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Identification of Photosynthesis-Associated C4 Candidate Genes through Comparative Leaf Gradient Transcriptome in Multiple Lineages of C3 and C4 Species
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86 genes are involved in the transition between C3 and C4 photosynthesis.
“As an example of the exploration of lists of a priori-defined candidate genes, we analyzed PAV of 86 genes shown to be involved in the transition between C3 and C4 photosynthesis (Ding et al., 2015), the latter permitting ecological dominance in arid climates and agricultural productivity under forecasted increased heat load of the next century.”
From GENESPACE tracks regions of interest and gene copy number variation across multiple genomes (2022) · cites this paper as Ding et al., 2015
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Improving photosynthetic efficiency for greater yield.
Zhu, X.-G., Long, S. P., & Ort, D. R. (2010) · Annual Review of Plant Biology · doi:10.1146/annurev-arplant-042809-112206 · Cited by 1,902
Divergence of human and mouse brain transcriptome highlights Alzheimer disease pathways
Miller, J. A., Horvath, S., & Geschwind, D. H. (2010) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0914257107 · Cited by 480
DiffCoEx: a simple and sensitive method to find differentially coexpressed gene modules
Tesson, B. M., Breitling, R., & Jansen, R. C. (2010) · BMC Bioinformatics · doi:10.1186/1471-2105-11-497 · Cited by 244
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Research works printed but not linked: 57
- JM Hibberd, 2008, Using C4 photosynthesis to increase the yield of rice—rationale and feasibility, Current opinion in plant biology, 11, 228, 10.1016/j.pbi.2007.11.002 · DOI
- P Mitchell, 2006, Supercharging rice photosynthesis to increase yield, New Phytologist, 171, 688, 10.1111/j.1469-8137.2006.01855.x · DOI
- RF Sage, 2004, The evolution of C4 photosynthesis, New phytologist, 161, 341, 10.1111/j.1469-8137.2004.00974.x · DOI
- C Peterhansel, 2011, Best practice procedures for the establishment of a C4 cycle in transgenic C3 plants, Journal of experimental botany, 62, 3011, 10.1093/jxb/err027 · DOI
- M Miyao, 2011, Lessons from engineering a single-cell C4 photosynthetic pathway into rice, Journal of experimental botany, 62, 3021, 10.1093/jxb/err023 · DOI
- K Kajala, 2011, Strategies for engineering a two-celled C4 photosynthetic pathway into rice, Journal of experimental botany, 62, 3001, 10.1093/jxb/err022 · DOI
- RF Sage, 2011, The C4 plant lineages of planet Earth, Journal of Experimental Botany, 62, 3155, 10.1093/jxb/err048 · DOI
- JM Hibberd, 2010, The regulation of gene expression required for C4 photosynthesis, Annual review of plant biology, 61, 181, 10.1146/annurev-arplant-042809-112238 · DOI
- S Aubry, 2011, The role of proteins in C3 plants prior to their recruitment into the C4 pathway, Journal of experimental botany, 62, 3049, 10.1093/jxb/err012 · DOI
- P-A Christin, 2013, Parallel recruitment of multiple genes into C4 photosynthesis, Genome biology and evolution, 5, 2174, 10.1093/gbe/evt168 · DOI
- PS Schnable, 2009, The B73 maize genome: complexity, diversity, and dynamics, science, 326, 1112, 10.1126/science.1178534 · DOI
- AH Paterson, 2009, The Sorghum bicolor genome and the diversification of grasses, Nature, 457, 551, 10.1038/nature07723 · DOI
- G Zhang, 2012, Genome sequence of foxtail millet (Setaria italica) provides insights into grass evolution and biofuel potential, Nature biotechnology, 30, 549, 10.1038/nbt.2195 · DOI
- JL Bennetzen, 2012, Reference genome sequence of the model plant Setaria, Nature biotechnology, 30, 555, 10.1038/nbt.2196 · DOI
- W Majeran, 2005, Functional differentiation of bundle sheath and mesophyll maize chloroplasts determined by comparative proteomics, The Plant Cell Online, 17, 3111, 10.1105/tpc.105.035519 · DOI
- W Majeran, 2008, Consequences of C4 differentiation for chloroplast membrane proteomes in maize mesophyll and bundle sheath cells, Molecular & Cellular Proteomics, 7, 1609, 10.1074/mcp.M800016-MCP200 · DOI
