Beyond Genomics: Studying Evolution with Gene Coexpression Networks

Trends in Plant Science

Volumn 22, Issue 4, 2017, Pages 298-307

  Ruprecht, Colin ^a   Vaid, Neha ^b   Proost, Sebastian ^b   Persson, Staffan ^c   Mutwil, Marek ^b  

^a MAX PLANCK INSTITUTE OF COLLOIDS AND INTERFACES   (Germany)

^b MAX PLANCK INSTITUTE OF MOLECULAR PLANT PHYSIOLOGY   (Germany)

^c UNIVERSITY OF MELBOURNE   (Australia)

Author keywords

[No Author keywords available]

Indexed keywords

EVOLUTION; GENE REGULATORY NETWORK; GENETICS; GENOMICS; MOLECULAR EVOLUTION; PHYLOGENY; PHYSIOLOGY; PROCEDURES;

BIOLOGICAL EVOLUTION; EVOLUTION, MOLECULAR; GENE REGULATORY NETWORKS; GENOMICS; PHYLOGENY;

EID: 85009997645     PISSN: 13601385     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.tplants.2016.12.011     Document Type: Review

References (88)

1. 1 Rensing, S.A., et al. The Physcomitrella genome reveals evolutionary insights into the conquest of land by plants. Science 319 (2008), 64–69.
2. 2 Merchant, S.S., et al. The Chlamydomonas genome reveals the evolution of key animal and plant functions. Science 318 (2010), 245–250.
3. 3 Chaney, L., et al. Genome mapping in plant comparative genomics. Trends Plant Sci. 21 (2016), 770–780.
4. 4 True, J.R., Carroll, S.B., Gene co-option in physiological and morphological evolution. Annu. Rev. Cell Dev. Biol. 18 (2002), 53–80.
5. 5 Zhong, R., et al. Evolutionary conservation of the transcriptional network regulating secondary cell wall biosynthesis. Trends Plant Sci. 15 (2010), 625–632.
6. 6 Banks, J.A., et al. The Selaginella genome identifies genetic changes associated with the evolution of vascular plants. Science 332 (2011), 960–963.
7. 7 Rhee, S.Y., Mutwil, M., Towards revealing the functions of all genes in plants. Trends Plant Sci. 19 (2014), 212–221.
8. 8 Radivojac, P., et al. A large-scale evaluation of computational protein function prediction. Nat. Methods 10 (2013), 221–227.
9. 9 Proost, S., Mutwil, M., Tools of the trade: studying molecular networks in plants. Curr. Opin. Plant Biol. 30 (2016), 130–140.
10. 10 Arabidopsis Interactome Mapping Consortium, Evidence for network evolution in an Arabidopsis interactome map. Science 333 (2011), 601–607.
11. 11 Movahedi, S., et al. Comparative co-expression analysis in plant biology. Plant Cell Environ. 35 (2012), 1787–1798.
12. 12 Lee, T., et al. AraNet v2: an improved database of co-functional gene networks for the study of Arabidopsis thaliana and 27 other nonmodel plant species. Nucleic Acids Res. 43 (2015), D996–D1002.
13. 13 Mutwil, M., et al. Assembly of an interactive correlation network for the Arabidopsis genome using a novel heuristic clustering algorithm. Plant Physiol. 152 (2010), 29–43.
14. 14 Stelzl, U., et al. A human protein-protein interaction network: a resource for annotating the proteome. Cell 122 (2005), 957–968.
15. 15 Maslov, S., Sneppen, K., Specificity and stability in topology of protein networks. Science 296 (2002), 910–913.
16. 16 Stuart, J.M., et al. A gene-coexpression network for global discovery of conserved genetic modules. Science 302 (2003), 249–255.
17. 17 Zarrineh, P., et al. Genome-scale co-expression network comparison across Escherichia coli and Salmonella enterica serovar Typhimurium reveals significant conservation at the regulon level of local regulators despite their dissimilar lifestyles. PLoS One, 9, 2014, e102871.
18. 18 Gerstein, M.B., et al. Comparative analysis of the transcriptome across distant species. Nature 512 (2014), 445–448.
