UMR1313 Génétique Animale et Biologie Intégrative, AgroParisTech, Jouy-en-Josas, France
- DSV/iRCM/SREIT/LREG, CEA, Jouy-en-Josas, France
| | | | - Patricia Lepage
- UMR1319 MICALIS, INRA, Jouy-en-Josas, France
- UMR1319 MICALIS, AgroParisTech, Jouy-en-Josas, France
| | - Isabelle P. Oswald
- UMR1331 TOXALIM, INRA, Toulouse, France
- UMR1331 TOXALIM-INP, Université de Toulouse III, Toulouse, France
| | - Joël Doré
- UMR1319 MICALIS, INRA, Jouy-en-Josas, France
- UMR1319 MICALIS, AgroParisTech, Jouy-en-Josas, France
| | - Claire Rogel-Gaillard
- UMR1313 Génétique Animale et Biologie Intégrative, INRA, Jouy-en-Josas, France
- UMR1313 Génétique Animale et Biologie Intégrative, AgroParisTech, Jouy-en-Josas, France
- DSV/iRCM/SREIT/LREG, CEA, Jouy-en-Josas, France
| | - Jordi Estellé
- UMR1313 Génétique Animale et Biologie Intégrative, INRA, Jouy-en-Josas, France
- UMR1313 Génétique Animale et Biologie Intégrative, AgroParisTech, Jouy-en-Josas, France
- DSV/iRCM/SREIT/LREG, CEA, Jouy-en-Josas, France
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616
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Analysis of porcine adipose tissue transcriptome reveals differences in de novo fatty acid synthesis in pigs with divergent muscle fatty acid composition. BMC Genomics 2013; 14:843. [PMID: 24289474 PMCID: PMC3879068 DOI: 10.1186/1471-2164-14-843] [Citation(s) in RCA: 68] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2013] [Accepted: 11/25/2013] [Indexed: 01/18/2023] Open
Abstract
Background In pigs, adipose tissue is one of the principal organs involved in the regulation of lipid metabolism. It is particularly involved in the overall fatty acid synthesis with consequences in other lipid-target organs such as muscles and the liver. With this in mind, we have used massive, parallel high-throughput sequencing technologies to characterize the porcine adipose tissue transcriptome architecture in six Iberian x Landrace crossbred pigs showing extreme phenotypes for intramuscular fatty acid composition (three per group). Results High-throughput RNA sequencing was used to generate a whole characterization of adipose tissue (backfat) transcriptome. A total of 4,130 putative unannotated protein-coding sequences were identified in the 20% of reads which mapped in intergenic regions. Furthermore, 36% of the unmapped reads were represented by interspersed repeats, SINEs being the most abundant elements. Differential expression analyses identified 396 candidate genes among divergent animals for intramuscular fatty acid composition. Sixty-two percent of these genes (247/396) presented higher expression in the group of pigs with higher content of intramuscular SFA and MUFA, while the remaining 149 showed higher expression in the group with higher content of PUFA. Pathway analysis related these genes to biological functions and canonical pathways controlling lipid and fatty acid metabolisms. In concordance with the phenotypic classification of animals, the major metabolic pathway differentially modulated between groups was de novo lipogenesis, the group with more PUFA being the one that showed lower expression of lipogenic genes. Conclusions These results will help in the identification of genetic variants at loci that affect fatty acid composition traits. The implications of these results range from the improvement of porcine meat quality traits to the application of the pig as an animal model of human metabolic diseases.
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617
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Beneventi MA, da Silva OB, de Sá MEL, Firmino AAP, de Amorim RMS, Albuquerque ÉVS, da Silva MCM, da Silva JP, Campos MDA, Lopes MJC, Togawa RC, Pappas GJ, Grossi–de–Sa MF. Transcription profile of soybean-root-knot nematode interaction reveals a key role of phythormones in the resistance reaction. BMC Genomics 2013; 14:322. [PMID: 23663436 PMCID: PMC3701510 DOI: 10.1186/1471-2164-14-322] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2013] [Accepted: 05/01/2013] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Root-knot nematodes (RKN- Meloidogyne genus) present extensive challenges to soybean crop. The soybean line (PI 595099) is known to be resistant against specific strains and races of nematode species, thus its differential gene expression analysis can lead to a comprehensive gene expression profiling in the incompatible soybean-RKN interaction. Even though many disease resistance genes have been studied, little has been reported about phytohormone crosstalk on modulation of ROS signaling during soybean-RKN interaction. RESULTS Using 454 technology to explore the common aspects of resistance reaction during both parasitism and resistance phases it was verified that hormone, carbohydrate metabolism and stress related genes were consistently expressed at high levels in infected roots as compared to mock control. Most noteworthy genes include those encoding glycosyltransferases, peroxidases, auxin-responsive proteins and gibberellin-regulated genes. Our data analysis suggests the key role of glycosyltransferases, auxins and components of gibberellin signal transduction, biosynthesis and deactivation pathways in the resistance reaction and their participation in jasmonate signaling and redox homeostasis in mediating aspects of plant growth and responses to biotic stress. CONCLUSIONS Based on this study we suggest a reasonable model regarding to the complex mechanisms of crosstalk between plant hormones, mainly gibberellins and auxins, which can be crucial to modulate the levels of ROS in the resistance reaction to nematode invasion. The model also includes recent findings concerning to the participation of DELLA-like proteins and ROS signaling controlling plant immune or stress responses. Furthermore, this study provides a dataset of potential candidate genes involved in both nematode parasitism and resistance, which can be tested further for their role in this biological process using functional genomics approaches.
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Affiliation(s)
- Magda Aparecida Beneventi
- Federal University of Rio Grande do Sul, Porto Alegre, RS 91501-970, Brazil
- Embrapa Genetic Resources and Biotechnology, Brasilia, DF 70770-917, Brazil
| | | | - Maria Eugênia Lisei de Sá
- Embrapa Genetic Resources and Biotechnology, Brasilia, DF 70770-917, Brazil
- Agricultural Research Company of Minas Gerais State, Uberaba, MG 38001-970, Brazil
| | - Alexandre Augusto Pereira Firmino
- Federal University of Rio Grande do Sul, Porto Alegre, RS 91501-970, Brazil
- Embrapa Genetic Resources and Biotechnology, Brasilia, DF 70770-917, Brazil
| | | | | | | | | | | | | | | | | | - Maria Fatima Grossi–de–Sa
- Embrapa Genetic Resources and Biotechnology, Brasilia, DF 70770-917, Brazil
- Catholic University of Brasília, Brasília, DF 70790-160, Brazil
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Abstract
The evolution of higher cognitive functions in humans is thought to be due, at least in part, to the molecular evolution of gene expression patterns specific to the human brain. In this article, we explore recent and past findings using comparative genomics in human and non-human primate brain to identify these novel human patterns. We suggest additional directions and lines of experimentation that should be taken to improve our understanding of these changes on the human lineage. Finally, we attempt to put into context these genomic changes with biological phenotypes and diseases in humans.
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Affiliation(s)
- Guang-Zhong Wang
- Department of Neuroscience; UT Southwestern Medical Center; Dallas, TX USA
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Lindner MS, Kollock M, Zickmann F, Renard BY. Analyzing genome coverage profiles with applications to quality control in metagenomics. Bioinformatics 2013; 29:1260-7. [DOI: 10.1093/bioinformatics/btt147] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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