Tissue and cell-type co-expression networks of transcription factors and wood component genes in Populus trichocarpa

Planta

Volumn 245, Issue 5, 2017, Pages 927-938

  Shi, Rui ^a   Wang, Jack P ^a,b   Lin, Ying Chung ^a,b,c   Li, Quanzi ^d   Sun, Ying Hsuan ^e   Chen, Hao ^a   Sederoff, Ronald R ^a   Chiang, Vincent L ^a,b  

^a NORTH CAROLINA STATE UNIVERSITY   (United States)

^b NORTHEAST FORESTRY UNIVERSITY   (China)

^c NATIONAL TAIWAN UNIVERSITY   (Taiwan)

^d RESEARCH INSTITUTE OF FORESTRY   (China)

^e NATIONAL CHUNG HSING UNIVERSITY   (Taiwan)

Author keywords

Cell wall biosynthesis; Co expression network; Fiber cells; Transcriptome; Vessel elements; Wood formation

Indexed keywords

CELLULOSE; LIGNIN; PLANT PROTEIN; TRANSCRIPTION FACTOR; TRANSCRIPTOME;

ANTIBODY SPECIFICITY; CELL WALL; CLUSTER ANALYSIS; GENE EXPRESSION REGULATION; GENETICS; GROWTH, DEVELOPMENT AND AGING; METABOLISM; MOLECULAR GENETICS; PHLOEM; PLANT LEAF; POPULUS; SEQUENCE ANALYSIS; WOOD; XYLEM;

CELL WALL; CELLULOSE; CLUSTER ANALYSIS; GENE EXPRESSION REGULATION, PLANT; LIGNIN; MOLECULAR SEQUENCE ANNOTATION; ORGAN SPECIFICITY; PHLOEM; PLANT LEAVES; PLANT PROTEINS; POPULUS; SEQUENCE ANALYSIS, RNA; TRANSCRIPTION FACTORS; TRANSCRIPTOME; WOOD; XYLEM;

EID: 85009291513     PISSN: 00320935     EISSN: 14322048     Source Type: Journal    
DOI: 10.1007/s00425-016-2640-1     Document Type: Article

References (48)

