101
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Lundin S, Jemt A, Terje-Hegge F, Foam N, Pettersson E, Käller M, Wirta V, Lexow P, Lundeberg J. Endonuclease specificity and sequence dependence of type IIS restriction enzymes. PLoS One 2015; 10:e0117059. [PMID: 25629514 PMCID: PMC4309577 DOI: 10.1371/journal.pone.0117059] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2014] [Accepted: 12/17/2014] [Indexed: 11/23/2022] Open
Abstract
Restriction enzymes that recognize specific sequences but cleave unknown sequence outside the recognition site are extensively utilized tools in molecular biology. Despite this, systematic functional categorization of cleavage performance has largely been lacking. We established a simple and automatable model system to assay cleavage distance variation (termed slippage) and the sequence dependence thereof. We coupled this to massively parallel sequencing in order to provide sensitive and accurate measurement. With this system 14 enzymes were assayed (AcuI, BbvI, BpmI, BpuEI, BseRI, BsgI, Eco57I, Eco57MI, EcoP15I, FauI, FokI, GsuI, MmeI and SmuI). We report significant variation of slippage ranging from 1–54%, variations in sequence context dependence, as well as variation between isoschizomers. We believe this largely overlooked property of enzymes with shifted cleavage would benefit from further large scale classification and engineering efforts seeking to improve performance. The gained insights of in-vitro performance may also aid the in-vivo understanding of these enzymes.
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Affiliation(s)
- Sverker Lundin
- Science for Life Laboratory, KTH, Gene Technology, Solna, 171 65, Sweden
| | - Anders Jemt
- Science for Life Laboratory, KTH, Gene Technology, Solna, 171 65, Sweden
| | | | | | | | | | | | | | - Joakim Lundeberg
- Science for Life Laboratory, KTH, Gene Technology, Solna, 171 65, Sweden
- * E-mail:
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102
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Wang X, Zhang X, Liu L, Xiang M, Wang W, Sun X, Che Y, Guo L, Liu G, Guo L, Wang C, Yin WB, Stadler M, Zhang X, Liu X. Genomic and transcriptomic analysis of the endophytic fungus Pestalotiopsis fici reveals its lifestyle and high potential for synthesis of natural products. BMC Genomics 2015; 16:28. [PMID: 25623211 PMCID: PMC4320822 DOI: 10.1186/s12864-014-1190-9] [Citation(s) in RCA: 84] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2014] [Accepted: 12/22/2014] [Indexed: 11/17/2022] Open
Abstract
Background In recent years, the genus Pestalotiopsis is receiving increasing attention, not only because of its economic impact as a plant pathogen but also as a commonly isolated endophyte which is an important source of bioactive natural products. Pestalotiopsis fici Steyaert W106-1/CGMCC3.15140 as an endophyte of tea produces numerous novel secondary metabolites, including chloropupukeananin, a derivative of chlorinated pupukeanane that is first discovered in fungi. Some of them might be important as the drug leads for future pharmaceutics. Results Here, we report the genome sequence of the endophytic fungus of tea Pestalotiopsis fici W106-1/CGMCC3.15140. The abundant carbohydrate-active enzymes especially significantly expanding pectinases allow the fungus to utilize the limited intercellular nutrients within the host plants, suggesting adaptation of the fungus to endophytic lifestyle. The P. fici genome encodes a rich set of secondary metabolite synthesis genes, including 27 polyketide synthases (PKSs), 12 non-ribosomal peptide synthases (NRPSs), five dimethylallyl tryptophan synthases, four putative PKS-like enzymes, 15 putative NRPS-like enzymes, 15 terpenoid synthases, seven terpenoid cyclases, seven fatty-acid synthases, and five hybrids of PKS-NRPS. The majority of these core enzymes distributed into 74 secondary metabolite clusters. The putative Diels-Alderase genes have undergone expansion. Conclusion The significant expansion of pectinase encoding genes provides essential insight in the life strategy of endophytes, and richness of gene clusters for secondary metabolites reveals high potential of natural products of endophytic fungi. Electronic supplementary material The online version of this article (doi:10.1186/s12864-014-1190-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Xiuna Wang
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China. .,Department of Plant Pathology, China Agricultural University, Beijing, China.
| | - Xiaoling Zhang
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.
| | - Ling Liu
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.
| | - Meichun Xiang
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.
| | - Wenzhao Wang
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.
| | - Xiang Sun
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.
| | - Yongsheng Che
- Department of Natural Products Chemistry, Beijing Institute of Pharmacology & Toxicology, Beijing, China.
| | - Liangdong Guo
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.
| | - Gang Liu
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.
| | - Liyun Guo
- Department of Plant Pathology, China Agricultural University, Beijing, China.
| | - Chengshu Wang
- Key Laboratory of Insect Development and Evolutionary Biology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China.
| | - Wen-Bing Yin
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.
| | - Marc Stadler
- Department Microbial Drugs, Helmholtz Centre for Infection Research, Braunschweig, Germany.
| | - Xinyu Zhang
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.
| | - Xingzhong Liu
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.
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103
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Sequencing of first-strand cDNA library reveals full-length transcriptomes. Nat Commun 2015; 6:6002. [PMID: 25607527 DOI: 10.1038/ncomms7002] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2014] [Accepted: 12/02/2014] [Indexed: 11/09/2022] Open
Abstract
Massively parallel strand-specific sequencing of RNA (ssRNA-seq) has emerged as a powerful tool for profiling complex transcriptomes. However, many current methods for ssRNA-seq suffer from the underrepresentation of both the 5' and 3' ends of RNAs, which can be attributed to second-strand cDNA synthesis. The 5' and 3' ends of RNA harbour crucial information for gene regulation; namely, transcription start sites (TSSs) and polyadenylation sites. Here we report a novel ssRNA-seq method that does not involve second-strand cDNA synthesis, as we Directly Ligate sequencing Adaptors to the First-strand cDNA (DLAF). This novel method with fewer enzymatic reactions results in a higher quality of the libraries than the conventional method. Sequencing of DLAF libraries followed by a novel analysis pipeline enables the profiling of both 5' ends and polyadenylation sites at near-base resolution. Therefore, DLAF offers the first genomics tool to obtain the 'full-length' transcriptome with a single library.
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104
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Chen Q, Ritt M, Sivaramakrishnan S, Sun Y, Fan X. Optofluidic lasers with a single molecular layer of gain. LAB ON A CHIP 2014; 14:4590-5. [PMID: 25312306 PMCID: PMC4229433 DOI: 10.1039/c4lc00872c] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
We achieve optofluidic lasers with a single molecular layer of gain, in which green fluorescent protein, dye-labeled bovine serum albumin, and dye-labeled DNA, are used as the gain medium and attached to the surface of a ring resonator via surface immobilization biochemical methods. It is estimated that the surface density of the gain molecules is on the order of 10(12) cm(-2), sufficient for lasing under pulsed optical excitation. It is further shown that the optofluidic laser can be tuned by energy transfer mechanisms through biomolecular interactions. This work not only opens a door to novel photonic devices that can be controlled at the level of a single molecular layer but also provides a promising sensing platform to analyze biochemical processes at the solid-liquid interface.
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Affiliation(s)
- Qiushu Chen
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, MI 48109, USA.
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105
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Carroll CJ, Brilhante V, Suomalainen A. Next-generation sequencing for mitochondrial disorders. Br J Pharmacol 2014; 171:1837-53. [PMID: 24138576 DOI: 10.1111/bph.12469] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2013] [Revised: 10/03/2013] [Accepted: 10/13/2013] [Indexed: 12/30/2022] Open
Abstract
A great deal of our understanding of mitochondrial function has come from studies of inherited mitochondrial diseases, but still majority of the patients lack molecular diagnosis. Furthermore, effective treatments for mitochondrial disorders do not exist. Development of therapies has been complicated by the fact that the diseases are extremely heterogeneous, and collecting large enough cohorts of similarly affected individuals to assess new therapies properly has been difficult. Next-generation sequencing technologies have in the last few years been shown to be an effective method for the genetic diagnosis of inherited mitochondrial diseases. Here we review the strategies and findings from studies applying next-generation sequencing methods for the genetic diagnosis of mitochondrial disorders. Detailed knowledge of molecular causes also enables collection of homogenous cohorts of patients for therapy trials, and therefore boosts development of intervention.
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Affiliation(s)
- C J Carroll
- Research Programs Unit, Molecular Neurology, Biomedicum-Helsinki, University of Helsinki, Helsinki, Finland
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106
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Luo H, Li J, Chia BKH, Robson P, Nagarajan N. The importance of study design for detecting differentially abundant features in high-throughput experiments. Genome Biol 2014; 15:527. [PMID: 25517037 PMCID: PMC4253014 DOI: 10.1186/s13059-014-0527-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2014] [Accepted: 11/03/2014] [Indexed: 12/20/2022] Open
Abstract
High-throughput assays, such as RNA-seq, to detect differential abundance are widely used. Variable performance across statistical tests, normalizations, and conditions leads to resource wastage and reduced sensitivity. EDDA represents a first, general design tool for RNA-seq, Nanostring, and metagenomic analysis, that rationally selects tests, predicts performance, and plans experiments to minimize resource wastage. Case studies highlight EDDA’s ability to model single-cell RNA-seq, suggesting ways to reduce sequencing costs up to five-fold and improving metagenomic biomarker detection through improved test selection. EDDA’s novel mode-based normalization for detecting differential abundance improves robustness by 10% to 20% and precision by up to 140%.
