Research Papers

Selected Research Papers by UBC Centre for Plant Research Faculty

Earlier publications are available through a PubMed search.


Rothfels CJ, Larsson A, Li FW, Sigel EM, Huiet L, Burge DO, Ruhsam M, Graham SW, Stevenson DW, Wong GK, Korall P, Pryer KM. 2013. Transcriptome-Mining for Single-Copy Nuclear Markers in Ferns. PLoS One.

Porth I, Klapšte J, Skyba O, Hannemann J, McKown AD, Guy RD, Difazio SP, Muchero W, Ranjan P, Tuskan GA, Friedmann MC, Ehlting J, Cronk QC, El-Kassaby YA, Douglas CJ, Mansfield SD. 2013. Genome-wide association mapping for wood characteristics in Populus identifies an array of candidate single nucleotide polymorphisms. New Phytologist (DOI: 10.1111/nph.12422)

Bao H, Li E, Mansfield SD, Cronk QC, El-Kassaby YA, Douglas CJ. 2013. The developing xylem transcriptome and genome-wide analysis of alternative splicing in Populus trichocarpa (black cottonwood) populations. BMC Genomics. (DOI: 10.1186/1471-2164-14-359)

Bell GD, Kane NC, Rieseberg LH, Adams KL. 2013. RNA-seq analysis of allele-specific expression, hybrid effects, and regulatory divergence in hybrids compared with their parents from natural populations. Genome Biol Evol. (DOI: 10.1093/gbe/evt072)

Darracq A, Adams KL. 2013. Features of evolutionarily conserved alternative splicing events between Brassica and Arabidopsis. New Phytologist. (DOI: 10.1111/nph.12238)

De Smet R, Adams KL, Vandepoele K, Van Montagu MC, Maere S, Van de Peer Y. 2013. Convergent gene loss following gene and genome duplications creates single-copy families in flowering plants. Proc Acad Natl Sci USA. (DOI: 10.1073/pnas.1300127110)

Geraldes A, Difazio SP, Slavov GT, Ranjan P, Muchero W, Hannemann J, Gunter LE, Wymore AM, Grassa CJ, Farzaneh N, Porth I, McKown AD, Skyba O, Li E, Fujita M, Klápště J, Martin J, Schackwitz W, Pennacchio C, Rokhsar D, Friedmann MC, Wasteneys GO, Guy RD, El-Kassaby YA, Mansfield SD, Cronk QC, Ehlting J, Douglas CJ, Tuskan GA. 2013. A 34K SNP genotyping array for Populus trichocarpa: design, application to the study of natural populations and transferability to other Populus species. Mol Ecol Resour. (DOI: 10.1111/1755-0998.12056)


Slavov GT, DiFazio SP, Martin J, Schackwitz W, Muchero W, Rodgers-Melnick E, Lipphardt MF, Pennacchio CP, Hellsten U, Pennacchio LA, Gunter LE, Ranjan P, Vining K, Pomraning KR, Wilhelm LJ, Pellegrini M, Mockler TC, Freitag M, Geraldes A, El-Kassaby YA, Mansfield SD, Cronk QC, Douglas CJ, Strauss SH, Rokhsar D, Tuskan GA. 2012. Genome resequencing reveals multiscale geographic structure and extensive linkage disequilibrium in the forest tree Populus trichocarpa. New Phytologist. (DOI: 10.1111/j.1469-8137.2012.04258.x)

Wang Z, Hobson N, Galindo L, Zhu S, Shi D, McDill J, Yang L, Hawkins S, Neutelings G, Datla R, Lambert G, Galbraith DW, Grassa CJ, Geraldes A, Cronk QC, Cullis C, Dash PK, Kumar PA, Cloutier S, Sharpe AG, Wong GK, Wang J, Deyholos MK. 2012. The genome of flax (Linum usitatissimum) assembled de novo from short shotgun sequence reads. Plant J.. (DOI: 10.1111/j.1365-313X.2012.05093.x)

Iles WJ, Rudall PJ, Sokoloff DD, Remizowa MV, Macfarlane TD, Logacheva MD, Graham SW. 2012. Molecular phylogenetics of Hydatellaceae (Nymphaeales): sexual-system homoplasy and a new sectional classification. American Journal of Botany. (DOI: 10.3732/ajb.1100524)


Yang JY, Motilal LA, Dempewolf H, Maharaj K, Cronk QC. 2011. Chloroplast microsatellite primers for cacao (Theobroma cacao) and other Malvaceae. American Journal of Botany. (DOI: 10.3732/ajb.1100306)