1. Brady SM, Orlando DA, Lee JY, Wang JY, Koch J, Dinneny JR, Mace D, Ohler U, Benfey PN (2007) A high-resolution root spatiotemporal map reveals dominant expression patterns. Science 318:801–806
2. Cai B, Li CH, Huang J (2014) Systematic identification of cell wall related genes in Populus based on analysis of functional modules in co-expression network. PLoS One 9:e95176
3. Carlowicz M (2012) Seeing forests for the trees and the carbon: Mapping the world’s forests in three dimensions. Earth Observatory (NASA). http://earthobservatory.nasa.gov/Features/ForestCarbon
4. Carpita NC (2011) Update on mechanisms of plant cell wall biosynthesis: how plants make cellulose and other (1 → 4)-β-d-glycans. Plant Physiol 155:171–184
5. Chen HC, Song J, Wang JP, Lin YC, Ducoste J, Shuford CM, Liu J, Li Q, Shi R, Nepomuceno A, Isik F (2014a) Systems biology of lignin biosynthesis in Populus trichocarpa: heteromeric 4-coumaric acid: coenzyme A ligase protein complex formation, regulation, and numerical modeling. Plant Cell 26:876–893
6. Chen Y, Lun AT, Smyth GK (2014b) Differential expression analysis of complex RNA-seq experiments using edgeR. In: Datta S, Nettleton D (eds) Statistical analysis of next generation sequencing data. Springer International Publishing, Switzerland, pp 51–74
7. Chiang VL (2002) From rags to riches. Nat Biotechnol 20:557–558
8. Cline MS, Smoot M, Cerami E, Kuchinsky A, Landys N, Workman C, Christmas R, Avila-Campilo I, Creech M, Gross B, Hanspers K (2007) Integration of biological networks and gene expression data using Cytoscape. Nat Protoc 2:2366–2382
9. D’haeseleer P, Liang S, Somogyi R (2000) Genetic network inference: from co-expression clustering to reverse engineering. Bioinformatics 16:707–726
10. Esau K (1965) Vascular differentiation in plants. Holt Rinehart and Winston, New York
11. Evert RF (2006) Esau’s plant anatomy: meristems, cells, and tissues of the plant body: their structure, function, and development. Wiley, Hoboken
12. Guitart-Pla O, Kustagi M, Rügheimer F, Califano A, Schwikowski B (2015) The Cyni framework for network inference in Cytoscape. Bioinformatics 31:1499–1501
13. Kumar M, Thammannagowda S, Bulone V, Chiang V, Han KH, Joshi CP, Mansfield SD, Mellerowicz E, Sundberg B, Teeri T, Ellis BE (2009) An update on the nomenclature for the cellulose synthase genes in Populus. Trends Plant Sci 14:248–254
14. Larson PR (1994) The vascular cambium: development and structure. Springer, Berlin
15. Li Q, Lin YC, Sun YH, Song J, Chen H, Zhang XH, Sederoff RR, Chiang VL (2012) Splice variant of the SND1 transcription factor is a dominant negative of SND1 members and their regulation in Populus trichocarpa. Proc Natl Acad Sci USA 109:14699–14704
16. Li Q, Min D, Wang JP, Peszlen I, Horvath L, Horvath B, Nishimura Y, Jameel H, Chang HM, Chiang VL (2011) Down-regulation of glycosyltransferase 8D genes in Populus trichocarpa caused reduced mechanical strength and xylan content in wood. Tree Physiol 31:226–236
17. Lin YC, Li W, Sun YH, Kumari S, Wei H, Li Q, Tunlaya-Anukit S, Sederoff RR, Chiang VL (2013) SND1 transcription factor-directed quantitative functional hierarchical genetic regulatory network in wood formation in Populus trichocarpa. Plant Cell 25:4324–4341
18. Liu L, Filkov V, Groover A (2014a) Modeling transcriptional networks regulating secondary growth and wood formation in forest trees. Physiol Plant 151:156–163
19. Liu Y, Zhou J, White KP (2014b) RNA-seq differential expression studies: more sequence or more replication? Bioinformatics 30:301–304
20. Lu S, Li Q, Wei H, Chang MJ, Tunlaya-Anukit S, Kim H, Liu J, Song J, Sun YH, Yuan L, Yeh TF (2013) Ptr-miR397a is a negative regulator of laccase genes affecting lignin content in Populus trichocarpa. Proc Natl Acad Sci USA 110:10848–10853
21. McCarthy DJ, Chen Y, Smyth GK (2012) Differential expression analysis of multifactor RNA-Seq experiments with respect to biological variation. Nucl Acids Res 40:4288–4297
22. Merkle SA, Dean JF (2000) Forest tree biotechnology. Curr Opin Biotechnol 11:298–302
23. Netotea S, Sundell D, Street NR, Hvidsten TR (2014) ComPlEx: conservation and divergence of co-expression networks in A. thaliana, Populus and O. sativa. BMC Genom 15:1
24. Perlin J (2005) A forest journey: the story of wood and civilization. The Countryman Press, Woodstock
25. Quinlan AR, Hall IM (2010) BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics 26:841–884
