51
|
Dasgupta MG, Dharanishanthi V, Agarwal I, Krutovsky KV. Development of genetic markers in Eucalyptus species by target enrichment and exome sequencing. PLoS One 2015; 10:e0116528. [PMID: 25602379 PMCID: PMC4300219 DOI: 10.1371/journal.pone.0116528] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2014] [Accepted: 12/08/2014] [Indexed: 02/02/2023] Open
Abstract
The advent of next-generation sequencing has facilitated large-scale discovery, validation and assessment of genetic markers for high density genotyping. The present study was undertaken to identify markers in genes supposedly related to wood property traits in three Eucalyptus species. Ninety four genes involved in xylogenesis were selected for hybridization probe based nuclear genomic DNA target enrichment and exome sequencing. Genomic DNA was isolated from the leaf tissues and used for on-array probe hybridization followed by Illumina sequencing. The raw sequence reads were trimmed and high-quality reads were mapped to the E. grandis reference sequence and the presence of single nucleotide variants (SNVs) and insertions/ deletions (InDels) were identified across the three species. The average read coverage was 216X and a total of 2294 SNVs and 479 InDels were discovered in E. camaldulensis, 2383 SNVs and 518 InDels in E. tereticornis, and 1228 SNVs and 409 InDels in E. grandis. Additionally, SNV calling and InDel detection were conducted in pair-wise comparisons of E. tereticornis vs. E. grandis, E. camaldulensis vs. E. tereticornis and E. camaldulensis vs. E. grandis. This study presents an efficient and high throughput method on development of genetic markers for family– based QTL and association analysis in Eucalyptus.
Collapse
Affiliation(s)
- Modhumita Ghosh Dasgupta
- Division of Plant Biotechnology, Institute of Forest Genetics and Tree Breeding, P.B. No. 1061, R.S. Puram, Coimbatore–641002, India
- * E-mail:
| | - Veeramuthu Dharanishanthi
- Division of Plant Biotechnology, Institute of Forest Genetics and Tree Breeding, P.B. No. 1061, R.S. Puram, Coimbatore–641002, India
| | - Ishangi Agarwal
- Genotypic Technology Private Limited, #2/13, Balaji Complex, Poojari Layout, 80, Feet Road, R. M. V. 2nd Stage, Bangalore-560094, India
| | - Konstantin V. Krutovsky
- Department of Forest Genetics and Forest Tree Breeding, Büsgen Institute, Georg August University of Göttingen, Büsgenweg 2, D-37077 Göttingen, Germany
- Department of Ecosystem Science and Management, Texas A&M University, 2138 TAMU, College Station, TX 77843-2138, United States of America
- N.I. Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow 119333, Russia
- Genome Research and Education Center, Siberian Federal University, 50a/2 Akademgorodok, Krasnoyarsk 660036, Russia
| |
Collapse
|
52
|
Guo K, Zou W, Feng Y, Zhang M, Zhang J, Tu F, Xie G, Wang L, Wang Y, Klie S, Persson S, Peng L. An integrated genomic and metabolomic framework for cell wall biology in rice. BMC Genomics 2014; 15:596. [PMID: 25023612 PMCID: PMC4112216 DOI: 10.1186/1471-2164-15-596] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2013] [Accepted: 07/09/2014] [Indexed: 11/21/2022] Open
Abstract
Background Plant cell walls are complex structures that full-fill many diverse functions during plant growth and development. It is therefore not surprising that thousands of gene products are involved in cell wall synthesis and maintenance. However, functional association for the majority of these gene products remains obscure. One useful approach to infer biological associations is via transcriptional coordination, or co-expression of genes. This approach has proved useful for several biological processes. Nevertheless, combining co-expression with other large-scale measurements may improve the biological inferences. Results In this study, we used a combined approach of co-expression and cell wall metabolomics to obtain new insight into cell wall synthesis in rice. We initially created a weighted gene co-expression network from publicly available datasets, and then established a comprehensive cell wall dataset by determining cell wall compositions from 29 tissues that almost cover the whole life cycle of rice. We subsequently combined the datasets through the conversion of co-expressed gene modules into eigen-vectors, representing expression profiles for the genes in the modules, and performed comparative analyses against the cell wall contents. Here, we made three major discoveries. First, we confirmed our approach by finding primary and secondary wall cellulose biosynthesis modules, respectively. Second, we found co-expressed modules that strongly correlated with re-organization of the secondary cell walls and with modifications and degradation of hemicellulosic structures. Third, we inferred that at least one module is likely to play a regulatory role in the production of G-rich lignification. Conclusions Here, we integrated transcriptomic associations and cell wall metabolism and found that certain co-expressed gene modules are positively correlated with distinct cell wall characteristics. We propose that combining multiple data-types, such as coordinated transcription and cell wall analyses, may be a useful approach to glean new insight into biological processes. The combination of multiple datasets, as illustrated here, can further improve the functional inferences that typically are generated via a single type of datasets. In addition, our data extend the typical co-expression approach to allow deeper insight into cell wall biology in rice. Electronic supplementary material The online version of this article (doi:10.1186/1471-2164-15-596) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | - Liangcai Peng
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei 430070, P, R, China.