Liu SL, Baute GJ, Adams KL. 2011. Organ and cell type-specific complementary expression patterns and regulatory neofunctionalization between duplicated genes in Arabidopsis thaliana. Genome Biol Evol. (DOI: 10.1093/gbe/evr114)

Lai Z, Kane NC, Kozik A, Hodgins KA, Dlugosch KM, Barker MS, Matvienko M, Yu Q, Turner KG, Pearl SA, Bell GD, Zou Y, Grassa C, Guggisberg A, Adams KL, Anderson JV, Horvath DP, Kesseli RV, Burke JM, Michelmore RW, Rieseberg LH. 2011. Genomics of Compositae weeds: EST libraries, microarrays, and evidence of introgression. American Journal of Botany. (DOI: 10.3732/ajb.1100313)

Zhou R, Moshgabadi N, Adams KL. 2011. Extensive changes to alternative splicing patterns following allopolyploidy in natural and resynthesized polyploids. Proc Natl Acad Sci USA. (DOI: 10.1073/pnas.1109551108)

Hollingsworth PM, Graham SW, Little DP. 2011. Choosing and using a plant DNA barcode. PLoS One. (DOI: 10.1371/journal.pone.0019254)

Ness RW, Graham SW, Barrett SC. 2011. Reconciling gene and genome duplication events: using multiple nuclear gene families to infer the phylogeny of the aquatic plant family Pontederiaceae. Mol Biol Evol. (DOI: 10.1093/molbev/msr119)

Kesanakurti PR, Fazekas AJ, Burgess KS, Percy DM, Newmaster SG, Graham SW, Barrett SC, Hajibabaei M, Husband BC (2011) Spatial patterns of plant diversity below-ground as revealed by DNA barcoding. Mol Ecol. 2011 20(6):1289-1302

Wang L, Beyer ST, Cronk QCB, Walus K (2011) Delivering high-resolution landmarks using inkjet micropatterning for spatial monitoring of leaf expansion. Plant Methods 2011, 7:1


Dempewolf H, Kane NC, Ostevik KL, Geleta M, Barker MS, Lai Z, Stewart ML, Bekele E, Engels JMM, Cronk QCB, Rieseberg LH (2010) Establishing genomic tools and resources for Guizotia abyssinica (L.f.) Cass.-the development of a library of expressed sequence tags, microsatellite loci, and the sequencing of its chloroplast genome. Molecular Ecology Resources 10, 1048-1058

Givnish TJ, Ames M, McNeal JR, McKain MR, Steele PR, dePamphilis CW, Graham SW, Pires JC, Stevenson DW, Zomlefer WB, Briggs BG, Duvall MR, Moore MJ, Heaney JM, Soltis DE, Soltis PS, Thiele K, and Leebens-Mack JH. 2010. Assembling the tree of the monocotyledons: plastome sequence phylogeny and evolution of Poales. Annals of the Missouri Botanical Garden 97:584-616

Liu S-L, and Adams KL. 2010. Dramatic change in function and expression pattern of a gene duplicated by polyploidy created a paternal effect gene in the Brassicaceae. Molecular Biology and Evolution, in press.

Nowak JS, Ono J, Cronk QCB (2010) Anatomical study of an aquatic mustard: Subularia aquatica (Brassicaceae). Aquatic Botany 93, 55-58

Rai HS, and Graham SW. 2010. Utility of a large, multigene plastid data set in inferring higher-order relationships in ferns and relatives (monilophytes). American Journal of Botany 97:1444-1456.

Saarela JM, and Graham SW. 2010. Inference of phylogenetic relationships among the subfamilies of grasses (Poaceae: Poales) using meso-scale exemplar-based sampling of the plastid genome. Botany 88: 65-84.

Scascitelli M, Cognet M, and Adams KL. 2010. An interspecific plant hybrid shows novel changes in parental alternative splice forms of genes for splicing factors. Genetics, 184: 975-983. Featured in Issue Highlights at the time of publication.

Zhang PG, Huang S, Pin A-L, and Adams KL. 2010. Extensive divergence in alternative splicing patterns after gene and genome duplication during the evolutionary history of Arabidopsis. Molecular Biology and Evolution, 27: 1686-1697.


Cronk QCB (2009) Evolution in reverse gear: the molecular genetics of loss and reversal. In: Evolution: The Molecular Landscape (Cold Spring Harbor Symposia on Quantitative Biology LXXIV). Pp. 259-266.