26. Ragauskas AJ, Nagy M, Kim DH, Eckert CA, Hallett JP, Liotta CL (2006) From wood to fuels: integrating biofuels and pulp production. Ind Biotechnol 2:55–65
27. Rehfuess E, Mehta S, Prüss-Üstün A (2006) Assessing household solid fuel use: multiple implications for the Millennium development goals. Environ Health Perspect 114:373–378
28. Reimand J, Arak T, Vilo J (2011) g:Profiler–a web server for functional interpretation of gene lists (2011 update). Nucl Acids Res 39:W307–W315
29. Robinson MD, Oshlack A (2010) A scaling normalization method for differential expression analysis of RNA-seq data. Genome Biol 11:R25
30. Sarkanen KV (1976) Renewable resources for the production of fuels and chemicals. Science 191:428
31. Shannon P, Markiel A, Ozier O, Baliga NS, Wang JT, Ramage D, Amin N, Schwikowski B, Ideker T (2003) Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Res 13:2498–2504
32. Shi R, Sun Y, Li Q, Heber S, Sederoff RR, Chiang VL (2010) Towards a systems approach for lignin biosynthesis in Populus trichocarpa: transcript abundance and specificity of the monolignol biosynthetic genes. Plant Cell Physiol 51:144–163
33. Shi R, Shuford CM, Wang JP, Sun YH, Yang Z, Chen HC, Tunlaya-Anukit S, Li Q, Liu J, Muddiman DC, Sederoff RR (2013) Regulation of phenylalanine ammonia-lyase (PAL) gene family in wood forming tissue of Populus trichocarpa. Planta 238:487–497
34. Song J, Lu S, Chen ZZ, Lourenco R, Chiang VL (2006) Genetic transformation of Populus trichocarpa genotype Nisqually-1: a functional genomic tool for woody plants. Plant Cell Physiol 47:1582–1589
35. Street NR, Jansson S, Hvidsten TR (2011) A systems biology model of the regulatory network in Populus leaves reveals interacting regulators and conserved regulation. BMC Plant Biol 11:13
36. Stuart JM, Segal E, Koller D, Kim SK (2003) A gene-coexpression network for global discovery of conserved genetic modules. Science 302:249–255
37. Suzuki S, Li L, Sun YH, Chiang VL (2006) The cellulose synthase gene superfamily and biochemical functions of xylem-specific cellulose synthase-like genes in Populus trichocarpa. Plant Physiol 142:1233–1245
38. Taylor-Teeples M, Lin L, de Lucas M, Turco G, Toal TW, Gaudinier A, Young NF, Trabucco GM, Veling MT, Lamothe R, Handakumbura PP (2015) An Arabidopsis gene regulatory network for secondary cell wall synthesis. Nature 517:571–575
39. Trapnell C, Pachter L, Salzberg SL (2009) TopHat: discovering splice junctions with RNA-Seq. Bioinformatics 25:1105–1111
40. Van Dongen S, Abreu-Goodger C (2012) Using MCL to extract clusters from networks. In: van Helden J, Toussaint A, Thieffry D (eds) Bacterial molecular networks: methods and protocols. Springer, New York, pp p281–p295
41. Vanholme R, Cesarino I, Rataj K, Xiao Y, Sundin L, Goeminne G, Kim H, Cross J, Morreel K, Araujo P, Welsh L (2013) Caffeoyl shikimate esterase (CSE) is an enzyme in the lignin biosynthetic pathway in Arabidopsis. Science 341:1103–1106
42. Vitousek PM, Mooney HA, Lubchenco J, Melillo JM (1997) Human domination of earth’s ecosystems. Science 277:494–499
43. Wang JP, Chuang L, Loziuk PL, Chen H, Lin YC, Shi R, Qu GZ, Muddiman DC, Sederoff RR, Chiang VL (2015) Phosphorylation is an on/off switch for 5-hydroxyconiferaldehyde O-methyltransferase activity in poplar monolignol biosynthesis. Proc Natl Acad Sci USA 112:8481–8486
44. Wang JP, Naik PP, Chen HC, Shi R, Lin CY, Liu J, Shuford CM, Li Q, Sun YH, Tunlaya-Anukit S, Williams CM, Muddiman DC, Ducoste JJ, Sederoff RR, Chiang VL (2014) Complete proteomic based enzyme reaction and inhibition kinetics reveal how monolignol biosynthetic enzyme families affect metabolic-flux and lignin. Plant Cell 26:894–914
45. Weirauch MT (2011) Gene coexpression networks for the analysis of DNA microarray data. In: Dehmer M, Emmert-Streib F, Graber A, Salvador A (eds) Applied statistics for network biology: methods in systems biology. Wiley, Hoboken, pp 215–250
46. Yang X, Ye CY, Bisaria A, Tuskan GA, Kalluri UC (2011) Identification of candidate genes in Arabidopsis and Populus cell wall biosynthesis using text-mining, co-expression network analysis and comparative genomics. Plant Sci 181:675–687
47. Zheng X, Moriyama EN (2013) Comparative studies of differential gene calling using RNA-Seq data. BMC Bioinform 14:S7
48. Zhong R, Ye ZH (2014) Complexity of the transcriptional network controlling secondary wall biosynthesis. Plant Sci 229:193–207