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107
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Ma T, Ma H, Zhao H, Qi H, Zhao J. Identification, characterization, and transcription analysis of xylogen-like arabinogalactan proteins in rice (Oryza sativa L.). BMC PLANT BIOLOGY 2014; 14:299. [PMID: 25407280 PMCID: PMC4239379 DOI: 10.1186/s12870-014-0299-y] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/09/2014] [Accepted: 09/24/2014] [Indexed: 05/08/2023]
Abstract
BACKGROUND Xylogen, a chimeric arabinogalactan protein containing a non-specific lipid transfer protein domain, can promote xylem cell differentiation. No comprehensive study has been carried out on the XYLP gene family in rice. As a first step in research on this gene family and as a useful strategy in general, a genome-wide analysis of the OsXYLP gene family is thus needed. RESULTS In this study, we identified 21 XYLP genes from the rice genome and comprehensively analyzed their protein structures, phylogenetic relationships, chromosomal locations, and gene duplication status. Our results indicate that gene duplication has played major roles in the expansion of the OsXYLP gene family. We used expressed sequence tag, microarray, massively parallel signature sequencing, and quantitative real-time PCR data to analyze OsXYLP gene expression during various developmental stages and under abiotic stress conditions. We found that many OsXYLP genes are abundantly expressed in vascular tissues and seeds, with some genes regulated under hormonal or abiotic stresses. In addition, we identified knockout mutants of OsXYLP7 and OsXYLP16 and discovered that the mutant xylp7 has a defect in stem height. CONCLUSIONS We analyzed expression profiles of 21 XYLP genes and characterized the structures and evolutionary relationships of their proteins. Our results demonstrate that the rice XYLP gene family may play roles in plant vascular system development and hormone signaling. Among the 21 detected OsXYLPs, 19 are newly identified genes encoding arabinogalactan proteins. Our results provide comprehensive insights that will assist future research on the biological functions of the rice XYLP gene family.
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Affiliation(s)
- Tengfei Ma
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, 430072 China
| | - Haoli Ma
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, 430072 China
| | - Heming Zhao
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, 430072 China
| | - Huandong Qi
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, 430072 China
| | - Jie Zhao
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, 430072 China
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108
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Christensen SA, Nemchenko A, Park YS, Borrego E, Huang PC, Schmelz EA, Kunze S, Feussner I, Yalpani N, Meeley R, Kolomiets MV. The novel monocot-specific 9-lipoxygenase ZmLOX12 is required to mount an effective jasmonate-mediated defense against Fusarium verticillioides in maize. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2014; 27:1263-76. [PMID: 25122482 DOI: 10.1094/mpmi-06-13-0184-r] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Fusarium verticillioides is a major limiting factor for maize production due to ear and stalk rot and the contamination of seed with the carcinogenic mycotoxin fumonisin. While lipoxygenase (LOX)-derived oxylipins have been implicated in defense against diverse pathogens, their function in maize resistance against F. verticillioides is poorly understood. Here, we functionally characterized a novel maize 9-LOX gene, ZmLOX12. This gene is distantly related to known dicot LOX genes, with closest homologs found exclusively in other monocot species. ZmLOX12 is predominantly expressed in mesocotyls in which it is strongly induced in response to F. verticillioides infection. The Mutator transposon-insertional lox12-1 mutant is more susceptible to F. verticillioides colonization of mesocotyls, stalks, and kernels. The infected mutant kernels accumulate a significantly greater amount of the mycotoxin fumonisin. Reduced resistance to the pathogen is accompanied by diminished levels of the jasmonic acid (JA) precursor 12-oxo phytodienoic acid, JA-isoleucine, and expression of jasmonate-biosynthetic genes. Supporting the strong defense role of jasmonates, the JA-deficient opr7 opr8 double mutant displayed complete lack of immunity to F. verticillioides. Unexpectedly, the more susceptible lox12 mutant accumulated higher levels of kauralexins, suggesting that F. verticillioides is tolerant to this group of antimicrobial phytoalexins. This study demonstrates that this unique monocot-specific 9-LOX plays a key role in defense against F. verticillioides in diverse maize tissues and provides genetic evidence that JA is the major defense hormone against this pathogen.
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109
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Agarwal P, Parida SK, Mahto A, Das S, Mathew IE, Malik N, Tyagi AK. Expanding frontiers in plant transcriptomics in aid of functional genomics and molecular breeding. Biotechnol J 2014; 9:1480-92. [PMID: 25349922 DOI: 10.1002/biot.201400063] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2014] [Revised: 09/02/2014] [Accepted: 10/01/2014] [Indexed: 12/30/2022]
Abstract
The transcript pool of a plant part, under any given condition, is a collection of mRNAs that will pave the way for a biochemical reaction of the plant to stimuli. Over the past decades, transcriptome study has advanced from Northern blotting to RNA sequencing (RNA-seq), through other techniques, of which real-time quantitative polymerase chain reaction (PCR) and microarray are the most significant ones. The questions being addressed by such studies have also matured from a solitary process to expression atlas and marker-assisted genetic enhancement. Not only genes and their networks involved in various developmental processes of plant parts have been elucidated, but also stress tolerant genes have been highlighted. The transcriptome of a plant with altered expression of a target gene has given information about the downstream genes. Marker information has been used for breeding improved varieties. Fortunately, the data generated by transcriptome analysis has been made freely available for ample utilization and comparison. The review discusses this wide variety of transcriptome data being generated in plants, which includes developmental stages, abiotic and biotic stress, effect of altered gene expression, as well as comparative transcriptomics, with a special emphasis on microarray and RNA-seq. Such data can be used to determine the regulatory gene networks, which can subsequently be utilized for generating improved plant varieties.
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Affiliation(s)
- Pinky Agarwal
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, India
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110
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Nesterov-Mueller A, Maerkle F, Hahn L, Foertsch T, Schillo S, Bykovskaya V, Sedlmayr M, Weber LK, Ridder B, Soehindrijo M, Muenster B, Striffler J, Bischoff FR, Breitling F, Loeffler FF. Particle-Based Microarrays of Oligonucleotides and Oligopeptides. MICROARRAYS 2014; 3:245-62. [PMID: 27600347 PMCID: PMC4979057 DOI: 10.3390/microarrays3040245] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/04/2014] [Revised: 10/15/2014] [Accepted: 10/16/2014] [Indexed: 01/02/2023]
Abstract
In this review, we describe different methods of microarray fabrication based on the use of micro-particles/-beads and point out future tendencies in the development of particle-based arrays. First, we consider oligonucleotide bead arrays, where each bead is a carrier of one specific sequence of oligonucleotides. This bead-based array approach, appearing in the late 1990s, enabled high-throughput oligonucleotide analysis and had a large impact on genome research. Furthermore, we consider particle-based peptide array fabrication using combinatorial chemistry. In this approach, particles can directly participate in both the synthesis and the transfer of synthesized combinatorial molecules to a substrate. Subsequently, we describe in more detail the synthesis of peptide arrays with amino acid polymer particles, which imbed the amino acids inside their polymer matrix. By heating these particles, the polymer matrix is transformed into a highly viscous gel, and thereby, imbedded monomers are allowed to participate in the coupling reaction. Finally, we focus on combinatorial laser fusing of particles for the synthesis of high-density peptide arrays. This method combines the advantages of particles and combinatorial lithographic approaches.
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Affiliation(s)
- Alexander Nesterov-Mueller
- Karlsruhe Institute of Technology, Hermann-von-Helmholtz-Platz 1, 76344 Eggenstein-Leopoldshafen, Germany.
| | - Frieder Maerkle
- Karlsruhe Institute of Technology, Hermann-von-Helmholtz-Platz 1, 76344 Eggenstein-Leopoldshafen, Germany.
| | - Lothar Hahn
- Karlsruhe Institute of Technology, Hermann-von-Helmholtz-Platz 1, 76344 Eggenstein-Leopoldshafen, Germany.
| | - Tobias Foertsch
- Karlsruhe Institute of Technology, Hermann-von-Helmholtz-Platz 1, 76344 Eggenstein-Leopoldshafen, Germany.
| | - Sebastian Schillo
- Karlsruhe Institute of Technology, Hermann-von-Helmholtz-Platz 1, 76344 Eggenstein-Leopoldshafen, Germany.
| | - Valentina Bykovskaya
- Karlsruhe Institute of Technology, Hermann-von-Helmholtz-Platz 1, 76344 Eggenstein-Leopoldshafen, Germany.
| | - Martyna Sedlmayr
- Karlsruhe Institute of Technology, Hermann-von-Helmholtz-Platz 1, 76344 Eggenstein-Leopoldshafen, Germany.
| | - Laura K Weber
- Karlsruhe Institute of Technology, Hermann-von-Helmholtz-Platz 1, 76344 Eggenstein-Leopoldshafen, Germany.
| | - Barbara Ridder
- Karlsruhe Institute of Technology, Hermann-von-Helmholtz-Platz 1, 76344 Eggenstein-Leopoldshafen, Germany.
| | - Miriam Soehindrijo
- Karlsruhe Institute of Technology, Hermann-von-Helmholtz-Platz 1, 76344 Eggenstein-Leopoldshafen, Germany.
| | - Bastian Muenster
- Karlsruhe Institute of Technology, Hermann-von-Helmholtz-Platz 1, 76344 Eggenstein-Leopoldshafen, Germany.
| | - Jakob Striffler
- Karlsruhe Institute of Technology, Hermann-von-Helmholtz-Platz 1, 76344 Eggenstein-Leopoldshafen, Germany.
| | - F Ralf Bischoff
- German Cancer Research Center, Im Neuenheimer Feld 280, 69120 Heidelberg, Germany.
| | - Frank Breitling
- Karlsruhe Institute of Technology, Hermann-von-Helmholtz-Platz 1, 76344 Eggenstein-Leopoldshafen, Germany.
| | - Felix F Loeffler
- Karlsruhe Institute of Technology, Hermann-von-Helmholtz-Platz 1, 76344 Eggenstein-Leopoldshafen, Germany.