Cronk, QCB, Percy DM (2009) Endemism. In Encyclopedia of Islands (RG Gillespie and DA Clague eds). University of California Press.

Fazekas AJ, Kesanakurti PR, Burgess KS, Percy DM, Graham SW, Barrett SCH, Newmaster SG, Hajibabaei M, and Husband BC. 2009. Are plant species inherently harder to discriminate than animal species using DNA barcoding markers? Molecular Ecology Resources 9 (Suppl. 1), 130–139.

Graham SW and Iles WJD. 2009. Different gymnosperm outgroups have (mostly) congruent signal regarding the root of flowering-plant phylogeny. American Journal of Botany 96: 207-215.

Hollingsworth PM [and 51 other authors]. 2009. A DNA barcode for land plants. Proceedings of the National Academy of Sciences, USA 106:12794-12797.

Liu S-L*, Zhuang Y*, Zhang P, and Adams KL. 2009. Comparative analysis of structural diversity and sequence evolution in plant mitochondrial genes transferred to the nucleus. Molecular Biology and Evolution, 26: 875-891. *equal contributions

Ojeda, I, Francisco-Ortega, J, Cronk, QCB (2009) Evolution of petal epidermal micromorphology in Leguminosae and its use as a marker of petal identity. Annals of Botany (epub ahead of print)


Adams KL 2008. Insights into the evolution of duplicated gene expression in polyploids from Gossypium. Botany 86: 827-834.

Case A.L., S.W. Graham, T.D. Macfarlane and S.C.H. Barrett. 2008. A phylogenetic study of transitions in sexual system in Australasian Wurmbea (Colchicaceae). International Journal of Plant Sciences 169:141-156.

Cronk, QCB, Ojeda, I (2008) Bird-pollinated flowers in an evolutionary and molecular context. Journal of Experimental Botany 59, 715-727

Dempewolf, H, Rieseberg, LH, Cronk, QCB (2008) Crop domestication in the Compositae: a family-wide trait assessment. Genetic Resources and Crop Evolution 55, 1141-1157.

Fazekas, A.J., K.S. Burgess, P.R. Kesanakurti, S.W. Graham, S.G. Newmaster, B.C. Husband, D.M. Percy, M. Hajibabaei and S.C.H. Barrett. 2008. Multiple multilocus DNA barcodes from the plastid genome discriminate plant species equally well. PLoS ONE 2:e2802.

Kane, NC, Cronk, QCB (2008) Botany without borders: barcoding in focus. Molecular Ecology 17, 5175-5176.

Liu S-L and Adams KL 2008. Molecular adaptation and expression evolution following duplication of genes for organellar ribosomal protein S13 in rosids. BMC Evolutionary Biology 8: 25 (15 pages).

Rai, H.S., P. A. Reeves, R. Peakall, R.G. Olmstead and S.W. Graham. 2008. Inference of higher-order conifer relationships from a multi-locus plastid data set. Botany 86:658-669

Saarela, J.M., P.J. Prentis, H.S. Rai and S.W. Graham. 2008. Phylogenetic relationships in the monocot order Commelinales, with a focus on Philydraceae. Botany (formerly Can. J. Botany) 86:719-731

Zgurski, J.M., H.S. Rai, Q.M. Fai, D.J. Bogler, J. Francisco-Ortega and S.W. Graham. 2008. How well do we understand the overall backbone of cycad phylogeny? New insights from a large, multigene plastid data set. Molecular Phylogenetics and Evolution 27:1232-1237.


Adams KL 2007. Evolution of duplicate gene expression in polyploid and hybrid plants. Journal of Heredity, 98: 136-141.

Cantino P.D., J.A. Doyle, S.W. Graham, W.S. Judd, R.G. Olmstead, D.E. Soltis, P.S. Soltis and M.J. Donoghue. 2007. Towards a phylogenetic nomenclature of Tracheophyta. Taxon 56:822-846 (an expanded online version of this article at Taxon is 44 pages long).

Denduangboripant, J, Cronk, QCB, Kokubugata, G, Moller, M. (2007) Variation and inheritance of nuclear ribosomal DNA clusters in Streptocarpus (Gesneriaceae) and their biological and phylogenetic implications. International Journal of Plant Sciences 168, 455-467

Liu Z and Adams KL 2007. Expression partitioning between genes duplicated by polyploidy under abiotic stress and during organ development. Current Biology 17: 1669-1674. Dispatches feature article about the paper: Hegarty, M., and Hiscock, S. Polyploidy: Doubling up for evolutionary success. Current Biology, 17: R927-929.