| |
Collapse
|
53
|
Mewalal R, Mizrachi E, Mansfield SD, Myburg AA. Cell wall-related proteins of unknown function: missing links in plant cell wall development. PLANT & CELL PHYSIOLOGY 2014; 55:1031-43. [PMID: 24683037 DOI: 10.1093/pcp/pcu050] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Lignocellulosic biomass is an important feedstock for the pulp and paper industry as well as emerging biofuel and biomaterial industries. However, the recalcitrance of the secondary cell wall to chemical or enzymatic degradation remains a major hurdle for efficient extraction of economically important biopolymers such as cellulose. It has been estimated that approximately 10-15% of about 27,000 protein-coding genes in the Arabidopsis genome are dedicated to cell wall development; however, only about 130 Arabidopsis genes thus far have experimental evidence validating cell wall function. While many genes have been implicated through co-expression analysis with known genes, a large number are broadly classified as proteins of unknown function (PUFs). Recently the functionality of some of these unknown proteins in cell wall development has been revealed using reverse genetic approaches. Given the large number of cell wall-related PUFs, how do we approach and subsequently prioritize the investigation of such unknown genes that may be essential to or influence plant cell wall development and structure? Here, we address the aforementioned question in two parts; we first identify the different kinds of PUFs based on known and predicted features such as protein domains. Knowledge of inherent features of PUFs may allow for functional inference and a concomitant link to biological context. Secondly, we discuss omics-based technologies and approaches that are helping identify and prioritize cell wall-related PUFs by functional association. In this way, hypothesis-driven experiments can be designed for functional elucidation of many proteins that remain missing links in our understanding of plant cell wall biosynthesis.
Collapse
Affiliation(s)
- Ritesh Mewalal
- Department of Genetics, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Private bag X20, Hatfield, Pretoria, 0028, South Africa
| | - Eshchar Mizrachi
- Department of Genetics, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Private bag X20, Hatfield, Pretoria, 0028, South Africa
| | - Shawn D Mansfield
- Department of Wood Science, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
| | - Alexander A Myburg
- Department of Genetics, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Private bag X20, Hatfield, Pretoria, 0028, South Africa
| |
Collapse
|
54
|
Bhatia R, Bosch M. Transcriptional regulators of Arabidopsis secondary cell wall formation: tools to re-program and improve cell wall traits. FRONTIERS IN PLANT SCIENCE 2014; 5:192. [PMID: 24860583 PMCID: PMC4030196 DOI: 10.3389/fpls.2014.00192] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2014] [Accepted: 04/23/2014] [Indexed: 05/25/2023]
|
55
|
Netotea S, Sundell D, Street NR, Hvidsten TR. ComPlEx: conservation and divergence of co-expression networks in A. thaliana, Populus and O. sativa. BMC Genomics 2014; 15:106. [PMID: 24498971 PMCID: PMC3925997 DOI: 10.1186/1471-2164-15-106] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2013] [Accepted: 01/29/2014] [Indexed: 01/16/2023] Open
Abstract
Background Divergence in gene regulation has emerged as a key mechanism underlying species differentiation. Comparative analysis of co-expression networks across species can reveal conservation and divergence in the regulation of genes. Results We inferred co-expression networks of A. thaliana, Populus spp. and O. sativa using state-of-the-art methods based on mutual information and context likelihood of relatedness, and conducted a comprehensive comparison of these networks across a range of co-expression thresholds. In addition to quantifying gene-gene link and network neighbourhood conservation, we also applied recent advancements in network analysis to do cross-species comparisons of network properties such as scale free characteristics and gene centrality as well as network motifs. We found that in all species the networks emerged as scale free only above a certain co-expression threshold, and that the high-centrality genes upholding this organization tended to be conserved. Network motifs, in particular the feed-forward loop, were found to be significantly enriched in specific functional subnetworks but where much less conserved across species than gene centrality. Although individual gene-gene co-expression had massively diverged, up to ~80% of the genes still had a significantly conserved network neighbourhood. For genes with multiple predicted orthologs, about half had one ortholog with conserved regulation and another ortholog with diverged or non-conserved regulation. Furthermore, the most sequence similar ortholog was not the one with the most conserved gene regulation in over half of the cases. Conclusions We have provided a comprehensive analysis of gene regulation evolution in plants and built a web tool for Comparative analysis of Plant co-Expression networks (ComPlEx, http://complex.plantgenie.org/). The tool can be particularly useful for identifying the ortholog with the most conserved regulation among several sequence-similar alternatives and can thus be of practical importance in e.g. finding candidate genes for perturbation experiments.
Collapse
Affiliation(s)
| | | | | | - Torgeir R Hvidsten
- Umeå Plant Science Center, Department of Plant Physiology, Umeå University, Umeå, Sweden.
| |
Collapse
|
56
|
Hansen BO, Vaid N, Musialak-Lange M, Janowski M, Mutwil M. Elucidating gene function and function evolution through comparison of co-expression networks of plants. FRONTIERS IN PLANT SCIENCE 2014; 5:394. [PMID: 25191328 PMCID: PMC4137175 DOI: 10.3389/fpls.2014.00394] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2014] [Accepted: 07/23/2014] [Indexed: 05/20/2023]
Abstract
The analysis of gene expression data has shown that transcriptionally coordinated (co-expressed) genes are often functionally related, enabling scientists to use expression data in gene function prediction. This Focused Review discusses our original paper (Large-scale co-expression approach to dissect secondary cell wall formation across plant species, Frontiers in Plant Science 2:23). In this paper we applied cross-species analysis to co-expression networks of genes involved in cellulose biosynthesis. We showed that the co-expression networks from different species are highly similar, indicating that whole biological pathways are conserved across species. This finding has two important implications. First, the analysis can transfer gene function annotation from well-studied plants, such as Arabidopsis, to other, uncharacterized plant species. As the analysis finds genes that have similar sequence and similar expression pattern across different organisms, functionally equivalent genes can be identified. Second, since co-expression analyses are often noisy, a comparative analysis should have higher performance, as parts of co-expression networks that are conserved are more likely to be functionally relevant. In this Focused Review, we outline the comparative analysis done in the original paper and comment on the recent advances and approaches that allow comparative analyses of co-function networks. We hypothesize that in comparison to simple co-expression analysis, comparative analysis would yield more accurate gene function predictions. Finally, by combining comparative analysis with genomic information of green plants, we propose a possible composition of cellulose biosynthesis machinery during earlier stages of plant evolution.
