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A Target Capture-Based Method to Estimate Ploidy From Herbarium Specimens.

Viruel J, Conejero M, Hidalgo O, Pokorny L, Powell RF, Forest F, Kantar MB, Soto Gomez M, Graham SW, Gravendeel B, Wilkin P, Leitch IJ.

Front Plant Sci. 2019 Jul 24;10:937. doi: 10.3389/fpls.2019.00937. eCollection 2019.


Mycoheterotrophic Epirixanthes (Polygalaceae) has a typical angiosperm mitogenome but unorthodox plastid genomes.

Petersen G, Darby H, Lam VKY, Pedersen HÆ, Merckx VSFT, Zervas A, Seberg O, Graham SW.

Ann Bot. 2019 Jul 26. pii: mcz114. doi: 10.1093/aob/mcz114. [Epub ahead of print]


A customized nuclear target enrichment approach for developing a phylogenomic baseline for Dioscorea yams (Dioscoreaceae).

Soto Gomez M, Pokorny L, Kantar MB, Forest F, Leitch IJ, Gravendeel B, Wilkin P, Graham SW, Viruel J.

Appl Plant Sci. 2019 Jun 13;7(6):e11254. doi: 10.1002/aps3.11254. eCollection 2019 Jun.


A comprehensive kelp phylogeny sheds light on the evolution of an ecosystem.

Starko S, Soto Gomez M, Darby H, Demes KW, Kawai H, Yotsukura N, Lindstrom SC, Keeling PJ, Graham SW, Martone PT.

Mol Phylogenet Evol. 2019 Jul;136:138-150. doi: 10.1016/j.ympev.2019.04.012. Epub 2019 Apr 10.


Monocot plastid phylogenomics, timeline, net rates of species diversification, the power of multi-gene analyses, and a functional model for the origin of monocots.

Givnish TJ, Zuluaga A, Spalink D, Soto Gomez M, Lam VKY, Saarela JM, Sass C, Iles WJD, de Sousa DJL, Leebens-Mack J, Chris Pires J, Zomlefer WB, Gandolfo MA, Davis JI, Stevenson DW, dePamphilis C, Specht CD, Graham SW, Barrett CF, Ané C.

Am J Bot. 2018 Nov;105(11):1888-1910. doi: 10.1002/ajb2.1178. Epub 2018 Oct 24.


A transcriptome-based resolution for a key taxonomic controversy in Cupressaceae.

Mao K, Ruhsam M, Ma Y, Graham SW, Liu J, Thomas P, Milne RI, Hollingsworth PM.

Ann Bot. 2019 Jan 1;123(1):221. doi: 10.1093/aob/mcy175. No abstract available.


A transcriptome-based resolution for a key taxonomic controversy in Cupressaceae.

Mao K, Ruhsam M, Ma Y, Graham SW, Liu J, Thomas P, Milne RI, Hollingsworth PM.

Ann Bot. 2019 Jan 1;123(1):153-167. doi: 10.1093/aob/mcy152. Erratum in: Ann Bot. 2019 Jan 1;123(1):221.


Comprehensive cross-genome survey and phylogeny of glycoside hydrolase family 16 members reveals the evolutionary origin of EG16 and XTH proteins in plant lineages.

Behar H, Graham SW, Brumer H.

Plant J. 2018 Sep;95(6):1114-1128. doi: 10.1111/tpj.14004. Epub 2018 Jul 13.


Phylogenomic inference in extremis: A case study with mycoheterotroph plastomes.

Lam VKY, Darby H, Merckx VSFT, Lim G, Yukawa T, Neubig KM, Abbott JR, Beatty GE, Provan J, Soto Gomez M, Graham SW.

Am J Bot. 2018 Mar;105(3):480-494. doi: 10.1002/ajb2.1070. Epub 2018 May 5.


10KP: A phylodiverse genome sequencing plan.

Cheng S, Melkonian M, Smith SA, Brockington S, Archibald JM, Delaux PM, Li FW, Melkonian B, Mavrodiev EV, Sun W, Fu Y, Yang H, Soltis DE, Graham SW, Soltis PS, Liu X, Xu X, Wong GK.

Gigascience. 2018 Mar 1;7(3):1-9. doi: 10.1093/gigascience/giy013.


Using herbarium-derived DNAs to assemble a large-scale DNA barcode library for the vascular plants of Canada.

Kuzmina ML, Braukmann TWA, Fazekas AJ, Graham SW, Dewaard SL, Rodrigues A, Bennett BA, Dickinson TA, Saarela JM, Catling PM, Newmaster SG, Percy DM, Fenneman E, Lauron-Moreau A, Ford B, Gillespie L, Subramanyam R, Whitton J, Jennings L, Metsger D, Warne CP, Brown A, Sears E, Dewaard JR, Zakharov EV, Hebert PDN.

