Cited by 55

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Identification of Photosynthesis-Associated C4 Candidate Genes through Comparative Leaf Gradient Transcriptome in Multiple Lineages of C3 and C4 Species

Ding, Zehong, Weissmann, Sarit, Wang, Minghui, Du, Baijuan, Huang, Lei, Wang, Lin, Tu, Xiaoyu, Zhong, Silin, Myers, Christopher, Brutnell, Thomas P., Sun, Qi, Li, Pinghua·2015·PLOS ONE

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Crossref · 10.1371/journal.pone.0140629

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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.”

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Research works printed but not linked: 57

  1. 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
  2. P Mitchell, 2006, Supercharging rice photosynthesis to increase yield, New Phytologist, 171, 688, 10.1111/j.1469-8137.2006.01855.x · DOI
  3. RF Sage, 2004, The evolution of C4 photosynthesis, New phytologist, 161, 341, 10.1111/j.1469-8137.2004.00974.x · DOI
  4. 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
  5. 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
  6. 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
  7. RF Sage, 2011, The C4 plant lineages of planet Earth, Journal of Experimental Botany, 62, 3155, 10.1093/jxb/err048 · DOI
  8. 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
  9. 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
  10. P-A Christin, 2013, Parallel recruitment of multiple genes into C4 photosynthesis, Genome biology and evolution, 5, 2174, 10.1093/gbe/evt168 · DOI
  11. PS Schnable, 2009, The B73 maize genome: complexity, diversity, and dynamics, science, 326, 1112, 10.1126/science.1178534 · DOI
  12. AH Paterson, 2009, The Sorghum bicolor genome and the diversification of grasses, Nature, 457, 551, 10.1038/nature07723 · DOI
  13. 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
  14. JL Bennetzen, 2012, Reference genome sequence of the model plant Setaria, Nature biotechnology, 30, 555, 10.1038/nbt.2196 · DOI
  15. 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
  16. 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
  17. 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
  18. 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
  19. 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
  20. 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
  21. 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
  22. 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
  23. P Li, 2010, The developmental dynamics of the maize leaf transcriptome, Nature genetics, 42, 1060, 10.1038/ng.703 · DOI
  24. 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
  25. L Wang, 2014, Comparative analyses of C4 and C3 photosynthesis in developing leaves of maize and rice, Nature biotechnology
  26. 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
  27. 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
  28. 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
  29. RF Sage, 2011, Exploiting the engine of C4 photosynthesis, Journal of Experimental Botany, 62, 2989, 10.1093/jxb/err179 · DOI
  30. 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
  31. 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
  32. 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
  33. 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
  34. 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
  35. 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
  36. 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
  37. C Trapnell, 2009, TopHat: discovering splice junctions with RNA-Seq, Bioinformatics, 25, 1105, 10.1093/bioinformatics/btp120 · DOI
  38. 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
  39. JC Schnable, 2012, Genome-wide analysis of syntenic gene deletion in the grasses, Genome biology and evolution, 4, 265, 10.1093/gbe/evs009 · DOI
  40. 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
  41. 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
  42. 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
  43. AM Smith, 2005, Starch degradation, Annu Rev Plant Biol, 56, 73, 10.1146/annurev.arplant.56.032604.144257 · DOI
  44. TL Slewinski, 2009, Sucrose transporter1 functions in phloem loading in maize leaves, Journal of Experimental Botany, 60, 881, 10.1093/jxb/ern335 · DOI
  45. M Bonke, 2003, APL regulates vascular tissue identity in Arabidopsis, Nature, 426, 181, 10.1038/nature02100 · DOI
  46. RK Monson, 2003, Gene duplication, neofunctionalization, and the evolution of C4 photosynthesis, International Journal of Plant Sciences, 164, S43, 10.1086/368400 · DOI
  47. 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
  48. DA Garfield, 2010, The evolution of gene regulatory interactions, BioScience, 60, 15, 10.1525/bio.2010.60.1.6 · DOI
  49. 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
  50. 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
  51. 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
  52. 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
  53. 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
  54. 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
  55. Y Wang, 2014, Three distinct biochemical subtypes of C4 photosynthesis? A modelling analysis, Journal of experimental botany, eru058
  56. 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
  57. 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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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
Published
2015-10-14
Volume
10
Issue
10
Pages
e0140629
ISSN
1932-6203
Cited by
55
References
3
Language
en

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