Collapse
|
57
|
Porth I, Klapšte J, Skyba O, Hannemann J, McKown AD, Guy RD, DiFazio SP, Muchero W, Ranjan P, Tuskan GA, Friedmann MC, Ehlting J, Cronk QCB, El-Kassaby YA, Douglas CJ, Mansfield SD. Genome-wide association mapping for wood characteristics in Populus identifies an array of candidate single nucleotide polymorphisms. THE NEW PHYTOLOGIST 2013; 200:710-726. [PMID: 23889164 DOI: 10.1111/nph.12422] [Citation(s) in RCA: 84] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2013] [Accepted: 06/18/2013] [Indexed: 05/02/2023]
Abstract
Establishing links between phenotypes and molecular variants is of central importance to accelerate genetic improvement of economically important plant species. Our work represents the first genome-wide association study to the inherently complex and currently poorly understood genetic architecture of industrially relevant wood traits. Here, we employed an Illumina Infinium 34K single nucleotide polymorphism (SNP) genotyping array that generated 29,233 high-quality SNPs in c. 3500 broad-based candidate genes within a population of 334 unrelated Populus trichocarpa individuals to establish genome-wide associations. The analysis revealed 141 significant SNPs (α ≤ 0.05) associated with 16 wood chemistry/ultrastructure traits, individually explaining 3-7% of the phenotypic variance. A large set of associations (41% of all hits) occurred in candidate genes preselected for their suggested a priori involvement with secondary growth. For example, an allelic variant in the FRA8 ortholog explained 21% of the total genetic variance in fiber length, when the trait's heritability estimate was considered. The remaining associations identified SNPs in genes not previously implicated in wood or secondary wall formation. Our findings provide unique insights into wood trait architecture and support efforts for population improvement based on desirable allelic variants.
Collapse
Affiliation(s)
- Ilga Porth
- Department of Wood Science, University of British Columbia, Vancouver, BC, Canada, V6T 1Z4
| | - Jaroslav Klapšte
- Department of Forest and Conservation Sciences, University of British Columbia, Vancouver, BC, Canada, V6T 1Z4
- Department of Dendrology and Forest Tree Breeding, Faculty of Forestry and Wood Sciences, Czech University of Life Sciences, Prague, 165 21, Czech Republic
| | - Oleksandr Skyba
- Department of Wood Science, University of British Columbia, Vancouver, BC, Canada, V6T 1Z4
| | - Jan Hannemann
- Department of Biology and Centre for Forest Biology, University of Victoria, Victoria, BC, Canada, V8W 3N5
| | - Athena D McKown
- Department of Forest and Conservation Sciences, University of British Columbia, Vancouver, BC, Canada, V6T 1Z4
| | - Robert D Guy
- Department of Forest and Conservation Sciences, University of British Columbia, Vancouver, BC, Canada, V6T 1Z4
| | - Stephen P DiFazio
- Department of Biology, West Virginia University, Morgantown, WV, 26506-6057, USA
| | - Wellington Muchero
- BioSciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - Priya Ranjan
- BioSciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - Gerald A Tuskan
- BioSciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - Michael C Friedmann
- Department of Botany, University of British Columbia, Vancouver, BC, Canada, V6T 1Z4
| | - Juergen Ehlting
- Department of Biology and Centre for Forest Biology, University of Victoria, Victoria, BC, Canada, V8W 3N5
| | - Quentin C B Cronk
- Department of Botany, University of British Columbia, Vancouver, BC, Canada, V6T 1Z4
| | - Yousry A El-Kassaby
- Department of Forest and Conservation Sciences, University of British Columbia, Vancouver, BC, Canada, V6T 1Z4
| | - Carl J Douglas
- Department of Botany, University of British Columbia, Vancouver, BC, Canada, V6T 1Z4
| | - Shawn D Mansfield
- Department of Wood Science, University of British Columbia, Vancouver, BC, Canada, V6T 1Z4
| |
Collapse
|
58
|
Hirano K, Aya K, Morinaka Y, Nagamatsu S, Sato Y, Antonio BA, Namiki N, Nagamura Y, Matsuoka M. Survey of Genes Involved in Rice Secondary Cell Wall Formation Through a Co-Expression Network. ACTA ACUST UNITED AC 2013; 54:1803-21. [DOI: 10.1093/pcp/pct121] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
|
59
|
Higashi Y, Saito K. Network analysis for gene discovery in plant-specialized metabolism. PLANT, CELL & ENVIRONMENT 2013; 36:1597-606. [PMID: 23336321 DOI: 10.1111/pce.12069] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2012] [Revised: 01/07/2013] [Accepted: 01/09/2013] [Indexed: 05/03/2023]
Abstract
Recent omics technologies provide information on multiple components of biological networks. Web-based data mining tools are continuously being developed. Because genes involved in specialized (secondary) metabolism are often co-ordinately regulated at the transcriptional level, a number of gene discovery studies have been successfully conducted using network analysis, especially by integrating gene co-expression network analysis and metabolomic investigation. In addition, next-generation sequencing technologies are currently utilized in functional genomics investigations of Arabidopsis and non-model plant species including medicinal plants. Systems-based approaches are expected to gain importance in medicinal plant research. This review discussed network analysis in Arabidopsis and gene discovery in plant-specialized metabolism in non-model plants.
