Conservation and divergence of gene expression plasticity following c. 140 million years of evolution in lodgepole pine (Pinus contorta) and interior spruce (Picea glauca × Picea engelmannii)

New Phytologist

Volumn 203, Issue 2, 2014, Pages 578-591

  Yeaman, Sam ^a   Hodgins, Kathryn A ^a,b   Suren, Haktan ^c   Nurkowski, Kristin A ^a   Rieseberg, Loren H ^a   Holliday, Jason A ^c   Aitken, Sally N ^a  

^a UNIVERSITY OF BRITISH COLUMBIA   (Canada)

^b MONASH UNIVERSITY   (Australia)

^c VIRGINIA POLYTECHNIC INSTITUTE AND STATE UNIVERSITY   (United States)

Author keywords

Climate; Divergence; Engelmann spruce; Gene expression; Lodgepole pine; Plasticity; RNAseq; White spruce

Indexed keywords

ADAPTATION; CONIFEROUS TREE; DIVERGENCE; ENVIRONMENTAL STRESS; GENE EXPRESSION; NATURAL SELECTION; PHENOTYPIC PLASTICITY; PHYSIOLOGICAL RESPONSE; TEMPERATURE EFFECT;

PICEA; PICEA ENGELMANNII; PICEA GLAUCA; PINUS CONTORTA;

ACCLIMATIZATION; EVOLUTION; GENE EXPRESSION REGULATION; GENE ONTOLOGY; GENETICS; PHYSIOLOGY; PINE; SEEDLING; SPRUCE;

ACCLIMATIZATION; BIOLOGICAL EVOLUTION; GENE EXPRESSION REGULATION, PLANT; GENE ONTOLOGY; PICEA; PINUS; SEEDLING;

EID: 84902547739     PISSN: 0028646X     EISSN: 14698137     Source Type: Journal    
DOI: 10.1111/nph.12819     Document Type: Article

References (61)