Mabee, PM, Ashburner, M, Cronk, Q, Gkoutos, GV, Haendel, M, Segerdell, E, Mungall, C, Westerfield, M (2007) Phenotype ontologies: the bridge between genomics and evolution. Trends in Ecology & Evolution 22, 345-350

Reaser, JK, Meyerson, LA, Cronk, Q, De Poorter, M, Eldrege, LG, Green, E, Kairo, M, Latasi, P, Mack, RN, Mauremootoo, J, O'Dowd, D, Orapa, W, Sastroutomo, S, Saunders, A, Shine, C, Thrainsson, S, Vaiutu, L (2007) Ecological and socioeconomic impacts of invasive alien species in island ecosystems. Environmental Conservation 34, 98-111

Saarela J.M., H.S. Rai, J.A. Doyle, P.K. Endress, S. Mathews, A.D. Marchant, B.G. Briggs and S.W. Graham. 2007. Hydatellaceae identified as a new branch near the base of the angiosperm phylogenetic tree. Nature 446:312-315.

Temmel, NA, Rai, HS, Cronk, QCB (2007). Sequence characterization of the putatively sex-linked Ssu72-like locus in willow and its homologue in poplar. Canadian Journal of Botany-Revue Canadienne de Botanique 85, 1092-1097

Zhuang Y and Adams KL 2007. Extensive allelic variation in gene expression in Populus F1 hybrids. Genetics 177: 1987-1996.


Chang Y., W.K. Chang, S.W. Graham and B.C. Tan. 2006. Molecular evidence for the systematic positions of two enigmatic mosses: Pterogonidium pulchellum (Sematophyllaceae, Musci) and Piloecium pseudorufescens (Myuriaceae, Musci). Canadian Journal of Botany 84:501-507.

Choi C, Liu Z, and Adams KL 2006. Evolutionary transfers of mitochondrial genes to the nucleus in the Populus lineage and co-expression of nuclear and mitochondrial Sdh4 genes. New Phytologist 172: 429-439. Feature article about the paper: Bonen L. 2006. Mitochondrial genes leave home. New Phytologist 172: 379-381.

Citerne, HL, Pennington, RT, Cronk, QCB (2006) An apparent reversal in floral symmetry in the legume Cadia is a homeotic transformation. Proceedings of the National Academy of Sciences of the United States of America 103, 12017-12020.

Cronk, QCB (2006) Legume flowers bear fruit. Proceedings of the National Academy of Sciences of The United States of America 103, 4801-4802.

Cronk, Q, Ojeda, I, Pennington, RT (2006) Legume comparative genomics: progress in phylogenetics and phylogenomics. Current Opinion in Plant Biology 9, 99-103.

Gilchrist, E.J., Haughn, G.W., Ying, C.C., Otto, S.P., Zhuang, J., Cheung, D., Hamberger, B., Aboutorabi, F., Kalynyak, T., Johnson, L., Bohlmann, J., Ellis, B.E., Douglas, C.J. and Cronk, Q.C.B. (2006). Use of Ecotilling as an efficient SNP discovery tool to survey genetic variation in wild populations of Populus trichocarpa. Molecular Ecology 15, 1367-1378.

Graham S.W., J.M. Zgurski, M.A. McPherson, D.M. Cherniawsky, J.M. Saarela, E.F.C. Horne,S.Y. Smith, W.A. Wong, H.E. O’Brien, V.L. Biron, J.C. Pires, R.G. Olmstead, M.W. Chase and H.S. Rai. 2006. Robust inference of monocot deep phylogeny using an expanded multigene plastid data set. In J.T. Columbus, E.A. Friar, J.M. Porter, L.M. Prince and M.G. Simpson [eds.], Monocots: comparative biology and evolution (excluding Poales). Rancho Santa Ana Botanic Garden, Claremont, California, USA, pages 3–21.

Tuskan, GA [and 109 other authors] (2006) The genome of black cottonwood, Populus trichocarpa (Torr. & Gray). Science 313, 1596-1604.

Whitton, J, Cronk, Q (2006) The origin of species - Genetics of speciation: American Genetics Association Annual Symposium, co-sponsored by Molecular Ecology, the University of British Columbia, Vancouver, Canada, 21-24 July 2006. New Phytologist 172, 390-392.

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