Collapse
Affiliation(s)
- Yasuhiro Higashi
- RIKEN Plant Science Center, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | | |
Collapse
|
60
|
Xu P, Kong Y, Li X, Li L. Identification of molecular processes needed for vascular formation through transcriptome analysis of different vascular systems. BMC Genomics 2013; 14:217. [PMID: 23548001 PMCID: PMC3620544 DOI: 10.1186/1471-2164-14-217] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2012] [Accepted: 03/22/2013] [Indexed: 11/24/2022] Open
Abstract
Background Vascular system formation has been studied through molecular and genetic approaches in Arabidopsis, a herbaceous dicot that is used as a model system. Different vascular systems have developed in other plants such as crops and trees. Uncovering shared mechanisms underlying vascular development by transcriptome analysis of different vascular systems may help to transfer knowledge acquired from Arabidopsis to other economically important species. Results Conserved vascular genes and biological processes fundamental to vascular development were explored across various plants. Through comparative transcriptome analysis, 226 genes from Arabidopsis, 217 genes from poplar and 281 genes from rice were identified as constituting 107 conserved vascular gene groups. These gene groups are expressed mainly in vascular tissues and form a complex coexpression network with multiple functional connections. To date, only half of the groups have been experimentally investigated. The conserved vascular gene groups were classified into 9 essential processes for vascular development. 18 groups (17%) lack of annotations were classified as having unknown functions. Conclusion The study provides a map of fundamental biological processes conserved across different vascular systems. It identifies gaps in the experimental investigation of pathways active in vascular formation, which if explored, could lead to a more complete understanding of vascular development.
Collapse
Affiliation(s)
- Peng Xu
- National Key Laboratory of Plant Molecular Genetics and Key Laboratory of Synthetic Biology, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, 300 Fenglin Rd, Shanghai 200032, China
| | | | | | | |
Collapse
|
61
|
Yang F, Mitra P, Zhang L, Prak L, Verhertbruggen Y, Kim JS, Sun L, Zheng K, Tang K, Auer M, Scheller HV, Loqué D. Engineering secondary cell wall deposition in plants. PLANT BIOTECHNOLOGY JOURNAL 2013; 11:325-35. [PMID: 23140549 PMCID: PMC3644865 DOI: 10.1111/pbi.12016] [Citation(s) in RCA: 131] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/25/2012] [Revised: 09/21/2012] [Accepted: 09/25/2012] [Indexed: 05/17/2023]
Abstract
Lignocellulosic biomass was used for thousands of years as animal feed and is now considered a great sugar source for biofuels production. It is composed mostly of secondary cell walls built with polysaccharide polymers that are embedded in lignin to reinforce the cell wall structure and maintain its integrity. Lignin is the primary material responsible for biomass recalcitrance to enzymatic hydrolysis. During plant development, deep reductions of lignin cause growth defects and often correlate with the loss of vessel integrity that adversely affects water and nutrient transport in plants. The work presented here describes a new approach to decrease lignin content while preventing vessel collapse and introduces a new strategy to boost transcription factor expression in native tissues. We used synthetic biology tools in Arabidopsis to rewire the secondary cell network by changing promoter-coding sequence associations. The result was a reduction in lignin and an increase in polysaccharide depositions in fibre cells. The promoter of a key lignin gene, C4H, was replaced by the vessel-specific promoter of transcription factor VND6. This rewired lignin biosynthesis specifically for vessel formation while disconnecting C4H expression from the fibre regulatory network. Secondly, the promoter of the IRX8 gene, secondary cell wall glycosyltransferase, was used to express a new copy of the fibre transcription factor NST1, and as the IRX8 promoter is induced by NST1, this also created an artificial positive feedback loop (APFL). The combination of strategies-lignin rewiring with APFL insertion-enhances polysaccharide deposition in stems without over-lignifying them, resulting in higher sugar yields after enzymatic hydrolysis.
Collapse
Affiliation(s)
- Fan Yang
- Joint BioEnergy Institute, Physical Biosciences Division, Lawrence Berkeley National LaboratoryOne Cyclotron Road, Berkeley, CA, USA
| | - Prajakta Mitra
- Joint BioEnergy Institute, Physical Biosciences Division, Lawrence Berkeley National LaboratoryOne Cyclotron Road, Berkeley, CA, USA
| | - Ling Zhang
- Joint BioEnergy Institute, Physical Biosciences Division, Lawrence Berkeley National LaboratoryOne Cyclotron Road, Berkeley, CA, USA
- FSN Plant Biotechnology R&D Centre, Shanghai Jiaotong UniversityShanghai, China
| | - Lina Prak
- Joint BioEnergy Institute, Physical Biosciences Division, Lawrence Berkeley National LaboratoryOne Cyclotron Road, Berkeley, CA, USA
| | - Yves Verhertbruggen
- Joint BioEnergy Institute, Physical Biosciences Division, Lawrence Berkeley National LaboratoryOne Cyclotron Road, Berkeley, CA, USA