1. Aitken SN, Yeaman S, Holliday JA, Wang T, Curtis-McLane S. 2008. Adaptation, migration or extirpation: climate change outcomes for tree populations. Evolutionary Applications 1: 95-111.
2. Alberto F, Aitken S, Alia R, González-Martínez S, Hanninen H, Kremer A, Lefèvre F, Lenormand T, Yeaman S, Whetten R et al. 2013. Potential for evolutionary response to climate change - evidence from tree populations. Global Change Biology 19: 1645-1661.
3. Allen CD, Macalady AK, Chenchouni H, Bachelet D, Mcdowell N, Vennetier M, Kitzberger T, Rigling A, Breshears DD, Hogg EHT et al. 2010. A global overview of drought and heat-induced tree mortality reveals emerging climate change risks for forests. Forest Ecology and Management 259: 660-684.
4. Beaulieu J, Giguère I, Deslauriers M, Boyle B, MacKay J. 2013. Differential gene expression patterns in white spruce newly formed tissue on board the International Space Station. Advances in Space Research 52: 760-772.
5. Birol I, Raymond A, Jackman SD, Pleasance S, Coope R, Taylor GA, Yuen MM, Keeling CI, Brand D, Vandervalk BP et al. 2013. Assembling the 20 Gb white spruce (Picea glauca) genome from whole-genome shotgun sequencing data. Bioinformatics 29: 1492-1497.
6. Bonan GB. 2008. Forests and climate change: forcings, feedbacks, and the climate benefits of forests. Science 320: 1444-1449.
7. De La Torre AR, Wang T, Jaquish B, Aitken SN. 2014. Adaptation and exogenous selection in a Picea glauca × Picea engelmannii hybrid zone: implications for forest management under climate change. New Phytologist 201: 687-699.
8. Eckert AJ, Shahi H, Datwyler SL, Neale DB. 2012. Spatially variable natural selection and the divergence between parapatric subspecies of lodgepole pine (Pinus contorta, Pinaceae). American Journal of Botany 99: 1323-1334.
9. Ekblom R, Galindo J. 2010. Applications of next generation sequencing in molecular ecology of non-model organisms. Heredity 107: 1-15.
10. El Kayal W, Allen CCG, Ju CJT, Adams E, King-Jones S, Zaharia LI, Abrams SR, Cooke JE. 2011. Molecular events of apical bud formation in white spruce, Picea glauca. Plant, Cell & Environment 34: 480-500.
11. Ewers BE, Gower ST, Bond-Lamberty B, Wang CK. 2005. Effects of stand age and tree species on canopy transpiration and average stomatal conductance of boreal forests. Plant, Cell & Environment 28: 660-678.
12. Franks S, Webber J, Aitken SN. 2013. Evolutionary and plastic responses to climate change in terrestrial plant populations. Evolutionary Applications 7: 123-139.
13. Grabherr MG, Haas BJ, Yassour M, Levin JZ, Thompson DA, Amit I, Adiconis X, Fan L, Raychowdhury R, Zeng Q et al. 2011. Full-length transcriptome assembly from RNA-seq data without a reference genome. Nature Biotechnology 29: 644-652.
14. Guan Y, Dunham MJ, Troyanskaya OG, Caudy AA. 2013. Comparative gene expression between two yeast species. BMC Genomics 14: 33.
15. Hamann A, Aitken SN. 2013. Conservation planning under climate change: accounting for adaptive potential and migration capacity in species distribution models. Diversity and Distributions 19: 268-280.
16. Hodgins KA, Lai Z, Oliveira LO, Still DW, Scascitelli M, Barker MS, Kane NC, Dempewolf H, Kozik A, Kesseli RV et al. 2014. Genomics of Compositae crops: reference transcriptome assemblies and evidence of hybridization with wild relatives. Molecular Ecology Resources 14: 166-177.
17. Hogg EH, Brandt JP, Michaelian M. 2008. Impacts of a regional drought on the productivity, dieback, and biomass of western Canadian aspen forests. Canadian Journal of Forest Research 38: 1373-1384.
18. Holliday JA, Ralph SG, White R, Bohlmann J, Aitken SN. 2008. Global monitoring of autumn gene expression within and among phenotypically divergent populations of Sitka spruce (Picea sitchensis). New Phytologist 178: 103-122.
19. IPCC. 2007. Climate change 2007: the physical science basis. Contribution of Working Group I to the fourth assessment report of the Intergovernmental Panel on Climate Change. Cambridge, UK and New York, NY, USA: Cambridge University Press.
20. Jiao Y, Ma L, Strickland E, Deng XW. 2005. Conservation and divergence of light-regulated genome expression patterns during seedling development in rice and Arabidopsis. Plant Cell 17: 3239-3256.