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111
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Renaud G, LaFave MC, Liang J, Wolfsberg TG, Burgess SM. trieFinder: an efficient program for annotating Digital Gene Expression (DGE) tags. BMC Bioinformatics 2014; 15:329. [PMID: 25311246 PMCID: PMC4287429 DOI: 10.1186/1471-2105-15-329] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2014] [Accepted: 09/05/2014] [Indexed: 01/31/2023] Open
Abstract
Background Quantification of a transcriptional profile is a useful way to evaluate the activity of a cell at a given point in time. Although RNA-Seq has revolutionized transcriptional profiling, the costs of RNA-Seq are still significantly higher than microarrays, and often the depth of data delivered from RNA-Seq is in excess of what is needed for simple transcript quantification. Digital Gene Expression (DGE) is a cost-effective, sequence-based approach for simple transcript quantification: by sequencing one read per molecule of RNA, this technique can be used to efficiently count transcripts while obviating the need for transcript-length normalization and reducing the total numbers of reads necessary for accurate quantification. Here, we present trieFinder, a program specifically designed to rapidly map, parse, and annotate DGE tags of various lengths against cDNA and/or genomic sequence databases. Results The trieFinder algorithm maps DGE tags in a two-step process. First, it scans FASTA files of RefSeq, UniGene, and genomic DNA sequences to create a database of all tags that can be derived from a predefined restriction site. Next, it compares the experimental DGE tags to this tag database, taking advantage of the fact that the tags are stored as a prefix tree, or “trie”, which allows for linear-time searches for exact matches. DGE tags with mismatches are analyzed by recursive calls in the data structure. We find that, in terms of alignment speed, the mapping functionality of trieFinder compares favorably with Bowtie. Conclusions trieFinder can quickly provide the user an annotation of the DGE tags from three sources simultaneously, simplifying transcript quantification and novel transcript detection, delivering the data in a simple parsed format, obviating the need to post-process the alignment results. trieFinder is available at http://research.nhgri.nih.gov/software/trieFinder/.
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Affiliation(s)
| | | | | | | | - Shawn M Burgess
- Translational and Functional Genomics Branch, Division of Intramural Research, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892-8004, USA.
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113
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El-Mahdy AFM, Ejupi V, Shibata T, Kabashima T, Lu J, Kai M. Facile preparation of streptavidin-coated sephadex beads and their application to chemiluminescence detection of a target DNA. Mikrochim Acta 2014. [DOI: 10.1007/s00604-014-1348-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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114
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Microfluidic bead-based assay for microRNAs using quantum dots as labels and enzymatic amplification. Mikrochim Acta 2014. [DOI: 10.1007/s00604-014-1372-9] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
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115
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Meijueiro ML, Santoyo F, Ramirez L, Pisabarro AG. Transcriptome characteristics of filamentous fungi deduced using high-throughput analytical technologies. Brief Funct Genomics 2014; 13:440-50. [DOI: 10.1093/bfgp/elu033] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
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116
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Egalite N, Groisman IJ, Godard B. Personalized medicine in oncology: ethical implications for the delivery of healthcare. Per Med 2014; 11:659-668. [PMID: 29764052 DOI: 10.2217/pme.14.53] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
While personalized medicine brings benefits for the treatment of cancer, there are still key ethical issues at stake in developing personalized medicine in oncology. We propose an ethical analysis of personalized medicine in oncology that highlights the particularities of cancer care, critically assesses the scientific advances behind personalized medicine in oncology and emphasizes fairness in resource allocation in the delivery of personalized healthcare. This allows for a broader understanding of the real impacts on both recipients and the healthcare system.
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Affiliation(s)
- Nathalie Egalite
- Omics-Ethics Research Group, Department of Preventive & Social Medicine, Public Health School, University of Montreal, C.P. 6128, succ. Centre-ville, Montreal, QC, H3C 3J7, Canada
| | - Iris Jaitovich Groisman
- Omics-Ethics Research Group, Department of Preventive & Social Medicine, Public Health School, University of Montreal, C.P. 6128, succ. Centre-ville, Montreal, QC, H3C 3J7, Canada
| | - Beatrice Godard
- Omics-Ethics Research Group, Department of Preventive & Social Medicine, Public Health School, University of Montreal, C.P. 6128, succ. Centre-ville, Montreal, QC, H3C 3J7, Canada
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117
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Bai Y, Zhang Z, Jin L, Kang H, Zhu Y, Zhang L, Li X, Ma F, Zhao L, Shi B, Li J, McManus DP, Zhang W, Wang S. Genome-wide sequencing of small RNAs reveals a tissue-specific loss of conserved microRNA families in Echinococcus granulosus. BMC Genomics 2014; 15:736. [PMID: 25168356 PMCID: PMC4156656 DOI: 10.1186/1471-2164-15-736] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2014] [Accepted: 08/20/2014] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND MicroRNAs (miRNAs) are important post-transcriptional regulators which control growth and development in eukaryotes. The cestode Echinococcus granulosus has a complex life-cycle involving different development stages but the mechanisms underpinning this development, including the involvement of miRNAs, remain unknown. RESULTS Using Illumina next generation sequencing technology, we sequenced at the genome-wide level three small RNA populations from the adult, protoscolex and cyst membrane of E. granulosus. A total of 94 pre-miRNA candidates (coding 91 mature miRNAs and 39 miRNA stars) were in silico predicted. Through comparison of expression profiles, we found 42 mature miRNAs and 23 miRNA stars expressed with different patterns in the three life stages examined. Furthermore, considering both the previously reported and newly predicted miRNAs, 25 conserved miRNAs families were identified in the E. granulosus genome. Comparing the presence or absence of these miRNA families with the free-living Schmidtea mediterranea, we found 13 conserved miRNAs are lost in E. granulosus, most of which are tissue-specific and involved in the development of ciliated cells, the gut and sensory organs. Finally, GO enrichment analysis of the differentially expressed miRNAs and their potential targets indicated that they may be involved in bi-directional development, nutrient metabolism and nervous system development in E. granulosus. CONCLUSIONS This study has, for the first time, provided a comprehensive description of the different expression patterns of miRNAs in three distinct life cycle stages of E. granulosus. The analysis supports earlier suggestions that the loss of miRNAs in the Platyhelminths might be related to morphological simplification. These results may help in the exploration of the mechanism of interaction between this parasitic worm and its definitive and intermediate hosts, providing information that can be used to develop new interventions and therapeutics for the control of cystic echinococcosis.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | - Wenbao Zhang
- Shanghai-MOST Key Laboratory of Health and Disease Genomics, Chinese National Human Genome Center at Shanghai, 250 Bibo Road, Shanghai 201203, China.
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118
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Mahdi JG. Biosynthesis and metabolism of β-d-salicin: A novel molecule that exerts biological function in humans and plants. ACTA ACUST UNITED AC 2014. [PMID: 28626665 PMCID: PMC5466123 DOI: 10.1016/j.btre.2014.08.005] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
β-d-Salicin 1 (Mahdi et al. [8]) is an interesting medicinal phytochemical that exhibits cross functions in plants and humans immunologically. This molecule 1 (Mahdi et al. [8]) has attracted the attention of scientists in various interdisciplinary fields, including chemistry, pharmacology and medicine. The biological cross functions of β-d-salicin 1 (Mahdi et al. [8]) serve in plant survival and healing processes via salicylic acid 2 (Pierpont [23]). Thus, this raise a question whether plant biosynthesis and human metabolism crosstalk to induce therapy via molecular recognition. If so, biotechnology and bioinformatics are significant techniques for new strategies in drug development. Thus, understanding the biosynthesis, metabolism and the cross-molecular setting of recognition may encourage further discussion and research on its medicinal and biological activity virtues.
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Affiliation(s)
- Jassem G Mahdi
- College of Medicine, Shagra University, Shaqra 11961, Saudi Arabia
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119
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Yin G, Xu H, Liu J, Gao C, Sun J, Yan Y, Hu Y. Screening and identification of soybean seed-specific genes by using integrated bioinformatics of digital differential display, microarray, and RNA-seq data. Gene 2014; 546:177-86. [PMID: 24929124 DOI: 10.1016/j.gene.2014.06.021] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2013] [Revised: 05/16/2014] [Accepted: 06/10/2014] [Indexed: 01/09/2023]
Abstract
Soybean is one of the most economically important crops in the world. Soybean seeds have abundant protein and lipid content and very high economic value. In this study, a total of 184 seed-specific genes were obtained using online microarray databases, DDD, and RNA-seq data. The reported seed-specific genes in soybean and the 184 seed-specific genes analyzed in this paper were compared. Of the screened genes, 26 were common to both previous reports and the current screening. Meanwhile, 90 of the 184 genes have homologous counterparts in Arabidopsis, among which 24 have seed-specific expression, as indicated by microarray data for Arabidopsis. Furthermore, promoter analysis showed that almost all seed-specific genes contain at least one seed specific-related element. Seed-specific element Skn-1 motif exists in most, if not all, of the seed-specific genes screened. Five genes were randomly selected from 184 soybean seed specific gene pool and their expressions were quantified using quantitative real time polymerase chain reaction (qRT-PCR) to further confirm the specificity of the screened genes. The results indicated that all five genes showed seed-specific expression. Moreover, the identification of genes with seed-specific expression screened in this study provides information valuable to the in-depth study of soybean.