| | - Jin-Sun Kim
- Joint BioEnergy Institute, Physical Biosciences Division, Lawrence Berkeley National LaboratoryOne Cyclotron Road, Berkeley, CA, USA
| | - Lan Sun
- Joint BioEnergy Institute, Physical Biosciences Division, Lawrence Berkeley National LaboratoryOne Cyclotron Road, Berkeley, CA, USA
| | - Kejian Zheng
- Joint BioEnergy Institute, Physical Biosciences Division, Lawrence Berkeley National LaboratoryOne Cyclotron Road, Berkeley, CA, USA
| | - Kexuan Tang
- FSN Plant Biotechnology R&D Centre, Shanghai Jiaotong UniversityShanghai, China
| | - Manfred Auer
- Joint BioEnergy Institute, Physical Biosciences Division, Lawrence Berkeley National LaboratoryOne Cyclotron Road, Berkeley, CA, USA
| | - Henrik V Scheller
- Joint BioEnergy Institute, Physical Biosciences Division, Lawrence Berkeley National LaboratoryOne Cyclotron Road, Berkeley, CA, USA
| | - Dominique Loqué
- Joint BioEnergy Institute, Physical Biosciences Division, Lawrence Berkeley National LaboratoryOne Cyclotron Road, Berkeley, CA, USA
- *Correspondence (fax 510 486 4252; email )
| |
Collapse
|
62
|
Valdivia ER, Herrera MT, Gianzo C, Fidalgo J, Revilla G, Zarra I, Sampedro J. Regulation of secondary wall synthesis and cell death by NAC transcription factors in the monocot Brachypodium distachyon. JOURNAL OF EXPERIMENTAL BOTANY 2013; 64:1333-43. [PMID: 23386682 PMCID: PMC3598421 DOI: 10.1093/jxb/ers394] [Citation(s) in RCA: 60] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
In several dicotyledonous species, NAC transcription factors act as master switches capable of turning on programmes of secondary cell-wall synthesis and cell death. This work used an oestradiol-inducible system to overexpress the NAC transcription factor BdSWN5 in the monocot model Brachypodium distachyon. This resulted in ectopic secondary cell-wall formation in both roots and shoots. Some of the genes upregulated in the process were a secondary cell-wall cellulose synthase (BdCESA4), a xylem-specific protease (BdXCP1) and an orthologue of AtMYB46 (BdMYB1). While activation of BdMYB1 may not be direct, this study showed that BdSWN5 is capable of transactivating the BdXCP1 promoter through two conserved binding sites. In the course of Brachypodium development, the BdXCP1 promoter was observed to be active in all types of differentiating tracheary elements. Together, these results suggest that Brachypodium SWNs can act as switches that turn on secondary cell-wall synthesis and programmed cell death.
Collapse
Affiliation(s)
- Elene R. Valdivia
- Dpto. Fisiología Vegetal, Facultad de Biología, Universidad de Santiago, Santiago de Compostela, 15782, Spain
| | - María Teresa Herrera
- Dpto. Fisiología Vegetal, Facultad de Biología, Universidad de Santiago, Santiago de Compostela, 15782, Spain
| | - Cristina Gianzo
- Dpto. Fisiología Vegetal, Facultad de Biología, Universidad de Santiago, Santiago de Compostela, 15782, Spain
| | - Javier Fidalgo
- Dpto. Fisiología Vegetal, Facultad de Biología, Universidad de Santiago, Santiago de Compostela, 15782, Spain
| | - Gloria Revilla
- Dpto. Fisiología Vegetal, Facultad de Biología, Universidad de Santiago, Santiago de Compostela, 15782, Spain
| | - Ignacio Zarra
- Dpto. Fisiología Vegetal, Facultad de Biología, Universidad de Santiago, Santiago de Compostela, 15782, Spain
| | - Javier Sampedro
- Dpto. Fisiología Vegetal, Facultad de Biología, Universidad de Santiago, Santiago de Compostela, 15782, Spain
| |
Collapse
|
63
|
Xie G, Yang B, Xu Z, Li F, Guo K, Zhang M, Wang L, Zou W, Wang Y, Peng L. Global identification of multiple OsGH9 family members and their involvement in cellulose crystallinity modification in rice. PLoS One 2013; 8:e50171. [PMID: 23308094 PMCID: PMC3537678 DOI: 10.1371/journal.pone.0050171] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2012] [Accepted: 10/22/2012] [Indexed: 11/19/2022] Open
Abstract
Plant glycoside hydrolase family 9 (GH9) comprises typical endo-β-1,4-glucanase (EGases, EC3.2.1.4). Although GH9A (KORRIGAN) family genes have been reported to be involved in cellulose biosynthesis in plants, much remains unknown about other GH9 subclasses. In this study, we observed a global gene co-expression profiling and conducted a correlation analysis between OsGH9 and OsCESA among 66 tissues covering most periods of life cycles in 2 rice varieties. Our results showed that OsGH9A3 and B5 possessed an extremely high co-expression with OsCESA1, 3, and 8 typical for cellulose biosynthesis in rice. Using two distinct rice non-GH9 mutants and wild type, we performed integrative analysis of gene expression level by qRT-PCR, cellulase activities in situ and in vitro, and lignocellulose crystallinity index (CrI) in four internodes of stem tissues. For the first time, OsGH9B1, 3, and 16 were characterized with the potential role in lignocellulose crystallinity alteration in rice, whereas OsGH9A3 and B5 were suggested for cellulose biosynthesis. In addition, phylogenetic analysis and gene co-expression comparison revealed GH9 function similarity in Arabidopsis and rice. Hence, the data can provide insights into GH9 function in plants and offer the potential strategy for genetic manipulation of plant cell wall using the five aforementioned novel OsGH9 genes.