Appl Plant Sci. 2017 Dec 22;5(12). pii: apps.1700079. doi: 10.3732/apps.1700079. eCollection 2017 Dec.


The Physcomitrella patens chromosome-scale assembly reveals moss genome structure and evolution.

Lang D, Ullrich KK, Murat F, Fuchs J, Jenkins J, Haas FB, Piednoel M, Gundlach H, Van Bel M, Meyberg R, Vives C, Morata J, Symeonidi A, Hiss M, Muchero W, Kamisugi Y, Saleh O, Blanc G, Decker EL, van Gessel N, Grimwood J, Hayes RD, Graham SW, Gunter LE, McDaniel SF, Hoernstein SNW, Larsson A, Li FW, Perroud PF, Phillips J, Ranjan P, Rokshar DS, Rothfels CJ, Schneider L, Shu S, Stevenson DW, Thümmler F, Tillich M, Villarreal Aguilar JC, Widiez T, Wong GK, Wymore A, Zhang Y, Zimmer AD, Quatrano RS, Mayer KFX, Goodstein D, Casacuberta JM, Vandepoele K, Reski R, Cuming AC, Tuskan GA, Maumus F, Salse J, Schmutz J, Rensing SA.

Plant J. 2018 Feb;93(3):515-533. doi: 10.1111/tpj.13801.


Evolution of strigolactone receptors by gradual neo-functionalization of KAI2 paralogues.

Bythell-Douglas R, Rothfels CJ, Stevenson DWD, Graham SW, Wong GK, Nelson DC, Bennett T.

BMC Biol. 2017 Jun 29;15(1):52. doi: 10.1186/s12915-017-0397-z.


The Unique Role of the ECERIFERUM2-LIKE Clade of the BAHD Acyltransferase Superfamily in Cuticular Wax Metabolism.

Haslam TM, Gerelle WK, Graham SW, Kunst L.

Plants (Basel). 2017 Jun 13;6(2). pii: E23. doi: 10.3390/plants6020023. Review.


Mitochondrial genome evolution in Alismatales: Size reduction and extensive loss of ribosomal protein genes.

Petersen G, Cuenca A, Zervas A, Ross GT, Graham SW, Barrett CF, Davis JI, Seberg O.

PLoS One. 2017 May 17;12(5):e0177606. doi: 10.1371/journal.pone.0177606. eCollection 2017.


Insights into the Evolution of Hydroxyproline-Rich Glycoproteins from 1000 Plant Transcriptomes.

Johnson KL, Cassin AM, Lonsdale A, Wong GK, Soltis DE, Miles NW, Melkonian M, Melkonian B, Deyholos MK, Leebens-Mack J, Rothfels CJ, Stevenson DW, Graham SW, Wang X, Wu S, Pires JC, Edger PP, Carpenter EJ, Bacic A, Doblin MS, Schultz CJ.

Plant Physiol. 2017 Jun;174(2):904-921. doi: 10.1104/pp.17.00295. Epub 2017 Apr 26.


Plastomes on the edge: the evolutionary breakdown of mycoheterotroph plastid genomes.

Graham SW, Lam VK, Merckx VS.

New Phytol. 2017 Apr;214(1):48-55. doi: 10.1111/nph.14398. Epub 2017 Jan 9. Review.


Planning the future of plant systematics: Report on a special colloquium at the Royal Netherlands Academy of Arts and Sciences.

Sauquet H, Graham SW.

Am J Bot. 2016 Dec;103(12):2022-2027. doi: 10.3732/ajb.1600327. Epub 2016 Dec 5. No abstract available.


Microbial-type terpene synthase genes occur widely in nonseed land plants, but not in seed plants.

Jia Q, Li G, Köllner TG, Fu J, Chen X, Xiong W, Crandall-Stotler BJ, Bowman JL, Weston DJ, Zhang Y, Chen L, Xie Y, Li FW, Rothfels CJ, Larsson A, Graham SW, Stevenson DW, Wong GK, Gershenzon J, Chen F.

Proc Natl Acad Sci U S A. 2016 Oct 25;113(43):12328-12333. Epub 2016 Oct 10.


The Evolution of HD2 Proteins in Green Plants.

Bourque S, Jeandroz S, Grandperret V, Lehotai N, Aimé S, Soltis DE, Miles NW, Melkonian M, Deyholos MK, Leebens-Mack JH, Chase MW, Rothfels CJ, Stevenson DW, Graham SW, Wang X, Wu S, Pires JC, Edger PP, Yan Z, Xie Y, Carpenter EJ, Wong GKS, Wendehenne D, Nicolas-Francès V.

Trends Plant Sci. 2016 Dec;21(12):1008-1016. doi: 10.1016/j.tplants.2016.10.001. Epub 2016 Oct 24. Review.


Localized Retroprocessing as a Model of Intron Loss in the Plant Mitochondrial Genome.