19. 19 Mutwil, M., et al. PlaNet: combined sequence and expression comparisons across plant networks derived from seven species. Plant Cell 23 (2011), 895–910.
20. 20 Ruprecht, C., et al. Large-scale co-expression approach to dissect secondary cell wall formation across plant species. Front. Plant Sci. 2 (2011), 1–13.
21. 21 Tzfadia, O., et al. The MORPH algorithm: ranking candidate genes for membership in Arabidopsis and tomato pathways. Plant Cell 24 (2012), 4389–4406.
22. 22 Park, C.Y., et al. Functional knowledge transfer for high-accuracy prediction of under-studied biological processes. PLoS Comput. Biol., 9, 2013, e1002957.
23. 23 Ruprecht, C., et al. FamNet: a framework to identify multiplied modules driving pathway expansion in plants. Plant Physiol. 170 (2016), 1878–1894.
24. 24 Movahedi, S., et al. Comparative network analysis reveals that tissue specificity and gene function are important factors influencing the mode of expression evolution in Arabidopsis and rice. Plant Physiol. 156 (2011), 1316–1330.
25. 25 Ficklin, S.P., Feltus, F.A., Gene coexpression network alignment and conservation of gene modules between two grass species: maize and rice. Plant Physiol. 156 (2011), 1244–1256.
26. 26 Humphry, M., et al. A regulon conserved in monocot and dicot plants defines a functional module in antifungal plant immunity. Proc. Natl. Acad. Sci. U. S. A. 107 (2010), 21896–21901.
27. 27 Kuzniar, A., et al. The quest for orthologs: finding the corresponding gene across genomes. Trends Genet. 24 (2008), 539–551.
28. 28 Proost, S., et al. PLAZA: a comparative genomics resource to study gene and genome evolution in plants. Plant Cell 21 (2009), 3718–3731.
29. 29 Van Bel, M., et al. Dissecting plant genomes with the PLAZA comparative genomics platform. Plant Physiol. 158 (2012), 590–600.
30. 30 Patel, R.V., et al. BAR expressolog identification: expression profile similarity ranking of homologous genes in plant species. Plant J. 71 (2012), 1038–1050.
31. 31 Das, M., et al. Expression pattern similarities support the prediction of orthologs retaining common functions after gene duplication events. Plant Physiol. 171 (2016), 2343–2357.
32. 32 Hansen, B.O., et al. Elucidating gene function and function evolution through comparison of co-expression networks of plants. Front. Plant Sci. 5 (2014), 1–9.
33. 33 Aoki, Y., et al. ATTED-II in 2016: a plant coexpression database towards lineage-specific coexpression. Plant Cell Physiol., 57, 2015, e5.
34. 34 Tzfadia, O., et al. CoExpNetViz: comparative co-expression networks construction and visualization tool. Front. Plant Sci., 6, 2016, 1194.
35. 35 Yee, D., Goring, D.R., The diversity of plant U-box E3 ubiquitin ligases: from upstream activators to downstream target substrates. J. Exp. Bot. 60 (2009), 1109–1121.
36. 36 Bullard, J.H., et al. Polygenic and directional regulatory evolution across pathways in Saccharomyces. Proc. Natl. Acad. Sci. U. S. A. 107 (2010), 5058–5063.
37. 37 Roop, J.I., et al. Polygenic evolution of a sugar specialization trade-off in yeast. Nature 530 (2016), 336–339.
38. 38 Matsuno, M., et al. Evolution of a novel phenolic pathway for pollen development. Science 325 (2009), 1688–1692.
39. 39 Ehlting, J., et al. An extensive (co-)expression analysis tool for the cytochrome P450 superfamily in Arabidopsis thaliana. BMC Plant Biol., 8, 2008, 47.
40. 40 Domazet-Loso, T., et al. A phylostratigraphy approach to uncover the genomic history of major adaptations in metazoan lineages. Trends Genet. 23 (2007), 533–539.