- G Friso, 2010, Reconstruction of metabolic pathways, protein expression, and homeostasis machineries across maize bundle sheath and mesophyll chloroplasts: large-scale quantitative proteomics using the first maize genome assembly, Plant physiology, 152, 1219, 10.1104/pp.109.152694 · DOI
- Y-M Chang, 2012, Characterizing regulatory and functional differentiation between maize mesophyll and bundle sheath cells by transcriptomic analysis, Plant physiology, 160, 165, 10.1104/pp.112.203810 · DOI
- SL Tausta, 2014, Developmental dynamics of Kranz cell transcriptional specificity in maize leaf reveals early onset of C4-related processes, Journal of experimental botany, eru152
- P Wang, 2013, Genome-wide transcript analysis of early maize leaf development reveals gene cohorts associated with the differentiation of C4 Kranz anatomy, The Plant Journal, 75, 656, 10.1111/tpj.12229 · DOI
- CR John, 2014, Evolutionary convergence of cell-specific gene expression in independent lineages of C4 grasses, Plant Physiol, 165, 62, 10.1104/pp.114.238667 · DOI
- Y Jiao, 2009, A transcriptome atlas of rice cell types uncovers cellular, functional and developmental hierarchies, Nature genetics, 41, 258, 10.1038/ng.282 · DOI
- P Li, 2010, The developmental dynamics of the maize leaf transcriptome, Nature genetics, 42, 1060, 10.1038/ng.703 · DOI
- TR Pick, 2011, Systems analysis of a maize leaf developmental gradient redefines the current C4 model and provides candidates for regulation, The Plant Cell Online, 23, 4208, 10.1105/tpc.111.090324 · DOI
- L Wang, 2014, Comparative analyses of C4 and C3 photosynthesis in developing leaves of maize and rice, Nature biotechnology
- A Bräutigam, 2008, Comparative proteomics of chloroplast envelopes from C3 and C4 plants reveals specific adaptations of the plastid envelope to C4 photosynthesis and candidate proteins required for maintaining C4 metabolite fluxes, Plant physiology, 148, 568, 10.1104/pp.108.121012 · DOI
- A Bräutigam, 2011, An mRNA blueprint for C4 photosynthesis derived from comparative transcriptomics of closely related C3 and C4 species, Plant Physiology, 155, 142, 10.1104/pp.110.159442 · DOI
- T Nelson, 2011, The grass leaf developmental gradient as a platform for a systems understanding of the anatomical specialization of C4 leaves, Journal of experimental botany, 62, 3039, 10.1093/jxb/err072 · DOI
- RF Sage, 2011, Exploiting the engine of C4 photosynthesis, Journal of Experimental Botany, 62, 2989, 10.1093/jxb/err179 · DOI
- B Usadel, 2009, Co-expression tools for plant biology: opportunities for hypothesis generation and caveats, Plant, cell & environment, 32, 1633, 10.1111/j.1365-3040.2009.02040.x · DOI
- BO Hansen, 2014, Elucidating gene function and function evolution through comparison of co-expression networks of plants, Frontiers in plant science, 5, 10.3389/fpls.2014.00394 · DOI
- P Langfelder, 2008, WGCNA: an R package for weighted correlation network analysis, BMC bioinformatics, 9, 559, 10.1186/1471-2105-9-559 · DOI · Paper page
- X Han, 2012, Co-expression Analysis Identifies CRC and AP1 the Regulator of Arabidopsis Fatty Acid Biosynthesis, Journal of integrative plant biology, 54, 486, 10.1111/j.1744-7909.2012.01132.x · DOI
- S Persson, 2005, Identification of genes required for cellulose synthesis by regression analysis of public microarray data sets, Proceedings of the National Academy of Sciences of the United States of America, 102, 8633, 10.1073/pnas.0503392102 · DOI
- SP Ficklin, 2010, The association of multiple interacting genes with specific phenotypes in rice using gene coexpression networks, Plant physiology, 154, 13, 10.1104/pp.110.159459 · DOI
- SP Ficklin, 2011, Gene coexpression network alignment and conservation of gene modules between two grass species: maize and rice, Plant Physiology, 156, 1244, 10.1104/pp.111.173047 · DOI
- C Trapnell, 2009, TopHat: discovering splice junctions with RNA-Seq, Bioinformatics, 25, 1105, 10.1093/bioinformatics/btp120 · DOI