Collapse
Affiliation(s)
- Guosheng Xie
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research (Wuhan), Biomass and Bioenergy Research Centre, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, People's Republic of China
| | - Bo Yang
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research (Wuhan), Biomass and Bioenergy Research Centre, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, People's Republic of China
| | - Zhengdan Xu
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research (Wuhan), Biomass and Bioenergy Research Centre, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, People's Republic of China
| | - Fengcheng Li
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research (Wuhan), Biomass and Bioenergy Research Centre, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, People's Republic of China
| | - Kai Guo
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research (Wuhan), Biomass and Bioenergy Research Centre, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, People's Republic of China
| | - Mingliang Zhang
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research (Wuhan), Biomass and Bioenergy Research Centre, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, People's Republic of China
| | - Lingqiang Wang
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research (Wuhan), Biomass and Bioenergy Research Centre, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, People's Republic of China
| | - Weihua Zou
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research (Wuhan), Biomass and Bioenergy Research Centre, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, People's Republic of China
| | - Yanting Wang
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research (Wuhan), Biomass and Bioenergy Research Centre, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, People's Republic of China
| | - Liangcai Peng
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research (Wuhan), Biomass and Bioenergy Research Centre, College of Plant Science and Technology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, People's Republic of China
- * E-mail:
| |
Collapse
|
64
|
Cassan-Wang H, Goué N, Saidi MN, Legay S, Sivadon P, Goffner D, Grima-Pettenati J. Identification of novel transcription factors regulating secondary cell wall formation in Arabidopsis. FRONTIERS IN PLANT SCIENCE 2013; 4:189. [PMID: 23781226 PMCID: PMC3677987 DOI: 10.3389/fpls.2013.00189] [Citation(s) in RCA: 62] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/27/2013] [Accepted: 05/23/2013] [Indexed: 05/17/2023]
Abstract
The presence of lignin in secondary cell walls (SCW) is a major factor preventing hydrolytic enzymes from gaining access to cellulose, thereby limiting the saccharification potential of plant biomass. To understand how lignification is regulated is a prerequisite for selecting plant biomass better adapted to bioethanol production. Because transcriptional regulation is a major mechanism controlling the expression of genes involved in lignin biosynthesis, our aim was to identify novel transcription factors (TFs) dictating lignin profiles in the model plant Arabidopsis. To this end, we have developed a post-genomic approach by combining four independent in-house SCW-related transcriptome datasets obtained from (1) the fiber cell wall-deficient wat1 Arabidopsis mutant, (2) Arabidopsis lines over-expressing either the master regulatory activator EgMYB2 or (3) the repressor EgMYB1 and finally (4) Arabidopsis orthologs of Eucalyptus xylem-expressed genes. This allowed us to identify 502 up- or down-regulated TFs. We preferentially selected those present in more than one dataset and further analyzed their in silico expression patterns as an additional selection criteria. This selection process led to 80 candidates. Notably, 16 of them were already proven to regulate SCW formation, thereby validating the overall strategy. Then, we phenotyped 43 corresponding mutant lines focusing on histological observations of xylem and interfascicular fibers. This phenotypic screen revealed six mutant lines exhibiting altered lignification patterns. Two of them [Bel-like HomeoBox6 (blh6) and a zinc finger TF] presented hypolignified SCW. Three others (myb52, myb-like TF, hb5) showed hyperlignified SCW whereas the last one (hb15) showed ectopic lignification. In addition, our meta-analyses highlighted a reservoir of new potential regulators adding to the gene network regulating SCW but also opening new avenues to ultimately improve SCW composition for biofuel production.
Collapse
Affiliation(s)
| | | | | | | | | | | | - Jacqueline Grima-Pettenati
- *Correspondence: Jacqueline Grima-Pettenati, Laboratoire de Recherche en Sciences Végétales, UMR5546, Centre National de la Recherche Scientifique, Université Toulouse III, UPS, 24 Chemin de Borde Rouge, BP 42617 Auzeville, 31326 Castanet-Tolosan, Toulouse, France e-mail:
| |
Collapse
|
65
|
Toubiana D, Fernie AR, Nikoloski Z, Fait A. Network analysis: tackling complex data to study plant metabolism. Trends Biotechnol 2012; 31:29-36. [PMID: 23245943 DOI: 10.1016/j.tibtech.2012.10.011] [Citation(s) in RCA: 75] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2012] [Revised: 10/18/2012] [Accepted: 10/24/2012] [Indexed: 11/18/2022]
Abstract
Incomplete knowledge of biochemical pathways makes the holistic description of plant metabolism a non-trivial undertaking. Sensitive analytical platforms, which are capable of accurately quantifying the levels of the various molecular entities of the cell, can assist in tackling this task. However, the ever-increasing amount of high-throughput data, often from multiple technologies, requires significant computational efforts for integrative analysis. Here we introduce the application of network analysis to study plant metabolism and describe the construction and analysis of correlation-based networks from (time-resolved) metabolomics data. By investigating the interactions between metabolites, network analysis can help to interpret complex datasets through the identification of key network components. The relationship between structural and biological roles of network components can be evaluated and employed to aid metabolic engineering.
Collapse
Affiliation(s)
- David Toubiana
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany
| | | | | | | |
Collapse
|
66
|
Han X, Chen C, Hyun TK, Kumar R, Kim JY. Metabolic module mining based on Independent Component Analysis in Arabidopsis thaliana. Mol Cells 2012; 34:295-304. [PMID: 22960738 PMCID: PMC3887838 DOI: 10.1007/s10059-012-0117-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2012] [Revised: 07/07/2012] [Accepted: 07/09/2012] [Indexed: 01/02/2023] Open
Abstract
Independent Component Analysis (ICA) has been introduced as one of the useful tools for gene-functional discovery in animals. However, this approach has been poorly utilized in the plant sciences. In the present study, we have exploited ICA combined with pathway enrichment analysis to address the statistical challenges associated with genome-wide analysis in plant system. To generate an Arabidopsis metabolic platform, we collected 4,373 Affy-metrix ATH1 microarray datasets. Out of the 3,232 metabolic genes and transcription factors, 99.47% of these genes were identified in at least one component, indicating the coverage of most of the metabolic pathways by the components. During the metabolic pathway enrichment analysis, we found components that indicate an independent regulation between the isoprenoid biosynthesis pathways. We also utilized this analysis tool to investigate some transcription factors involved in secondary cell wall biogenesis. This approach has identified remarkably more transcription factors compared to previously reported analysis tools. A website providing user-friendly searching and downloading of the entire dataset analyzed by ICA is available at http://kimjy.gnu.ac.kr/ICA.files/slide0002.htm . ICA combined with pathway enrichment analysis might provide a powerful approach for the extraction of the components responsible for a biological process of interest in plant systems.