41. 41 Geldner, N., et al. Auxin transport inhibitors block PIN1 cycling and vesicle trafficking. Nature 413 (2001), 425–428.
42. 42 Benková, E., et al. Local, efflux-dependent auxin gradients as a common module for plant organ formation. Cell 115 (2003), 591–602.
43. 43 Reinhardt, D., Auxin regulates the initiation and radial position of plant lateral organs. Plant Cell 12 (2000), 507–518.
44. 44 Petrasek, J., Friml, J., Auxin transport routes in plant development. Development 136 (2009), 2675–2688.
45. 45 Michniewicz, M., et al. Antagonistic regulation of PIN phosphorylation by PP2A and PINOID directs auxin flux. Cell 130 (2007), 1044–1056.
46. 46 Feraru, E., et al. Evolution and structural diversification of PILS putative auxin carriers in plants. Front. Plant Sci., 3, 2012, 227.
47. 47 Abel, S., Theologis, A., Early genes and auxin action. Plant Physiol. 111 (1996), 9–17.
48. 48 Ranocha, P., et al. Arabidopsis WAT1 is a vacuolar auxin transport facilitator required for auxin homoeostasis. Nat. Commun., 4, 2013, 2625.
49. 49 Ruzicka, K., et al. Arabidopsis PIS1 encodes the ABCG37 transporter of auxinic compounds including the auxin precursor indole-3-butyric acid. Proc. Natl. Acad. Sci. U. S. A. 107 (2010), 10749–10753.
50. 50 Emery, J.F., et al. Radial patterning of Arabidopsis shoots by class III HD-ZIP and KANADI genes. Curr. Biol. 13 (2003), 1768–1774.
51. 51 Dean, G., et al. KNAT6 gene of Arabidopsis is expressed in roots and is required for correct lateral root formation. Plant Mol. Biol. 54 (2004), 71–84.
52. 52 Berleth, T., et al. Vascular continuity and auxin signals. Trends Plant Sci. 5 (2000), 387–393.
53. 53 Ilegems, M., et al. Interplay of auxin, KANADI and class III HD-ZIP transcription factors in vascular tissue formation. Development 137 (2010), 975–984.
54. 54 Fisher, K., Turner, S., PXY, a receptor-like kinase essential for maintaining polarity during plant vascular-tissue development. Curr. Biol. 17 (2007), 1061–1066.
55. 55 Mähönen, A.P., et al. A novel two-component hybrid molecule regulates vascular morphogenesis of the Arabidopsis root. Genes Dev. 14 (2000), 2938–2943.
56. 56 Gursanscky, N.R., et al. MOL1 is required for cambium homeostasis in Arabidopsis. Plant J. 86 (2016), 210–220.
57. 57 Kakimoto, T., CKI1, a histidine kinase homolog implicated in cytokinin signal transduction. Science 274 (1996), 982–985.
58. 58 Zhang, Q.C., et al. Structure-based prediction of protein–protein interactions on a genome-wide scale. Nature 490 (2012), 556–560.
59. 59 Zhang, K., et al. Arabidopsis ABCG14 protein controls the acropetal translocation of root-synthesized cytokinins. Nat. Commun., 5, 2014, 3274.
60. 60 Lavy, M., et al. Constitutive auxin response in Physcomitrella reveals complex interactions between Aux/IAA and ARF proteins. Elife, 2016, 10.7554/elife.13325 Published online June 1, 2016.
61. 61 De Smet, R., Van de Peer, Y., Redundancy and rewiring of genetic networks following genome-wide duplication events. Curr. Opin. Plant Biol. 15 (2012), 168–176.
62. 62 Blanc, G., Wolfe, K.H., Widespread paleopolyploidy in model plant species inferred from age distributions of duplicate genes. Plant Cell 16 (2004), 1667–1678.
63. 63 Conant, G.C., Wolfe, K.H., Functional partitioning of yeast co-expression networks after genome duplication. PLoS Biol., 4, 2006, e109.
64. 64 Wapinski, I., et al. Natural history and evolutionary principles of gene duplication in fungi. Nature 449 (2007), 54–61.