- B Usadel, 2009, A guide to using MapMan to visualize and compare Omics data in plants: a case study in the crop species, Maize, Plant, cell & environment, 32, 1211, 10.1111/j.1365-3040.2009.01978.x · DOI
- JC Schnable, 2012, Genome-wide analysis of syntenic gene deletion in the grasses, Genome biology and evolution, 4, 265, 10.1093/gbe/evs009 · DOI
- S Aubry, 2014, Deep Evolutionary Comparison of Gene Expression Identifies Parallel Recruitment of Trans-Factors in Two Independent Origins of C4 Photosynthesis, PLoS genetics, 10, e1004365, 10.1371/journal.pgen.1004365 · DOI
- W Majeran, 2010, Structural and metabolic transitions of C4 leaf development and differentiation defined by microscopy and quantitative proteomics in maize, The Plant Cell Online, 22, 3509, 10.1105/tpc.110.079764 · DOI
- T Niittylä, 2006, Similar protein phosphatases control starch metabolism in plants and glycogen metabolism in mammals, Journal of Biological Chemistry, 281, 11815, 10.1074/jbc.M600519200 · DOI
- AM Smith, 2005, Starch degradation, Annu Rev Plant Biol, 56, 73, 10.1146/annurev.arplant.56.032604.144257 · DOI
- TL Slewinski, 2009, Sucrose transporter1 functions in phloem loading in maize leaves, Journal of Experimental Botany, 60, 881, 10.1093/jxb/ern335 · DOI
- M Bonke, 2003, APL regulates vascular tissue identity in Arabidopsis, Nature, 426, 181, 10.1038/nature02100 · DOI
- RK Monson, 2003, Gene duplication, neofunctionalization, and the evolution of C4 photosynthesis, International Journal of Plant Sciences, 164, S43, 10.1086/368400 · DOI
- X Wang, 2009, Comparative genomic analysis of C4 photosynthetic pathway evolution in grasses, Genome Biol, 10, R68, 10.1186/gb-2009-10-6-r68 · DOI
- DA Garfield, 2010, The evolution of gene regulatory interactions, BioScience, 60, 15, 10.1525/bio.2010.60.1.6 · DOI
- JM Ranz, 2006, Uncovering evolutionary patterns of gene expression using microarrays, Trends in Ecology & Evolution, 21, 29, 10.1016/j.tree.2005.09.002 · DOI
- MM Babu, 2006, Adaptive evolution by optimizing expression levels in different environments, Trends in microbiology, 14, 11, 10.1016/j.tim.2005.11.005 · DOI
- L López-Maury, 2008, Tuning gene expression to changing environments: from rapid responses to evolutionary adaptation, Nature Reviews Genetics, 9, 583, 10.1038/nrg2398 · DOI · Paper page
- W Yamori, 2014, Temperature response of photosynthesis in C3, C4, and CAM plants: temperature acclimation and temperature adaptation, Photosynthesis research, 119, 101, 10.1007/s11120-013-9874-6 · DOI
- J Sheen, 1991, Molecular mechanisms underlying the differential expression of maize pyruvate, orthophosphate dikinase genes, The Plant Cell Online, 3, 225, 10.1105/tpc.3.3.225 · DOI
- AJ Studer, 2014, A limited role for carbonic anhydrase in C4 photosynthesis as revealed by a ca1ca2 double mutant in maize, Plant physiology, 165, 608, 10.1104/pp.114.237602 · DOI
- Y Wang, 2014, Three distinct biochemical subtypes of C4 photosynthesis? A modelling analysis, Journal of experimental botany, eru058
- W Majeran, 2009, Cell-type-specific differentiation of chloroplasts in C4 plants, Trends in plant science, 14, 100, 10.1016/j.tplants.2008.11.006 · DOI
- AP Weber, 2010, Plastid transport and metabolism of C< sub> 3 and C< sub> 4 plants—comparative analysis and possible biotechnological exploitation, Current opinion in plant biology, 13, 256, 10.1016/j.pbi.2010.01.007 · DOI
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Sorted by citations
GENESPACE tracks regions of interest and gene copy number variation across multiple genomes
Lovell, J. T., Sreedasyam, A., Schranz, M. E., Wilson, M., Carlson, J. W., Harkess, A., Emms, D., Goodstein, D. M., & Schmutz, J. (2022) · eLife · doi:10.7554/elife.78526 · Cited by 391
Metadata
- Authors
- Ding, Z., Weissmann, S., Wang, M., Du, B., Huang, L., Wang, L., Tu, X., Zhong, S., Myers, C., Brutnell, T. P., Sun, Q., & Li, P.
- Venue
- PLOS ONE
- Publisher
- Public Library of Science (PLoS)
- Published
- 2015-10-14
- Volume
- 10
- Issue
- 10
- Pages
- e0140629
- ISSN
- 1932-6203
- PMC
- PMC4605685
- Cited by
- 55
- References
- 3
- Language
- en
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