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Affiliation(s)
- Guangjun Yin
- College of Life Sciences, Capital Normal University, Beijing 100048, China.
| | - Hongliang Xu
- Biochemistry, Molecular Biology & Biophysics, University of Minnesota, Minneapolis, MN 55455, USA.
| | - Jingyi Liu
- College of Life Sciences, Capital Normal University, Beijing 100048, China.
| | - Cong Gao
- College of Life Sciences, Capital Normal University, Beijing 100048, China.
| | - Jinyue Sun
- Plant Biotechnology Institute, National Research Council Canada, Saskatoon S7N 0W9, Canada.
| | - Yueming Yan
- College of Life Sciences, Capital Normal University, Beijing 100048, China.
| | - Yingkao Hu
- College of Life Sciences, Capital Normal University, Beijing 100048, China.
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Abstract
Pseudogenes are defined as non-functional relatives of genes whose protein-coding abilities are lost and are no longer expressed within cells. They are an outcome of accumulation of mutations within a gene whose end product is not essential for survival. Proper investigation of the procedure of pseudogenization is relevant for estimating occurrence of duplications in genomes. Frankineae houses an interesting group of microorganisms, carving a niche in the microbial world. This study was undertaken with the objective of determining the abundance of pseudogenes, understanding strength of purifying selection, investigating evidence of pseudogene expression, and analysing their molecular nature, their origin, evolution and deterioration patterns amongst domain families. Investigation revealed the occurrence of 956 core pFAM families sharing common characteristics indicating co-evolution. WD40, Rve_3, DDE_Tnp_IS240 and phage integrase core domains are larger families, having more pseudogenes, signifying a probability of harmful foreign genes being disabled within transposable elements. High selective pressure depicted that gene families rapidly duplicating and evolving undoubtedly facilitated creation of a number of pseudogenes in Frankineae. Codon usage analysis between protein-coding genes and pseudogenes indicated a wide degree of variation with respect to different factors. Moreover, the majority of pseudogenes were under the effect of purifying selection. Frankineae pseudogenes were under stronger selective constraints, indicating that they were functional for a very long time and became pseudogenes abruptly. The origin and deterioration of pseudogenes has been attributed to selection and mutational pressure acting upon sequences for adapting to stressed soil environments.
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Abstract
From the investigation of disease-associated loci in humans, to monitoring the changing genomes of pathogenic viruses and bacteria, sequencing is a powerful and versatile tool. A new generation of sequencing technologies will increase the speed and lower the cost of sequencing, and promises to expand the utility of sequencing in drug discovery and development.:
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Quiñones-Mateu ME, Avila S, Reyes-Teran G, Martinez MA. Deep sequencing: becoming a critical tool in clinical virology. J Clin Virol 2014; 61:9-19. [PMID: 24998424 DOI: 10.1016/j.jcv.2014.06.013] [Citation(s) in RCA: 90] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2014] [Revised: 06/12/2014] [Accepted: 06/14/2014] [Indexed: 02/07/2023]
Abstract
Population (Sanger) sequencing has been the standard method in basic and clinical DNA sequencing for almost 40 years; however, next-generation (deep) sequencing methodologies are now revolutionizing the field of genomics, and clinical virology is no exception. Deep sequencing is highly efficient, producing an enormous amount of information at low cost in a relatively short period of time. High-throughput sequencing techniques have enabled significant contributions to multiples areas in virology, including virus discovery and metagenomics (viromes), molecular epidemiology, pathogenesis, and studies of how viruses to escape the host immune system and antiviral pressures. In addition, new and more affordable deep sequencing-based assays are now being implemented in clinical laboratories. Here, we review the use of the current deep sequencing platforms in virology, focusing on three of the most studied viruses: human immunodeficiency virus (HIV), hepatitis C virus (HCV), and influenza virus.
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Affiliation(s)
- Miguel E Quiñones-Mateu
- University Hospital Translational Laboratory, University Hospitals Case Medical Center, Cleveland, OH, USA; Department of Pathology, Case Western Reserve University, Cleveland, OH, USA
| | - Santiago Avila
- Instituto Nacional de Enfermedades Respiratorias, Mexico City, Mexico; Centro de Investigaciones en Enfermedades Infecciosas, Mexico City, Mexico
| | - Gustavo Reyes-Teran
- Instituto Nacional de Enfermedades Respiratorias, Mexico City, Mexico; Centro de Investigaciones en Enfermedades Infecciosas, Mexico City, Mexico
| | - Miguel A Martinez
- Fundació irsicaixa, Universitat Autònoma de Barcelona, Hospital Universitari Germans Trias i Pujol, Badalona, Spain
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123
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Mishra R, Hegner M. Effect of non-specific species competition from total RNA on the static mode hybridization response of nanomechanical assays of oligonucleotides. NANOTECHNOLOGY 2014; 25:225501. [PMID: 24807191 DOI: 10.1088/0957-4484/25/22/225501] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
We investigate here the nanomechanical response of microcantilever sensors in real-time for detecting a range of ultra-low concentrations of oligonucleotides in a complex background of total cellular RNA extracts from cell lines without labeling or amplification. Cantilever sensor arrays were functionalized with probe single stranded DNA (ssDNA) and reference ssDNA to obtain a differential signal. They were then exposed to complementary target ssDNA strands that were spiked in a fragmented total cellular RNA background in biologically relevant concentrations so as to provide clinically significant analysis. We present a model for prediction of the sensor behavior in competitive backgrounds with parameters that are indicators of the change in nanomechanical response with variation in the target and background concentration. For nanomechanical assays to compete with current technologies it is essential to comprehend such responses with eventual impact on areas like understanding non-coding RNA pharmacokinetics, nucleic acid biomarker assays and miRNA quantification for disease monitoring and diagnosis to mention a few. Additionally, we also achieved a femtomolar sensitivity limit for online oligonucleotide detection in a non-competitive environment with these sensors.
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Affiliation(s)
- Rohit Mishra
- Centre for Research on Adaptive Nanostructures and Nanodevices, School of Physics, Trinity College, Dublin 2, Ireland
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124
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Kumar S, Shah N, Garg V, Bhatia S. Large scale in-silico identification and characterization of simple sequence repeats (SSRs) from de novo assembled transcriptome of Catharanthus roseus (L.) G. Don. PLANT CELL REPORTS 2014; 33:905-918. [PMID: 24482265 DOI: 10.1007/s00299-014-1569-8] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/25/2013] [Revised: 12/17/2013] [Accepted: 01/09/2014] [Indexed: 06/03/2023]
Abstract
Transcriptomic data of C. roseus offering ample sequence resources for providing better insights into gene diversity: large resource of genic SSR markers to accelerate genomic studies and breeding in Catharanthus . Next-generation sequencing is an efficient system for generating high-throughput complete transcripts/genes and developing molecular markers. We present here the transcriptome sequencing of a 26-day-old Catharanthus roseus seedling tissue using Illumina GAIIX platform that resulted in a total of 3.37 Gb of nucleotide sequence data comprising 29,964,104 reads which were de novo assembled into 26,581 unigenes. Based on similarity searches 58 % of the unigenes were annotated of which 13,580 unique transcripts were assigned 5016 gene ontology terms. Further, 7,687 of the unigenes were found to have Cluster of Orthologous Group classifications, and 4,006 were assigned to 289 Kyoto Encyclopedia of Genes and Genome pathways. Also, 5,221 (19.64 %) of transcripts were distributed to 81 known transcription factor (TF) families. In-silico analysis of the transcriptome resulted in identification of 11,004 SSRs in 26.62 % transcripts from which 2,520 SSR markers were designed which exhibited a non-random pattern of distribution. The most abundant was the trinucleotide repeats (AAG/CTT) followed by the dinucleotide repeats (AG/CT). Location specific analysis of SSRs revealed that SSRs were preferentially associated with the 5'-UTRs with a predicted role in regulation of gene expression. A PCR validation of a set of 48 primers revealed 97.9 % successful amplification, and 76.6 % of them showed polymorphism across different Catharanthus species as well as accessions of C. roseus. In summary, this study will provide an insight into understanding the seedling development and resources for novel gene discovery and SSR development for utilization in marker-assisted selective breeding in C. roseus.
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Affiliation(s)
- Santosh Kumar
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, PO Box 10531, New Delhi, 110067, India
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125
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Xiong D, Wang Y, Ma J, Klosterman SJ, Xiao S, Tian C. Deep mRNA sequencing reveals stage-specific transcriptome alterations during microsclerotia development in the smoke tree vascular wilt pathogen, Verticillium dahliae. BMC Genomics 2014; 15:324. [PMID: 24884698 PMCID: PMC4035056 DOI: 10.1186/1471-2164-15-324] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2013] [Accepted: 04/22/2014] [Indexed: 11/16/2022] Open
Abstract
Background Verticillium dahliae is a soil-borne fungus that causes vascular wilt diseases in a wide range of plant hosts. V. dahliae produces multicelled, melanized resting bodies, also known as microsclerotia (MS) that can survive for years in the soil. The MS are the primary source of infection of the Verticillium disease cycle. Thus, MS formation marks an important event in the disease cycle of V. dahliae. Results In this study, next generation sequencing technology of RNA-Seq was employed to investigate the global transcriptomic dynamics of MS development to identify differential gene expression at several stages of MS formation in strain XS11 of V. dahliae, isolated from smoke tree. We observed large-scale changes in gene expression during MS formation, such as increased expression of genes involved in protein metabolism and carbohydrate metabolism. Genes involved in glycolytic pathway and melanin biosynthesis were dramatically up-regulated in MS. Cluster analyses revealed increased expression of genes encoding products involved in primary metabolism and stress responses throughout MS development. Differential expression of ubiquitin-dependent protein catabolism and cell death-associated genes during MS development were revealed. Homologs of genes located in the lineage-specific (LS) regions of V. dahliae strain VdLs.17, were either not expressed or showed low expression. Furthermore, alternative splicing (AS) events were analyzed, revealing that over 95.0% AS events involve retention of introns (RI). Conclusions These data reveal the dynamics of transcriptional regulation during MS formation and were used to construct a comprehensive high-resolution gene expression map. This map provides a key resource for understanding the biology and molecular basis of MS development of V. dahliae. Electronic supplementary material The online version of this article (doi:10.1186/1471-2164-15-324) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | | | | | | | | | - Chengming Tian
- The Key Laboratory for Silviculture and Conservation of Ministry of Education, College of Forestry, Beijing Forestry University, Beijing, China.