Collapse
Affiliation(s)
- Xiao Han
- Division of Applied Life Science (Brain Korea 21-World Class University Program), Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju 660-701,
Korea
| | - Cong Chen
- Institute of Mitochondrial Biology and Medicine, The Key Laboratory of Biomedical Information Engineering of Ministry of Education, Xi’an Jiaotong University School of Life Science and Technology, Xi’an,
China
| | - Tae Kyung Hyun
- Division of Applied Life Science (Brain Korea 21-World Class University Program), Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju 660-701,
Korea
| | - Ritesh Kumar
- Division of Applied Life Science (Brain Korea 21-World Class University Program), Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju 660-701,
Korea
| | - Jae-Yean Kim
- Division of Applied Life Science (Brain Korea 21-World Class University Program), Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju 660-701,
Korea
| |
Collapse
|
67
|
4-O-methylation of glucuronic acid in Arabidopsis glucuronoxylan is catalyzed by a domain of unknown function family 579 protein. Proc Natl Acad Sci U S A 2012; 109:14253-8. [PMID: 22893684 DOI: 10.1073/pnas.1208097109] [Citation(s) in RCA: 121] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
The hemicellulose 4-O-methyl glucuronoxylan is one of the principle components present in the secondary cell walls of eudicotyledonous plants. However, the biochemical mechanisms leading to the formation of this polysaccharide and the effects of modulating its structure on the physical properties of the cell wall are poorly understood. We have identified and functionally characterized an Arabidopsis glucuronoxylan methyltransferase (GXMT) that catalyzes 4-O-methylation of the glucuronic acid substituents of this polysaccharide. AtGXMT1, which was previously classified as a domain of unknown function (DUF) 579 protein, specifically transfers the methyl group from S-adenosyl-L-methionine to O-4 of α-D-glucopyranosyluronic acid residues that are linked to O-2 of the xylan backbone. Biochemical characterization of the recombinant enzyme indicates that GXMT1 is localized in the Golgi apparatus and requires Co(2+) for optimal activity in vitro. Plants lacking GXMT1 synthesize glucuronoxylan in which the degree of 4-O-methylation is reduced by 75%. This result is correlated to a change in lignin monomer composition and an increase in glucuronoxylan release during hydrothermal treatment of secondary cell walls. We propose that the DUF579 proteins constitute a previously undescribed family of cation-dependent, polysaccharide-specific O-methyl-transferases. This knowledge provides new opportunities to selectively manipulate polysaccharide O-methylation and extends the portfolio of structural targets that can be modified either alone or in combination to modulate biopolymer interactions in the plant cell wall.
Collapse
|
68
|
Wang S, Yin Y, Ma Q, Tang X, Hao D, Xu Y. Genome-scale identification of cell-wall related genes in Arabidopsis based on co-expression network analysis. BMC PLANT BIOLOGY 2012; 12:138. [PMID: 22877077 PMCID: PMC3463447 DOI: 10.1186/1471-2229-12-138] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/14/2012] [Accepted: 07/30/2012] [Indexed: 05/21/2023]
Abstract
BACKGROUND Identification of the novel genes relevant to plant cell-wall (PCW) synthesis represents a highly important and challenging problem. Although substantial efforts have been invested into studying this problem, the vast majority of the PCW related genes remain unknown. RESULTS Here we present a computational study focused on identification of the novel PCW genes in Arabidopsis based on the co-expression analyses of transcriptomic data collected under 351 conditions, using a bi-clustering technique. Our analysis identified 217 highly co-expressed gene clusters (modules) under some experimental conditions, each containing at least one gene annotated as PCW related according to the Purdue Cell Wall Gene Families database. These co-expression modules cover 349 known/annotated PCW genes and 2,438 new candidates. For each candidate gene, we annotated the specific PCW synthesis stages in which it is involved and predicted the detailed function. In addition, for the co-expressed genes in each module, we predicted and analyzed their cis regulatory motifs in the promoters using our motif discovery pipeline, providing strong evidence that the genes in each co-expression module are transcriptionally co-regulated. From the all co-expression modules, we infer that 108 modules are related to four major PCW synthesis components, using three complementary methods. CONCLUSIONS We believe our approach and data presented here will be useful for further identification and characterization of PCW genes. All the predicted PCW genes, co-expression modules, motifs and their annotations are available at a web-based database: http://csbl.bmb.uga.edu/publications/materials/shanwang/CWRPdb/index.html.
