Research Papers

Selected Research Papers by UBC Centre for Plant Research Faculty and UBC Botanical Garden Staff

Earlier publications are available through a PubMed search.


Vasco A, Smalls TL, Graham SW, Cooper ED, Wong GK, Stevenson DW, Moran RC, Ambrose BA. Challenging the paradigms of leaf evolution: Class III HD-Zips in ferns and lycophytes. New Phytologist. 2016, July 17. doi: 10.1111/nph.14075. [Epub ahead of print]

Lam VKY, Merckx VSFT, Graham SW. A few-gene plastid phylogenetic framework for mycoheterotrophic monocots. Am. J. Bot.. 2016 Apr;103(4):692-708. doi: 10.3732/ajb.1500412.


Marques I, Montgomery SA, Barker MS, Macfarlane TD, Conran JG, Catalán P, Rieseberg LH, Rudall PJ, Graham SW. Transcriptome-derived evidence supports recent polyploidization and a major phylogeographic division in Trithuria submersa (Hydatellaceae, Nymphaeales). New Phytol. 2015 Nov 27. doi: 10.1111/nph.13755. [Epub ahead of print] PubMed PMID: 26612464.

Von Spreckelsen RM, Harris MT, Wigzell JM, Fraser RC, Carletto A, Mosquin DP, Justice D, Badyal JS. Bioinspired Breathable Architecture for Water Harvesting. Scientific Reports. 2015 Nov 18; 5:16798. doi:10.1038/srep16798

Bailey S, Percy DM, Hefer CA, Cronk QC. The transcriptional landscape of insect galls: psyllid (Hemiptera) gall formation in Hawaiian Metrosideros polymorpha (Myrtaceae). BMC Genomics. 2015 Nov 16;16(1):943. doi: 10.1186/s12864-015-2109-9. PubMed PMID: 26572921; PubMed Central PMCID: PMC4647832.

Arsovski AA, Pradinuk J, Guo XQ, Wang S, Adams KL. Evolution of cis-regulatory elements and regulatory networks in duplicated genes of Arabidopsis thaliana. Plant Physiol. 2015 Oct 16. pii: pp.00717.2015. [Epub ahead of print] PubMed PMID: 26474639.

Huang DI, Cronk QC. Plann: A command-line application for annotating plastome sequences. Appl Plant Sci. 2015 Aug 10;3(8). pii: apps.1500026. doi: 10.3732/apps.1500026. eCollection 2015 Aug. PubMed PMID: 26312193; PubMed Central PMCID: PMC4542940.

Geraldes A, Hefer CA, Capron A, Kolosova N, Martinez-Nuñez F, Soolanayakanahally RY, Stanton B, Guy RD, Mansfield SD, Douglas CJ, Cronk QC. Recent Y chromosome divergence despite ancient origin of dioecy in poplars (Populus). Mol Ecol. 2015 Jul;24(13):3243-56. doi: 10.1111/mec.13126. Epub 2015 Apr 2. PubMed PMID: 25728270.

Lam VK, Soto Gomez M, Graham SW. The Highly Reduced Plastome of Mycoheterotrophic Sciaphila (Triuridaceae) Is Colinear with Its Green Relatives and Is under Strong Purifying Selection. Genome Biol Evol. 2015 Jul 13;7(8):2220-36. doi: 10.1093/gbe/evv134. PubMed PMID: 26170229; PubMed Central PMCID: PMC4558852.

Wang S, Adams KL. Duplicate gene divergence by changes in microRNA binding sites in Arabidopsis and Brassica. Genome Biol Evol. 2015 Feb 2;7(3):646-55. doi: 10.1093/gbe/evv023. PubMed PMID: 25644246.


Tack DC, Pitchers WR, Adams KL. Transcriptome analysis indicates considerable divergence in alternative splicing between duplicated genes in Arabidopsis thaliana. Genetics. 2014 Dec;198(4):1473-81. doi: 10.1534/genetics.114.169466. Epub 2014 Oct 16. PubMed PMID: 25326238; PubMed Central PMCID: PMC4256766.

Huang DI, Hefer CA, Kolosova N, Douglas CJ, Cronk QC. Whole plastome sequencing reveals deep plastid divergence and cytonuclear discordance between closely related balsam poplars, Populus balsamifera and P. trichocarpa (Salicaceae). New Phytol. 2014 Nov;204(3):693-703. doi: 10.1111/nph.12956. Epub 2014 Jul 31. PubMed PMID: 25078531.

Geraldes A, Farzaneh N, Grassa CJ, McKown AD, Guy RD, Mansfield SD, Douglas CJ, Cronk QC. Landscape genomics of Populus trichocarpa: the role of hybridization, limited gene flow, and natural selection in shaping patterns of population structure. Evolution. 2014 Nov;68(11):3260-80. doi: 10.1111/evo.12497. Epub 2014 Sep 4. PubMed PMID: 25065449.

Percy DM, Argus GW, Cronk QC, Fazekas AJ, Kesanakurti PR, Burgess KS, Husband BC, Newmaster SG, Barrett SC, Graham SW. Understanding the spectacular failure of DNA barcoding in willows (Salix): does this result from a trans-specific selective sweep? Mol Ecol. 2014 Oct;23(19):4737-56. doi: 10.1111/mec.12837. Epub 2014 Jul 15. PubMed PMID: 24944007

Liu SL, Pan AQ, Adams KL. Protein subcellular relocalization of duplicated genes in Arabidopsis. Genome Biol Evol. 2014 Sep 4;6(9):2501-15. doi: 10.1093/gbe/evu191. PubMed PMID: 25193306; PubMed Central PMCID: PMC4202327.

Qiu Y, Liu SL, Adams KL. Frequent changes in expression profile and accelerated sequence evolution of duplicated imprinted genes in arabidopsis. Genome Biol Evol. 2014 Jul;6(7):1830-42. PubMed PMID: 25115008; PubMed Central PMCID: PMC4122942.

Iles WJ, Lee C, Sokoloff DD, Remizowa MV, Yadav SR, Barrett MD, Barrett RL, Macfarlane TD, Rudall PJ, Graham SW. Reconstructing the age and historical biogeography of the ancient flowering-plant family Hydatellaceae (Nymphaeales). BMC Evol Biol. 2014 May 13;14:102. doi: 10.1186/1471-2148-14-102. PubMed PMID: 24884487; PubMed Central PMCID: PMC4030046.

Sveinsson S, McDill J, Wong GK, Li J, Li X, Deyholos MK, Cronk QC. Phylogenetic pinpointing of a paleopolyploidy event within the flax genus (Linum) using transcriptomics. Ann Bot. 2014 Apr;113(5):753-61. doi: 10.1093/aob/mct306. Epub 2013 Dec 30. PubMed PMID: 24380843; PubMed Central PMCID: PMC3962240.


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