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126
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Marty F, Rockel-Bauer C, Simigdala N, Brunner E, Basler K. Large-scale imaginal disc sorting: A protocol for "omics"-approaches. Methods 2014; 68:260-4. [PMID: 24736056 DOI: 10.1016/j.ymeth.2014.04.005] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2014] [Revised: 04/03/2014] [Accepted: 04/07/2014] [Indexed: 12/29/2022] Open
Abstract
Imaginal discs, especially the wing imaginal disc, are powerful model systems to study organ development. The traditional methods to analyze wing imaginal discs depend on the laborious and time-consuming dissection of larvae. "Omics"-based approaches, such as RNA-seq, ChIP-seq, proteomics and lipidomics, offer new opportunities for the systems-level investigation of organ development. However, it is impractical to manually isolate the required starting material. This is even more problematic when experiments strive for enhanced temporal and spatial resolution. The mass isolation workflow discussed in this review, solves this problem. The semi-automated sorting of 1000 wing imaginal discs in less than 3h forms the basis of a workflow that can be connected to biochemical analyses of organ patterning and growth. In addition to the mass isolation workflow we briefly describe key "omics" technologies and their applications. The combination of mass isolation and "omics"-approaches ensures that the wing imaginal disc will continue to be a key model organ for studying developmental processes, both on the genetic, but increasingly also on the biochemical level.
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Affiliation(s)
- Florian Marty
- Institute of Molecular Life Sciences, University of Zurich, Winterthurerstrasse 190, CH 8057 Zurich, Switzerland
| | - Claudia Rockel-Bauer
- Institute of Molecular Life Sciences, University of Zurich, Winterthurerstrasse 190, CH 8057 Zurich, Switzerland
| | - Nikiana Simigdala
- Institute of Molecular Life Sciences, University of Zurich, Winterthurerstrasse 190, CH 8057 Zurich, Switzerland
| | - Erich Brunner
- Institute of Molecular Life Sciences, University of Zurich, Winterthurerstrasse 190, CH 8057 Zurich, Switzerland
| | - Konrad Basler
- Institute of Molecular Life Sciences, University of Zurich, Winterthurerstrasse 190, CH 8057 Zurich, Switzerland.
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127
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Rödiger S, Liebsch C, Schmidt C, Lehmann W, Resch-Genger U, Schedler U, Schierack P. Nucleic acid detection based on the use of microbeads: a review. Mikrochim Acta 2014. [DOI: 10.1007/s00604-014-1243-4] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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128
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Sun J, Wang S, Li C, Ren Y, Wang J. Novel expression profiles of microRNAs suggest that specific miRNAs regulate gene expression for the sexual maturation of female Schistosoma japonicum after pairing. Parasit Vectors 2014; 7:177. [PMID: 24721600 PMCID: PMC4021575 DOI: 10.1186/1756-3305-7-177] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2013] [Accepted: 03/26/2014] [Indexed: 02/06/2023] Open
Abstract
Background Schistosoma japonicum is one of the major causative agents of schistosomiasis. The pairing of males and females leads to female sexual maturation and maintains this mature state. However, the mechanisms by which pairing facilitates sexual maturation are yet to be investigated. Methods Parasites isolated from single- and double-sex cercariae-infected mice were analyzed by Solexa to uncover pair-regulated miRNA profiles. To reveal the biological functions of differentially expressed miRNAs among the samples, we predicted the target genes of these differentially expressed miRNAs and compared the gene expression between 23-d-old female schistosomula from double-sex infections (23DSI) and 23-d-old female schistosomula from single-sex infections (23SSI) by analyzing digital gene expression profiling (DGE). KEGG pathway analysis was used to investigate the relevant biological processes of these target genes to understand the significance of differentially expressed miRNAs after pairing. Results The differentially expressed miRNA profiles of female 18- and 23-d post-single- and double-sex infections were analysed by Solexa. Similar miRNA profiles were observed in 18SSI and 18DSI, with the presence of identically expressed high-abundance miRNA, such as miRNA-1, miRNA-71b-5p and let-7. By contrast, in 23DSI and 23SSI, most of these high-abundance miRNAs were down-regulated. Furthermore, among all samples, bantam was distinctly up-regulated in 23 DSI, and miR-1, miR-71, miR-7-5p, and miR-7 were distinctly up-regulated in 23SSI. The transcriptomes of 23DSI and 23SSI revealed that the predicted target genes of miRNA-1, miRNA-71, miRNA-7, and miR-7-5p were associated with the ribonucleoprotein complex assembly and microtubule-based process. Conversely, the predicted target genes of bantam were related to the embryo development, development of primary sexual characteristics and regulation of transcription. KEGG pathway analysis revealed that in unpaired females, the highly-expressed miRNA-1, miRNA-71, miRNA-7, and miR-7-5p only inhibited the limited pathways, such as proteasome and ribosome assembly. Meanwhile, in paired mature females, highly-expressed bantam inhibited more biological pathways, such as the citrate cycle, glycolysis, fatty acid biosynthesis and RNA degradation. Conclusions The differentially expressed miRNAs between 23SSI and 23DSI and their different functions indicated that more genes or metabolic pathways in paired mature females were inhibited than those in unpaired ones. The results suggested that after pairing, specific miRNAs regulated gene expression to lead to female sexual maturation.
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Affiliation(s)
- Jun Sun
- Institute for Infectious Diseases and Vaccine Development, Tongji University School of Medicine, Shanghai 200092, People's Republic of China.
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129
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Moresco EMY, Li X, Beutler B. Going forward with genetics: recent technological advances and forward genetics in mice. THE AMERICAN JOURNAL OF PATHOLOGY 2014; 182:1462-73. [PMID: 23608223 DOI: 10.1016/j.ajpath.2013.02.002] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2012] [Accepted: 02/05/2013] [Indexed: 12/24/2022]
Abstract
Forward genetic analysis is an unbiased approach for identifying genes essential to defined biological phenomena. When applied to mice, it is one of the most powerful methods to facilitate understanding of the genetic basis of human biology and disease. The speed at which disease-causing mutations can be identified in mutagenized mice has been markedly increased by recent advances in DNA sequencing technology. Creating and analyzing mutant phenotypes may therefore become rate-limiting in forward genetic experimentation. We review the forward genetic approach and its future in the context of recent technological advances, in particular massively parallel DNA sequencing, induced pluripotent stem cells, and haploid embryonic stem cells.
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Affiliation(s)
- Eva Marie Y Moresco
- Center for Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX 75235-8505, USA
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130
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Egalite N, Groisman IJ, Godard B. Genetic Counseling Practice in Next Generation Sequencing Research: Implications for the Ethical Oversight of the Informed Consent Process. J Genet Couns 2014; 23:661-70. [DOI: 10.1007/s10897-014-9703-x] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2013] [Accepted: 02/14/2014] [Indexed: 12/20/2022]
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131
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Swanson A, Ramos E, Snyder H. Next Generation Sequencing is the Impetus for the Next Generation of Laboratory-Based Genetic Counselors. J Genet Couns 2014; 23:647-54. [DOI: 10.1007/s10897-013-9684-1] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2013] [Accepted: 12/12/2013] [Indexed: 02/04/2023]
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132
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Hu Z, Lausted C, Yoo H, Yan X, Brightman A, Chen J, Wang W, Bu X, Hood L. Quantitative liver-specific protein fingerprint in blood: a signature for hepatotoxicity. Am J Cancer Res 2014; 4:215-28. [PMID: 24465277 PMCID: PMC3900804 DOI: 10.7150/thno.7868] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2013] [Accepted: 12/04/2013] [Indexed: 02/06/2023] Open
Abstract
We discuss here a new approach to detecting hepatotoxicity by employing concentration changes of liver-specific blood proteins during disease progression. These proteins are capable of assessing the behaviors of their cognate liver biological networks for toxicity or disease perturbations. Blood biomarkers are highly desirable diagnostics as blood is easily accessible and baths virtually all organs. Fifteen liver-specific blood proteins were identified as markers of acetaminophen (APAP)-induced hepatotoxicity using three proteomic technologies: label-free antibody microarrays, quantitative immunoblotting, and targeted iTRAQ mass spectrometry. Liver-specific blood proteins produced a toxicity signature of eleven elevated and four attenuated blood protein levels. These blood protein perturbations begin to provide a systems view of key mechanistic features of APAP-induced liver injury relating to glutathione and S-adenosyl-L-methionine (SAMe) depletion, mitochondrial dysfunction, and liver responses to the stress. Two markers, elevated membrane-bound catechol-O-methyltransferase (MB-COMT) and attenuated retinol binding protein 4 (RBP4), report hepatic injury significantly earlier than the current gold standard liver biomarker, alanine transaminase (ALT). These biomarkers were perturbed prior to onset of irreversible liver injury. Ideal markers should be applicable for both rodent model studies and human clinical trials. Five of these mouse liver-specific blood markers had human orthologs that were also found to be responsive to human hepatotoxicity. This panel of liver-specific proteins has the potential to effectively identify the early toxicity onset, the nature and extent of liver injury and report on some of the APAP-perturbed liver networks.