65. 65 Pereira-Leal, J.B., Teichmann, S.A., Novel specificities emerge by stepwise duplication of functional modules. Genome Res. 15 (2005), 552–559.
66. 66 Papp, B., et al. Dosage sensitivity and the evolution of gene families in yeast. Nature 424 (2003), 194–197.
67. 67 Vanneste, K., et al. Inference of genome duplications from age distributions revisited. Mol. Biol. Evol. 30 (2013), 177–190.
68. 68 Price, D.C., et al. Cyanophora paradoxa genome elucidates origin of photosynthesis in algae and plants. Science 335 (2012), 843–847.
69. 69 Matsuzaki, M., et al. Genome sequence of the ultrasmall unicellular red alga Cyanidioschyzon merolae 10D. Nature 428 (2004), 653–657.
70. 70 Hori, K., et al. Klebsormidium flaccidum genome reveals primary factors for plant terrestrial adaptation. Nat. Commun., 5, 2014, 3978.
71. 71 Nystedt, B., et al. The Norway spruce genome sequence and conifer genome evolution. Nature 497 (2013), 579–584.
72. 72 Albert, V.A., et al. The Amborella genome and the evolution of flowering plants. Science, 342, 2013, 1241089.
73. 73 International Rice Genome Sequencing Project, The map-based sequence of the rice genome. Nature 436 (2005), 793–800.
74. 74 The Arabidopsis Genome Initiative, Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. Nature 408 (2000), 796–815.
75. 75 Linder, C.R., Rieseberg, L.H., Reconstructing patterns of reticulate evolution in plants. Am. J. Bot. 91 (2004), 1700–1708.
76. 76 Goodstein, D.M., et al. Phytozome: a comparative platform for green plant genomics. Nucleic Acids Res. 40 (2012), D1178–D1186.
77. 77 Conte, M.G., et al. GreenPhylDB: a database for plant comparative genomics. Nucleic Acids Res. 36 (2008), D991–D998.
78. 78 Duvick, J., et al. PlantGDB: a resource for comparative plant genomics. Nucleic Acids Res. 36 (2008), D959–D965.
79. 79 Usadel, B., et al. Co-expression tools for plant biology: opportunities for hypothesis generation and caveats. Plant Cell Environ. 32 (2009), 1633–1651.
80. 80 Serin, E.A.R., et al. Learning from co-expression networks: possibilities and challenges. Front. Plant Sci., 7, 2016, 444.
81. 81 Brown, D.M., et al. Identification of novel genes in Arabidopsis involved in secondary cell wall formation using expression profiling and reverse genetics. Plant Cell 17 (2005), 2281–2295.
82. 82 Persson, S., et al. Identification of genes required for cellulose synthesis by regression analysis of public microarray data sets. Proc. Natl. Acad. Sci. U. S. A. 102 (2005), 8633–8638.
83. 83 Maier, T., et al. Correlation of mRNA and protein in complex biological samples. FEBS Lett. 583 (2009), 3966–3973.
84. 84 Efroni, I., Birnbaum, K.D., The potential of single-cell profiling in plants. Genome Biol., 17, 2016, 65.
85. 85 Ogata, Y., et al. CoP: a database for characterizing co-expressed gene modules with biological information in plants. Bioinformatics 26 (2010), 1267–1268.
86. 86 Jupiter, D., et al. STARNET 2: a web-based tool for accelerating discovery of gene regulatory networks using microarray co-expression data. BMC Bioinformatics, 10, 2009, 332.
87. 87 Obayashi, T., et al. ATTED-II updates: condition-specific gene coexpression to extend coexpression analyses and applications to a broad range of flowering plants. Plant Cell Physiol. 52 (2011), 213–219.
88. 88 De Bodt, S., et al. CORNET 2. 0: integrating plant coexpression, protein-protein interactions, regulatory interactions, gene associations and functional annotations. New Phytol. 195 (2012), 707–720.