21. Joosen RVL, Lammers M, Balk PA, Bronnum P, Konings M, Perks M, Stattin E, van Wordragen MF, van der Geest AL. 2006. Correlating gene expression to physiological parameters and environmental conditions during cold acclimation of Pinus sylvestris, identification of molecular markers using cDNA microarrays. Tree Physiology 26: 1297-1313.
22. Kolosova N, Miller B, Ralph S, Ellis BE, Douglas C, Ritland K, Bohlmann J. 2004. Isolation of high-quality RNA from gymnosperm and angiosperm trees. BioTechniques 36: 821-824.
23. Kreps JA, Wu Y, Chang H, Zhu T, Wang X, Harper JF, Mesa T, Row M, Diego S, California JAK et al. 2002. Transcriptome changes for Arabidopsis in response to salt, osmotic, and cold stress. Plant Physiology 130: 2129-2141.
24. Lai Z, Kane NC, Kozik A, Hodgins KA, Dlugosch KM, Barker MS, Matvienko M, Yu Q, Turner KG, Pearl SA et al. 2012. Genomics of Compositae weeds: EST libraries, microarrays, and evidence of introgression. American Journal of Botany 99: 1-10.
25. Langfelder P, Horvath S. 2008. WGCNA: an R package for weighted correlation network analysis. BMC Bioinformatics 9: 559.
26. Li B, Dewey CN. 2011. RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome. BMC Bioinformatics 12: 323.
27. Li L, Stoeckert CJ, Roos DS. 2003. OrthoMCL: identification of ortholog groups for eukaryotic genomes. Genome Research 13: 2178-2189.
28. Liu Q, Kasuga M, Sakuma Y, Abe H, Miura S, Yamaguchi-Shinozaki K, Shinozaki K. 1998. Two transcription factors, DREB1 and DREB2, with an EREBP/AP2 DNA binding domain separate two cellular signal transduction pathways in drought- and low-temperature-responsive gene expression, respectively, in Arabidopsis. Plant Cell 10: 1391-1406.
29. Ma L, Chen C, Liu X, Jiao Y, Su N, Li L, Wang X, Cao M, Sun N, Zhang X et al. 2005. A microarray analysis of the rice transcriptome and its comparison to Arabidopsis. Genome Research 15: 1274-1283.
30. Mbogga MS, Hamann A, Wang T. 2009. Historical and projected climate data for natural resource management in western Canada. Agricultural and Forest Meteorology 149: 881-890.
31. Movahedi S, Van Bel M, Heyndrickx KS, Vandepoele K. 2012. Comparative co-expression analysis in plant biology. Plant, Cell & Environment 35: 1787-1798.
32. Namroud M-C, Beaulieu J, Juge N, Laroche J, Bousquet J. 2008. Scanning the genome for gene single nucleotide polymorphisms involved in adaptive population differentiation in white spruce. Molecular Ecology 17: 3599-3613.
33. Parchman TL, Gompert Z, Mudge J, Schilkey FD, Benkman CW, Buerkle CA. 2012. Genome-wide association genetics of an adaptive trait in lodgepole pine. Molecular Ecology 21: 2991-3005.
34. Porth I, White R, Jaquish B, Alfaro R, Ritland C, Ritland K. 2012. Genetical genomics identifies the genetic architecture for growth and weevil resistance in spruce. PLoS One 7: e44397.
35. Qin D, Wu H, Peng H, Yao Y, Ni Z, Li Z, Zhou C, Sun Q. 2008. Heat stress-responsive transcriptome analysis in heat susceptible and tolerant wheat (Triticum aestivum L.) by using Wheat Genome Array. BMC Genomics 9: 432.
36. Raherison E, Rigault P, Caron S, Poulin P-L, Boyle B, Verta J-P, Giguère I, Bomal C, Bohlmann J, MacKay J. 2013. Transcriptome profiling in conifers and the PiceaGenExpress database show patterns of diversification within gene families and interspecific conservation in vascular gene expression. BMC Genomics 13: 434.
37. Rehfeldt GE, Wykoff WR, Ying CC. 2001. Physiologic plasticity, evolution, and impacts of a changing climate on Pinus contorta. Climatic Change 50: 355-376.
38. Rehfeldt GE, Ying CC, Spittlehouse DL, Hamilton DA Jr. 1999. Genetic responses to climate in Pinus contorta: niche breadth, climate change, and reforestation. Ecological Monographs 59: 375-407.
39. Reid KE, Holliday JA, Yuen M, Nguyen A, Aitken SN, Bohlmann J. 2013. Sequencing of Sitka spruce (Picea sitchensis) cDNA libraries constructed from autumn buds and foliage reveals autumn-specific spruce transcripts. Tree Genetics & Genomes 9: 683-691.
40. Robinson MD, McCarthy DJ, Smyth GK. 2010. edgeR: a Bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics 26: 139-140.