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133
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Gao J, Chen Z, Luo M, Peng H, Lin H, Qin C, Yuan G, Shen Y, Ding H, Zhao M, Pan G, Zhang Z. Genome expression profile analysis of the maize sheath in response to inoculation to R. solani. Mol Biol Rep 2014; 41:2471-83. [PMID: 24420865 PMCID: PMC3968446 DOI: 10.1007/s11033-014-3103-z] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2012] [Accepted: 01/06/2014] [Indexed: 12/27/2022]
Abstract
Currently, the molecular regulation mechanisms of disease-resistant involved in maize leaf sheaths infected by banded leaf and sheath blight (BLSB) are poorly known. To gain insight into the transcriptome dynamics that are associated with their disease-resistant, genome-wide gene expression profiling was conducted by Solexa sequencing. More than four million tags were generated from sheath tissues without any leaf or development leaf, including 193,222 and 204,824 clean tags in the two libraries, respectively. Of these, 82,864 (55.4 %) and 91,678 (51.5 %) tags were matched to the reference genes. The most differentially expressed tags with log2 ratio >2 or <-2 (P < 0.001) were further analyzed, representing 1,476 up-regulated and 1,754 down-regulated genes, except for unknown transcripts, which were classified into 11 functional categories. The most enriched categories were those of metabolism, signal transduction and cellular transport. Next, the expression patterns of 12 genes were assessed by quantitative real-time PCR, and it is showed the results were general agreement with the Solexa analysis, although the degree of change was lower in amplitude. In conclusion, we first reveal the complex changes in the transcriptome during the early development of maize sheath infected by BLSB and provide a comprehensive set of data that are essential for understanding its molecular regulation mechanism.
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Affiliation(s)
- Jian Gao
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, Maize Research Institute of Sichuan Agricultural University, Wenjiang, 611130 Sichuan China
| | - Zhe Chen
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, Maize Research Institute of Sichuan Agricultural University, Wenjiang, 611130 Sichuan China
| | - Mao Luo
- Drug Discovery Research Center of Luzhou Medical College, Luzhou, 646000 Sichuan China
| | - Hua Peng
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, Maize Research Institute of Sichuan Agricultural University, Wenjiang, 611130 Sichuan China
| | - Haijian Lin
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, Maize Research Institute of Sichuan Agricultural University, Wenjiang, 611130 Sichuan China
| | - Cheng Qin
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, Maize Research Institute of Sichuan Agricultural University, Wenjiang, 611130 Sichuan China
| | - Guangsheng Yuan
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, Maize Research Institute of Sichuan Agricultural University, Wenjiang, 611130 Sichuan China
| | - Yaou Shen
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, Maize Research Institute of Sichuan Agricultural University, Wenjiang, 611130 Sichuan China
| | - Haiping Ding
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, Maize Research Institute of Sichuan Agricultural University, Wenjiang, 611130 Sichuan China
| | - Maojun Zhao
- Life Science College of Sichuan Agricultural University, Ya’an, 625014 Sichuan China
| | - Guangtang Pan
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, Maize Research Institute of Sichuan Agricultural University, Wenjiang, 611130 Sichuan China
| | - Zhiming Zhang
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, Maize Research Institute of Sichuan Agricultural University, Wenjiang, 611130 Sichuan China
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135
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Davies WI. Challenges using diagnostic next-generation sequencing in the clinical environment for inherited retinal disorders. Per Med 2014; 11:99-111. [PMID: 29751394 DOI: 10.2217/pme.13.95] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Visual impairment, and in particular the inherited retinopathies, is a significant problem worldwide. Many disorders are progressive so their early and accurate detection is crucial to the development and application of appropriate disease management and treatment strategies, some of which are currently being tested in clinical trials. Over the past few decades, the identification of genetic causes that mediate many inherited diseases has largely been based on traditional 'Sanger sequencing' and microchip approaches that are expensive and time consuming. However, with the advent of next-generation sequencing it is now possible to apply high-throughput technologies to the clinical arena and sequence the entire exome or genome of an affected individual. Despite the potential for a paradigm shift in the clinical diagnosis of retinal disease, it may prove difficult to interpret and confirm the pathogenicity of any variants discovered by next-generation sequencing pipelines. In this review, I examine the application of next-generation sequencing to inherited retinal disorders and discuss current limitations and future perspectives.
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Affiliation(s)
- Wayne Il Davies
- School of Animal Biology & University of Western Australia Oceans Institute, University of Western Australia, 35 Stirling Highway, Perth, Western Australia, WA 6009, Australia.
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136
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Abstract
The differential abundance of transcripts from alternative alleles of a gene, for example in a hybrid plant or an outbred natural population, can provide information about the nature of interindividual or interstrain variation in gene expression. Allele-specific expression (ASE) can result from epigenetic phenomena, such as imprinting (when the overexpressed allele is inherited consistently from one parent) or allele-specific chromatin modifications. Alternatively, DNA sequence variants in the promoter or within the transcribed region of a gene can affect the rate of transcription or the rate of decay of the transcript, respectively. The existence of this allelic variation and the insights it provides into the nature of the gene regulation are of significant interest. With the recent widespread availability of sequencing based transcriptomics, the power to detect ASE has increased; however, inference of ASE from transcriptome sequencing data is subject to several caveats and potential biases and the results need to be interpreted with care.
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Affiliation(s)
- Paul K Korir
- School of Mathematics, Statistics and Applied Mathematics, National University of Ireland, Galway (NUI Galway), Ireland
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137
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Application of “Omics” Technologies to In Vitro Toxicology. METHODS IN PHARMACOLOGY AND TOXICOLOGY 2014. [DOI: 10.1007/978-1-4939-0521-8_18] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/06/2022]
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138
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Qian X, Ba Y, Zhuang Q, Zhong G. RNA-Seq technology and its application in fish transcriptomics. OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY 2013; 18:98-110. [PMID: 24380445 DOI: 10.1089/omi.2013.0110] [Citation(s) in RCA: 177] [Impact Index Per Article: 16.1] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
High-throughput sequencing technologies, also known as next-generation sequencing (NGS) technologies, have revolutionized the way that genomic research is advancing. In addition to the static genome, these state-of-art technologies have been recently exploited to analyze the dynamic transcriptome, and the resulting technology is termed RNA sequencing (RNA-seq). RNA-seq is free from many limitations of other transcriptomic approaches, such as microarray and tag-based sequencing method. Although RNA-seq has only been available for a short time, studies using this method have completely changed our perspective of the breadth and depth of eukaryotic transcriptomes. In terms of the transcriptomics of teleost fishes, both model and non-model species have benefited from the RNA-seq approach and have undergone tremendous advances in the past several years. RNA-seq has helped not only in mapping and annotating fish transcriptome but also in our understanding of many biological processes in fish, such as development, adaptive evolution, host immune response, and stress response. In this review, we first provide an overview of each step of RNA-seq from library construction to the bioinformatic analysis of the data. We then summarize and discuss the recent biological insights obtained from the RNA-seq studies in a variety of fish species.
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Affiliation(s)
- Xi Qian
- 1 Department of Animal Science, University of Vermont , Burlington, Vermont
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139
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Wankhede DP, Kumar K, Singh P, Sinha AK. Involvement of mitogen activated protein kinase kinase 6 in UV induced transcripts accumulation of genes in phytoalexin biosynthesis in rice. RICE (NEW YORK, N.Y.) 2013; 6:35. [PMID: 24295067 PMCID: PMC4883730 DOI: 10.1186/1939-8433-6-35] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2012] [Accepted: 08/12/2013] [Indexed: 05/04/2023]
Abstract
BACKGROUND Ultra violet radiation leads to accumulation of phytoalexins (PA) in rice (Oryza sativa) which are typically accumulated when the plants are infected with rice blast pathogen Magnaporthe oryzae. Although extensive works have been done in elucidating phytoalexin biosynthesis, UV stress signal transduction leading to accumulations of rice phytoalexin is largely unknown. RESULTS In the present study, the involvement of mitogen activated protein kinase (MAPK) cascade has been shown in UV induced regulation of genes in phytoalexin biosynthesis in rice. UV induced activation of MAPK and expression of PA biosynthesis genes were shown to be inhibited with staurosporin and MAPK inhibitors. Transcript regulation studies and kinase assays indicated involvement of OsMKK6 in the process. Transgenic rice overexpressing constitutive active OsMKK6EE exhibited higher expression of genes of PA biosynthesis pathway upon UV stress and also upon infection with M. oryzae. CONCLUSION These results suggest a key role of OsMKK6 in regulation of UV responsive expression of genes of PA biosynthesis in rice. This study will help to elucidate the intricate signalling components of UV leading to phytoalexins biosynthesis in rice.
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Affiliation(s)
| | - Kundan Kumar
- />National Institute of Plant Genome Research, Aruna Asaf Ali Road, New Delhi, India
- />Department of Biological Sciences, Birla Institute of Technology and Science-Pilani, KK Birla Goa Campus, Zuarinagar, Goa India
| | - Pallavi Singh
- />National Institute of Plant Genome Research, Aruna Asaf Ali Road, New Delhi, India
| | - Alok Krishna Sinha
- />National Institute of Plant Genome Research, Aruna Asaf Ali Road, New Delhi, India
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Kudapa H, Ramalingam A, Nayakoti S, Chen X, Zhuang WJ, Liang X, Kahl G, Edwards D, Varshney RK. Functional genomics to study stress responses in crop legumes: progress and prospects. FUNCTIONAL PLANT BIOLOGY : FPB 2013; 40:1221-1233. [PMID: 32481190 DOI: 10.1071/fp13191] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/25/2013] [Accepted: 08/22/2013] [Indexed: 06/11/2023]
Abstract
Legumes are important food crops worldwide, contributing to more than 33% of human dietary protein. The production of crop legumes is frequently impacted by abiotic and biotic stresses. It is therefore important to identify genes conferring resistance to biotic stresses and tolerance to abiotic stresses that can be used to both understand molecular mechanisms of plant response to the environment and to accelerate crop improvement. Recent advances in genomics offer a range of approaches such as the sequencing of genomes and transcriptomes, gene expression microarray as well as RNA-seq based gene expression profiling, and map-based cloning for the identification and isolation of biotic and abiotic stress-responsive genes in several crop legumes. These candidate stress associated genes should provide insights into the molecular mechanisms of stress tolerance and ultimately help to develop legume varieties with improved stress tolerance and productivity under adverse conditions. This review provides an overview on recent advances in the functional genomics of crop legumes that includes the discovery as well as validation of candidate genes.