Collapse
Affiliation(s)
- Shan Wang
- Computational Systems Biology Laboratory, Department of Biochemistry and Molecular Biology, and Institute of Bioinformatics, Athens, GA, USA
- Key Lab for Molecular Enzymology and Engineering of the Ministry of Education, Jilin University, Changchun, China
- Biotechnology Research Centre, Jilin Academy of Agricultural Sciences (JAAS), Changchun, China
| | - Yanbin Yin
- Computational Systems Biology Laboratory, Department of Biochemistry and Molecular Biology, and Institute of Bioinformatics, Athens, GA, USA
- BESC BioEerngy Science Center, University of Georgia, Athens, GA, USA
| | - Qin Ma
- Computational Systems Biology Laboratory, Department of Biochemistry and Molecular Biology, and Institute of Bioinformatics, Athens, GA, USA
- BESC BioEerngy Science Center, University of Georgia, Athens, GA, USA
| | - Xiaojia Tang
- Computational Systems Biology Laboratory, Department of Biochemistry and Molecular Biology, and Institute of Bioinformatics, Athens, GA, USA
| | - Dongyun Hao
- Key Lab for Molecular Enzymology and Engineering of the Ministry of Education, Jilin University, Changchun, China
- Biotechnology Research Centre, Jilin Academy of Agricultural Sciences (JAAS), Changchun, China
| | - Ying Xu
- Computational Systems Biology Laboratory, Department of Biochemistry and Molecular Biology, and Institute of Bioinformatics, Athens, GA, USA
- BESC BioEerngy Science Center, University of Georgia, Athens, GA, USA
- College of Computer Science and Technology, Jilin University, Changchun, China
| |
Collapse
|
69
|
Affiliation(s)
- Anett Doering
- Max-Planck-Institute for Molecular Plant Physiology, Potsdam, Germany
| | | | | |
Collapse
|
70
|
Handakumbura PP, Hazen SP. Transcriptional Regulation of Grass Secondary Cell Wall Biosynthesis: Playing Catch-Up with Arabidopsis thaliana. FRONTIERS IN PLANT SCIENCE 2012; 3:74. [PMID: 22639662 PMCID: PMC3355686 DOI: 10.3389/fpls.2012.00074] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2012] [Accepted: 03/31/2012] [Indexed: 05/17/2023]
Abstract
Secondary cell wall synthesis occurs in specialized cell types following completion of cell enlargement. By virtue of mechanical strength provided by a wall thickened with cellulose, hemicelluloses, and lignin, these cells can function as water-conducting vessels and provide structural support. Several transcription factor families regulate genes encoding wall synthesis enzymes. Certain NAC and MYB proteins directly bind to the SNBE and AC elements upstream of structural genes and other transcription factors. The most detailed model of this regulatory network is established predominantly for a eudicot, Arabidopsis thaliana. In grasses, both the patterning and the composition of secondary cell walls are distinct from that of eudicots. These differences suggest transcriptional regulation is similarly distinct. Putative rice and maize orthologs of several eudicot cell wall regulators genetically complement mutants of A. thaliana or result in wall defects when constitutively overexpressed; nevertheless, aside from a maize, ZmMYB31, and a switchgrass protein, PvMYB4, function has not been tested in a grass. Similar to the seminal work conducted in A. thaliana, gene expression profiling in maize, rice, and other grasses implicates additional genes as regulators. Characterization of these genes will continue to elucidate the relationship between the transcription regulatory networks of eudicots and grasses.
Collapse
Affiliation(s)
- Pubudu P. Handakumbura
- Biology Department, University of MassachusettsAmherst, MA, USA
- Plant Biology Graduate Program, University of MassachusettsAmherst, MA, USA
| | - Samuel P. Hazen
- Biology Department, University of MassachusettsAmherst, MA, USA
- *Correspondence: Samuel P. Hazen, Biology Department, University of Massachusetts, 221 Morrill Science Center, Amherst, MA 01003, USA. e-mail:
| |
Collapse
|
71
|
Tohge T, Fernie AR. Co-expression and co-responses: within and beyond transcription. FRONTIERS IN PLANT SCIENCE 2012; 3:248. [PMID: 23162560 PMCID: PMC3492870 DOI: 10.3389/fpls.2012.00248] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/25/2012] [Accepted: 10/20/2012] [Indexed: 05/04/2023]
Abstract
Whole genome sequencing, the relative ease of transcript profiling by the use of microarrays and latterly RNA sequencing approaches have facilitated the capture of vast amounts of transcript data. However, despite the enormous progress made in gene annotation a substantial proportion of genes remain to be annotated at the functional level. Considerable progress has, however, been made by searching for transcriptional coordination between genes of known function and non-annotated genes on the premise that such co-expressed genes tend to be functionally related. Here we review progress made following this approach as well as its expansion to include phenotypic information from other levels of cellular organization such as proteomic and metabolomic data as well as physiological and developmental phenotypes.
Collapse
Affiliation(s)
- Takayuki Tohge
- *Correspondence: Takayuki Tohge, Max-Planck-Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany. e-mail:
| | | |
Collapse
|
72
|
Ruprecht C, Persson S. Co-expression of cell-wall related genes: new tools and insights. FRONTIERS IN PLANT SCIENCE 2012; 3:83. [PMID: 22645599 PMCID: PMC3355730 DOI: 10.3389/fpls.2012.00083] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/29/2012] [Accepted: 04/13/2012] [Indexed: 05/02/2023]
Abstract
Global transcript analyses based on publicly available microarray dataset have revealed that genes with similar function tend to be transcriptionally coordinated. Indeed, many genes involved in the formation of cellulose, hemicelluloses, and lignin have been identified using co-expression approaches in Arabidopsis. To facilitate these transcript analyses, several web-based tools have been developed that allow researchers to investigate co-expression relationships of their gene(s) of interest. In addition, several tools now also provide the possibility of comparative transcriptional analyses across species, which potentially increases the predictive power. In this short review, we describe recent developments and updates of plant-related co-expression tools, and summarize studies that have successfully used expression profiling in cell wall research. Finally, we illustrate the value of comparative co-expression relationships across species using genes involved in lignin biosynthesis.
Collapse
Affiliation(s)
| | - Staffan Persson
- *Correspondence: Staffan Persson, Max Planck Institute of Molecular Plant Physiology, Am Muehlenberg 1, 14476 Potsdam-Golm, Germany. e-mail:
| |
Collapse
|
73
|
Fernie AR. Editorial overview - computational approaches in aid of advancing understanding in plant physiology. FRONTIERS IN PLANT SCIENCE 2011; 2:78. [PMID: 22639611 PMCID: PMC3355588 DOI: 10.3389/fpls.2011.00078] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2011] [Accepted: 10/26/2011] [Indexed: 06/01/2023]
|