41. Roche L. 1969. A genecological study of the genus Picea in British Columbia. New Phytologist 68: 505-554.
42. Ruttink T, Arend M, Morreel K, Storme V, Rombauts S et al. 2007. A molecular timetable for apical bud formation and dormancy induction in poplar. Plant Cell 19: 2370-2390.
43. Rweyongeza DM, Yang R-C, Dhir NK, Barnhardt LK, Hansen C. 2007. Genetic variation and climatic impacts on survival and growth of White spruce in Alberta, Canada. Silvae Genetica 56: 3-4.
44. Savard L, Li P, Strauss SH, Chase MW, Michaud M, Bousquet J. 1994. Chloroplast and nuclear gene sequences indicate Late Pennsylvanian time for the last common ancestor of extant seed plants. Proceedings of the National Academy of Sciences, USA 91: 5163-5167.
45. Schramm F, Larkindale J, Kiehlmann E, Ganguli A, Englich G, Vierling E, von Koskull-Doring P. 2008. A cascade of transcription factor DREB2A and heat stress transcription factor HsfA3 regulates the heat stress response of Arabidopsis. Plant Journal 53: 264-274.
46. Snell-Rood EC, Van Dyken JD, Cruickshank T, Wade MJ, Moczek AP. 2010. Toward a population genetic framework of developmental evolution: the costs, limits, and consequences of phenotypic plasticity. BioEssays 32: 71-81.
47. Sork VL, Aitken SN, Dyer RJ, Eckert AJ, Legendre P, Neal DB. 2013. Putting the landscape into the genomics of trees: approaches for understanding local adaptation and population responses to changing climate. Tree Genetics & Genomes 9: 901-911.
48. Sun WN, Van Montagu M, Verbruggen N. 2002. Small heat shock proteins and stress tolerance in plants. Biochimica Et Biophysica Acta 1577: 1-9.
49. Swindell WR, Huebner M, Weber AP. 2007. Transcriptional profiling of Arabidopsis heat shock proteins and transcription factors reveals extensive overlap between heat and non-heat stress response pathways. BMC Genomics 8: 125.
50. Tirosh I, Barkai N. 2011. Inferring regulatory mechanisms from patterns of evolutionary divergence. Molecular Systems Biology 7: 530.
51. Ukrainetz NK, O'Neill GA, Jaquish B. 2011. Comparison of fixed and focal point seed transfer systems for reforestation and assisted migration: a case study for interior spruce in British Columbia. Canadian Journal of Forestry Research 41: 1452-1464.
52. Walia H, Wilson C, Ismail AM, Close TJ, Cui X. 2009. Comparing genomic expression patterns across plant species reveals highly diverged transcriptional dynamics in response to salt stress. BMC Genomics 10: 398.
53. Wall PK, Leebens-Mack J, Chanderbali AS, Barakat A, Wolcott E, Liang H, Landherr L, Tomsho LP, Hu Y, Carlson JE et al. 2009. Comparison of next generation sequencing technologies for transcriptome characterization. BMC Genomics 10: 347.
54. Wang T, Campbell EM, O'Neill GA, Aitken SN. 2012. Projecting future distributions of ecosystem climate niches: uncertainties and management applications. Forest Ecology and Management 279: 128-140.
55. Wang T, Hamann A, Yanchuk A, O'Neill GA, Aitken SN. 2006. Use of response functions in selecting lodgepole pine populations for future climate. Global Change Biology 12: 2404-2416.
56. Wang WX, Vinocur B, Altman A. 2003. Plant responses to drought, salinity and extreme temperatures: towards genetic engineering for stress tolerance. Planta 218: 1-14.
57. Wang X-Q, Tank DC, Sang T. 2000. Phylogeny and divergence times in Pinaceae: evidence from three genomes. Molecular Biology and Evolution 17: 773-781.
58. Wegrzyn JL, Liechty JD, Stevens KA, Wu LS, Loopstra CA, Vasquez-Gross H, Dougherty WM, Lin BY, Zieve JJ, Martinez-Garcia PJ et al. 2014. Unique features of the lobololly pine (Pinus taeda L.) megagenome revealed through sequence annotation. Genetics 196: 891-909.
59. Woods A, Coates KD, Hamann A. 2005. Is an unprecedented Dothistroma needle blight epidemic related to climate change? BioScience 55: 761.
60. Wu TD, Watanabe CK. 2005. GMAP: a genomic mapping and alignment program for mRNA and EST sequences. Bioinformatics 21: 1859-1875.
61. Wu HX, Ying CC. 2004. Geographic pattern of local optimality in natural populations of lodgepole pine. Forest Ecology and Management 194: 177-198.