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Affiliation(s)
- Himabindu Kudapa
- International Crops Research Institute for the Semiarid Tropics (ICRISAT), Patancheru 502324, India
| | - Abirami Ramalingam
- International Crops Research Institute for the Semiarid Tropics (ICRISAT), Patancheru 502324, India
| | - Swapna Nayakoti
- International Crops Research Institute for the Semiarid Tropics (ICRISAT), Patancheru 502324, India
| | - Xiaoping Chen
- Crops Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Wei-Jian Zhuang
- Fujian Provincial Key Laboratory of Plant Molecular and Cell Biology, Fujian Agriculture and Forestry University, Fuzhou 350002, PR China
| | - Xuanqiang Liang
- Crops Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Guenter Kahl
- Goethe University Frankfurt am Main, Institute for Molecular BioSciences, Max-von-Laue-Str. 9, Frankfurt am Main 60438, Germany
| | - David Edwards
- School of Agriculture and Food Sciences, University of Queensland, Brisbane, St Lucia, Qld 4072, Australia
| | - Rajeev K Varshney
- International Crops Research Institute for the Semiarid Tropics (ICRISAT), Patancheru 502324, India
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Abstract
Deep sequencing of transcriptomes has become an indispensable tool for biology, enabling expression levels for thousands of genes to be compared across multiple samples. Since transcript counts scale with sequencing depth, counts from different samples must be normalized to a common scale prior to comparison. We analyzed fifteen existing and novel algorithms for normalizing transcript counts, and evaluated the effectiveness of the resulting normalizations. For this purpose we defined two novel and mutually independent metrics: (1) the number of “uniform” genes (genes whose normalized expression levels have a sufficiently low coefficient of variation), and (2) low Spearman correlation between normalized expression profiles of gene pairs. We also define four novel algorithms, one of which explicitly maximizes the number of uniform genes, and compared the performance of all fifteen algorithms. The two most commonly used methods (scaling to a fixed total value, or equalizing the expression of certain ‘housekeeping’ genes) yielded particularly poor results, surpassed even by normalization based on randomly selected gene sets. Conversely, seven of the algorithms approached what appears to be optimal normalization. Three of these algorithms rely on the identification of “ubiquitous” genes: genes expressed in all the samples studied, but never at very high or very low levels. We demonstrate that these include a “core” of genes expressed in many tissues in a mutually consistent pattern, which is suitable for use as an internal normalization guide. The new methods yield robustly normalized expression values, which is a prerequisite for the identification of differentially expressed and tissue-specific genes as potential biomarkers.
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Meerupati T, Andersson KM, Friman E, Kumar D, Tunlid A, Ahrén D. Genomic mechanisms accounting for the adaptation to parasitism in nematode-trapping fungi. PLoS Genet 2013; 9:e1003909. [PMID: 24244185 PMCID: PMC3828140 DOI: 10.1371/journal.pgen.1003909] [Citation(s) in RCA: 76] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2013] [Accepted: 09/09/2013] [Indexed: 01/12/2023] Open
Abstract
Orbiliomycetes is one of the earliest diverging branches of the filamentous ascomycetes. The class contains nematode-trapping fungi that form unique infection structures, called traps, to capture and kill free-living nematodes. The traps have evolved differently along several lineages and include adhesive traps (knobs, nets or branches) and constricting rings. We show, by genome sequencing of the knob-forming species Monacrosporium haptotylum and comparison with the net-forming species Arthrobotrys oligospora, that two genomic mechanisms are likely to have been important for the adaptation to parasitism in these fungi. Firstly, the expansion of protein domain families and the large number of species-specific genes indicated that gene duplication followed by functional diversification had a major role in the evolution of the nematode-trapping fungi. Gene expression indicated that many of these genes are important for pathogenicity. Secondly, gene expression of orthologs between the two fungi during infection indicated that differential regulation was an important mechanism for the evolution of parasitism in nematode-trapping fungi. Many of the highly expressed and highly upregulated M. haptotylum transcripts during the early stages of nematode infection were species-specific and encoded small secreted proteins (SSPs) that were affected by repeat-induced point mutations (RIP). An active RIP mechanism was revealed by lack of repeats, dinucleotide bias in repeats and genes, low proportion of recent gene duplicates, and reduction of recent gene family expansions. The high expression and rapid divergence of SSPs indicate a striking similarity in the infection mechanisms of nematode-trapping fungi and plant and insect pathogens from the crown groups of the filamentous ascomycetes (Pezizomycotina). The patterns of gene family expansions in the nematode-trapping fungi were more similar to plant pathogens than to insect and animal pathogens. The observation of RIP activity in the Orbiliomycetes suggested that this mechanism was present early in the evolution of the filamentous ascomycetes.
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Affiliation(s)
- Tejashwari Meerupati
- Microbial Ecology Group, Department of Biology, Lund University, Ecology Building, Lund, Sweden
| | - Karl-Magnus Andersson
- Microbial Ecology Group, Department of Biology, Lund University, Ecology Building, Lund, Sweden
| | - Eva Friman
- Microbial Ecology Group, Department of Biology, Lund University, Ecology Building, Lund, Sweden
| | - Dharmendra Kumar
- Microbial Ecology Group, Department of Biology, Lund University, Ecology Building, Lund, Sweden
- Department of Genetics and Plant Breeding, N.D. University of Agriculture and Technology, Faizabad, India
| | - Anders Tunlid
- Microbial Ecology Group, Department of Biology, Lund University, Ecology Building, Lund, Sweden
| | - Dag Ahrén
- Microbial Ecology Group, Department of Biology, Lund University, Ecology Building, Lund, Sweden
- BILS Bioinformatics Infrastructure for Life Sciences, Department of Biology, Lund University, Ecology Building, Lund, Sweden
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143
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Kumar K, Sinha AK. Overexpression of constitutively active mitogen activated protein kinase kinase 6 enhances tolerance to salt stress in rice. RICE (NEW YORK, N.Y.) 2013; 6:25. [PMID: 24280045 PMCID: PMC4883705 DOI: 10.1186/1939-8433-6-25] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2013] [Accepted: 08/01/2013] [Indexed: 05/04/2023]
Abstract
BACKGROUND Salinity is one of the most common abiotic stresses encountered by plants in the environment and transgenic approaches offer new opportunities to improve tolerance. The mitogen activated protein kinase (MAPK) kinase (MKK) is a key component of MAPK cascade that plays important roles in intra and extra cellular signaling in plants. In the present study, a MKK from rice (Oryza sativa), OsMKK6 was functionally characterized in salt stress by transforming its constitutively active form. FINDINGS OsMKK6 was made constitutively active by mutating serine and threonine to glutamic acid by site directed mutagenesis, and transformed in indica cultivar rice var. Pusa Basmati-1. The transgenic seedlings growing in 200 mM NaCl solution showed increased root/shoot length and weight, less chlorophyll beaching and higher MAPK activity compared to the wild types. CONCLUSION Present work suggest role of OsMKK6 gene in salt stress signaling in rice.
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Affiliation(s)
- Kundan Kumar
- />National Institute of Plant Genome Research, Aruna Asaf Ali Road, New Delhi, 110067 India
- />Birla Institute of Technology & Science Pilani, K K Birla Goa Campus, Zuarinagar, Goa 403726 India
| | - Alok Krishna Sinha
- />National Institute of Plant Genome Research, Aruna Asaf Ali Road, New Delhi, 110067 India
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Saha J, Chatterjee C, Sengupta A, Gupta K, Gupta B. Genome-wide analysis and evolutionary study of sucrose non-fermenting 1-related protein kinase 2 (SnRK2) gene family members in Arabidopsis and Oryza. Comput Biol Chem 2013; 49:59-70. [PMID: 24225178 DOI: 10.1016/j.compbiolchem.2013.09.005] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2013] [Revised: 09/27/2013] [Accepted: 09/27/2013] [Indexed: 10/26/2022]
Abstract
The over-expression of plant specific SnRK2 gene family members by hyperosmotic stress and some by abscisic acid is well established. In this report, we have analyzed the evolution of SnRK2 gene family in different plant lineages including green algae, moss, lycophyte, dicot and monocot. Our results provide some evidences to indicate that the natural selection pressure had considerable influence on cis-regulatory promoter region and coding region of SnRK2 members in Arabidopsis and Oryza independently through time. Observed degree of sequence/motif conservation amongst SnRK2 homolog in all the analyzed plant lineages strongly supported their inclusion as members of this family. The chromosomal distributions of duplicated SnRK2 members have also been analyzed in Arabidopsis and Oryza. Massively Parallel Signature Sequencing (MPSS) database derived expression data and the presence of abiotic stress related promoter elements within the 1 kb upstream promoter region of these SnRK2 family members further strengthen the observations of previous workers. Additionally, the phylogenetic relationships of SnRK2 have been studied in all plant lineages along with their respective exon-intron structural patterns. Our results indicate that the ancestral SnRK2 gene of land plants gradually evolved by duplication and diversification and modified itself through exon-intron loss events to survive under environmental stress conditions.
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Affiliation(s)
- Jayita Saha
- Department of Biological Sciences (Section Biotechnology), Presidency University, 86/1 College Street, Kolkata 700073, India; Department of Biological Sciences (Section Botany), Presidency University, 86/1 College Street, Kolkata 700073, India
| | - Chitrita Chatterjee
- Department of Biological Sciences (Section Biotechnology), Presidency University, 86/1 College Street, Kolkata 700073, India
| | - Atreyee Sengupta
- Department of Biological Sciences (Section Biotechnology), Presidency University, 86/1 College Street, Kolkata 700073, India; Department of Biological Sciences (Section Botany), Presidency University, 86/1 College Street, Kolkata 700073, India
| | - Kamala Gupta
- Department of Biological Sciences (Section Botany), Presidency University, 86/1 College Street, Kolkata 700073, India.
| | - Bhaskar Gupta
- Department of Biological Sciences (Section Biotechnology), Presidency University, 86/1 College Street, Kolkata 700073, India.
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145
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Armenta-Medina A, Huanca-Mamani W, Sanchez-León N, Rodríguez-Arévalo I, Vielle-Calzada JP. Functional analysis of sporophytic transcripts repressed by the female gametophyte in the ovule of Arabidopsis thaliana. PLoS One 2013; 8:e76977. [PMID: 24194852 PMCID: PMC3806734 DOI: 10.1371/journal.pone.0076977] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2013] [Accepted: 08/28/2013] [Indexed: 01/07/2023] Open
Abstract
To investigate the genetic and molecular regulation that the female gametophyte could exert over neighboring sporophytic regions of the ovule, we performed a quantitative comparison of global expression in wild-type and nozzle/sporocyteless (spl) ovules of Arabidopsis thaliana (Arabidopsis), using Massively Parallel Signature Sequencing (MPSS). This comparison resulted in 1517 genes showing at least 3-fold increased expression in ovules lacking a female gametophyte, including those encoding 89 transcription factors, 50 kinases, 25 proteins containing a RNA-recognition motif (RRM), and 20 WD40 repeat proteins. We confirmed that eleven of these genes are either preferentially expressed or exclusive of spl ovules lacking a female gametophyte as compared to wild-type, and showed that six are also upregulated in determinant infertile1 (dif1), a meiotic mutant affected in a REC8-like cohesin that is also devoided of female gametophytes. The sporophytic misexpression of IOREMPTE, a WD40/transducin repeat gene that is preferentially expressed in the L1 layer of spl ovules, caused the arrest of female gametogenesis after differentiation of a functional megaspore. Our results show that in Arabidopsis, the sporophytic-gametophytic cross talk includes a negative regulation of the female gametophyte over specific genes that are detrimental for its growth and development, demonstrating its potential to exert a repressive control over neighboring regions in the ovule.
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Affiliation(s)
- Alma Armenta-Medina
- Grupo de Desarrollo Reproductivo y Apomixis, Laboratorio Nacional de Genómica para la Biodiversidad y Departamento de Ingeniería Genética de Plantas, CINVESTAV Irapuato, Irapuato, Mexico
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146
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Dong Z, Chen Y. Transcriptomics: advances and approaches. SCIENCE CHINA-LIFE SCIENCES 2013; 56:960-7. [PMID: 24091688 DOI: 10.1007/s11427-013-4557-2] [Citation(s) in RCA: 69] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/14/2013] [Accepted: 09/06/2013] [Indexed: 11/25/2022]
Abstract
Transcriptomics is one of the most developed fields in the post-genomic era. Transcriptome is the complete set of RNA transcripts in a specific cell type or tissue at a certain developmental stage and/or under a specific physiological condition, including messenger RNA, transfer RNA, ribosomal RNA, and other non-coding RNAs. Transcriptomics focuses on the gene expression at the RNA level and offers the genome-wide information of gene structure and gene function in order to reveal the molecular mechanisms involved in specific biological processes. With the development of next-generation high-throughput sequencing technology, transcriptome analysis has been progressively improving our understanding of RNA-based gene regulatory network. Here, we discuss the concept, history, and especially the recent advances in this inspiring field of study.
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Affiliation(s)
- Zhicheng Dong
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China,
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147
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Next generation sequencing in psychiatric research: what study participants need to know about research findings. Int J Neuropsychopharmacol 2013; 16:2119-27. [PMID: 23725748 DOI: 10.1017/s1461145713000527] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
The use of next generation sequencing (NGS) technologies in psychiatric genetics research and its potential to generate individual research results will likely have far reaching implications for predictive and diagnostic practices. The extent of this impact may not be easily understood by psychiatric research participants during the consent process. The traditional consent process for studies involving human subjects does not address critical issues specific to NGS research, such as the return of results. We examined which type of research findings should be communicated, how this information should be conveyed during the consent process and what guidance is required by researchers and IRBs to help psychiatric research participants understand the peculiarities, the limits and the impact of NGS. Strong standards are needed to ensure appropriate use of data generated by NGS, to meet participants' expectations and needs, and to clarify researchers' duties regarding the disclosure of data and their subsequent management. In the short term, researchers and IRBs need to be proactive in revising current consent processes that deal with the disclosure of research findings.
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148
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Bush SJ, Castillo-Morales A, Tovar-Corona JM, Chen L, Kover PX, Urrutia AO. Presence-absence variation in A. thaliana is primarily associated with genomic signatures consistent with relaxed selective constraints. Mol Biol Evol 2013; 31:59-69. [PMID: 24072814 PMCID: PMC3879440 DOI: 10.1093/molbev/mst166] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
The sequencing of multiple genomes of the same plant species has revealed polymorphic gene and exon loss. Genes associated with disease resistance are overrepresented among those showing structural variations, suggesting an adaptive role for gene and exon presence–absence variation (PAV). To shed light on the possible functional relevance of polymorphic coding region loss and the mechanisms driving this process, we characterized genes that have lost entire exons or their whole coding regions in 17 fully sequenced Arabidopsis thaliana accessions. We found that although a significant enrichment in genes associated with certain functional categories is observed, PAV events are largely restricted to genes with signatures of reduced essentiality: PAV genes tend to be newer additions to the genome, tissue specific, and lowly expressed. In addition, PAV genes are located in regions of lower gene density and higher transposable element density. Partial coding region PAV events were associated with only a marginal reduction in gene expression level in the affected accession and occurred in genes with higher levels of alternative splicing in the Col-0 accession. Together, these results suggest that although adaptive scenarios cannot be ruled out, PAV events can be explained without invoking them.
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Affiliation(s)
- Stephen J Bush
- Department of Biology and Biochemistry, University of Bath, Bath, United Kingdom
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149
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Fujii G, Imamura S, Hanaoka M, Tanaka K. Nuclear-encoded chloroplast RNA polymerase sigma factor SIG2 activates chloroplast-encoded phycobilisome genes in a red alga, Cyanidioschyzon merolae. FEBS Lett 2013; 587:3354-9. [PMID: 24036445 DOI: 10.1016/j.febslet.2013.08.031] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2013] [Revised: 08/23/2013] [Accepted: 08/23/2013] [Indexed: 10/26/2022]
Abstract
The phycobilisome (PBS) is a photosynthetic light-harvesting complex in red algae, whose structural genes are separately encoded by both the nuclear and chloroplast genomes. While the expression of PBS genes in both genomes is responsive to environmental changes to modulate light-harvesting efficiency, little is known about how gene expression of the two genomes is coordinated. In this study, we focused on the four nuclear-encoded chloroplast sigma factors to understand aspects of this coordination, and found that SIG2 directs the expression of chloroplast PBS genes in the red alga Cyanidioschyzon merolae.
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Affiliation(s)
- Gaku Fujii
- Chemical Resources Laboratory, Tokyo Institute of Technology, 4259-R1-29 Nagatsuta, Midori-ku, Yokohama 226-8503, Japan; Graduate School of Horticulture, Chiba University, 648 Matsudo, Matsudo, Chiba 271-8510, Japan
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150
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Morey M, Fernández-Marmiesse A, Castiñeiras D, Fraga JM, Couce ML, Cocho JA. A glimpse into past, present, and future DNA sequencing. Mol Genet Metab 2013; 110:3-24. [PMID: 23742747 DOI: 10.1016/j.ymgme.2013.04.024] [Citation(s) in RCA: 80] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/27/2013] [Revised: 04/30/2013] [Accepted: 04/30/2013] [Indexed: 12/21/2022]
Abstract
Current advances in DNA sequencing technologies are dropping down sequencing cost while increasing throughput at a pace never shown before. Past-decade great milestones, as the establishment of a reference human genome (amongst others) and large-scale human genetic variation study in the 1000 Genome project are, in conjunction with the use of these techniques, triggering advances in many areas of basic and applied science. These tools, stored in and combined with the vast amount of information present in biological online databases are, with the use of automated interpretation and analysis tools, allowing the fulfillment of increasingly ambitious studies in many areas and also are democratizing the access to information, interpretation and technologies, being the first opportunity for researchers to assess the influence of genetics in complex events as multifactorial diseases, evolutionary studies, metagenomics, transcriptomics, etc. In this review, we present the current state of the art of these technologies, focusing on second generation sequencing, from sample and library preparation to sequencing chemistries and bioinformatic software available for final data analysis and visualisation, with its possible applications. We also make an overview of first and third generation, due to its historical importance and for being the upcoming future tools for genetic analysis, respectively.
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Affiliation(s)
- Marcos Morey
- Unidad de Diagnóstico y Tratamiento de Enfermedades Metabólicas Congénitas, Hospital Clínico Universitario de Santiago, A Choupana s/n, 15706 Santiago de Compostela, Spain.
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