Cuenca A, Ross TG, Graham SW, Barrett CF, Davis JI, Seberg O, Petersen G.

Genome Biol Evol. 2016 Aug 3;8(7):2176-89. doi: 10.1093/gbe/evw148.


Challenging the paradigms of leaf evolution: Class III HD-Zips in ferns and lycophytes.

Vasco A, Smalls TL, Graham SW, Cooper ED, Wong GK, Stevenson DW, Moran RC, Ambrose BA.

New Phytol. 2016 Nov;212(3):745-758. doi: 10.1111/nph.14075. Epub 2016 Jul 7.


Diversity of ABC transporter genes across the plant kingdom and their potential utility in biotechnology.

Lane TS, Rempe CS, Davitt J, Staton ME, Peng Y, Soltis DE, Melkonian M, Deyholos M, Leebens-Mack JH, Chase M, Rothfels CJ, Stevenson D, Graham SW, Yu J, Liu T, Pires JC, Edger PP, Zhang Y, Xie Y, Zhu Y, Carpenter E, Wong GK, Stewart CN Jr.

BMC Biotechnol. 2016 May 31;16(1):47. doi: 10.1186/s12896-016-0277-6.


A few-gene plastid phylogenetic framework for mycoheterotrophic monocots.

Lam VK, Merckx VS, Graham SW.

Am J Bot. 2016 Apr;103(4):692-708. doi: 10.3732/ajb.1500412. Epub 2016 Apr 7.


Early genome duplications in conifers and other seed plants.

Li Z, Baniaga AE, Sessa EB, Scascitelli M, Graham SW, Rieseberg LH, Barker MS.

Sci Adv. 2015 Nov 20;1(10):e1501084. doi: 10.1126/sciadv.1501084. eCollection 2015 Nov.


Transcriptome-derived evidence supports recent polyploidization and a major phylogeographic division in Trithuria submersa (Hydatellaceae, Nymphaeales).

Marques I, Montgomery SA, Barker MS, Macfarlane TD, Conran JG, Catalán P, Rieseberg LH, Rudall PJ, Graham SW.

New Phytol. 2016 Apr;210(1):310-23. doi: 10.1111/nph.13755. Epub 2015 Nov 27.


The origin and evolution of phototropins.

Li FW, Rothfels CJ, Melkonian M, Villarreal JC, Stevenson DW, Graham SW, Wong GK, Mathews S, Pryer KM.

Front Plant Sci. 2015 Aug 12;6:637. doi: 10.3389/fpls.2015.00637. eCollection 2015.


Phytochrome diversity in green plants and the origin of canonical plant phytochromes.

Li FW, Melkonian M, Rothfels CJ, Villarreal JC, Stevenson DW, Graham SW, Wong GK, Pryer KM, Mathews S.

Nat Commun. 2015 Jul 28;6:7852. doi: 10.1038/ncomms8852.


The evolutionary history of ferns inferred from 25 low-copy nuclear genes.

Rothfels CJ, Li FW, Sigel EM, Huiet L, Larsson A, Burge DO, Ruhsam M, Deyholos M, Soltis DE, Stewart CN Jr, Shaw SW, Pokorny L, Chen T, dePamphilis C, DeGironimo L, Chen L, Wei X, Sun X, Korall P, Stevenson DW, Graham SW, Wong GK, Pryer KM.

Am J Bot. 2015 Jul;102(7):1089-107. doi: 10.3732/ajb.1500089. Epub 2015 Jul 16.


Data access for the 1,000 Plants (1KP) project.

Matasci N, Hung LH, Yan Z, Carpenter EJ, Wickett NJ, Mirarab S, Nguyen N, Warnow T, Ayyampalayam S, Barker M, Burleigh JG, Gitzendanner MA, Wafula E, Der JP, dePamphilis CW, Roure B, Philippe H, Ruhfel BR, Miles NW, Graham SW, Mathews S, Surek B, Melkonian M, Soltis DE, Soltis PS, Rothfels C, Pokorny L, Shaw JA, DeGironimo L, Stevenson DW, Villarreal JC, Chen T, Kutchan TM, Rolf M, Baucom RS, Deyholos MK, Samudrala R, Tian Z, Wu X, Sun X, Zhang Y, Wang J, Leebens-Mack J, Wong GK.

Gigascience. 2014 Oct 27;3:17. doi: 10.1186/2047-217X-3-17. eCollection 2014. Review.


Does complete plastid genome sequencing improve species discrimination and phylogenetic resolution in Araucaria?

Ruhsam M, Rai HS, Mathews S, Ross TG, Graham SW, Raubeson LA, Mei W, Thomas PI, Gardner MF, Ennos RA, Hollingsworth PM.

Mol Ecol Resour. 2015 Sep;15(5):1067-78. doi: 10.1111/1755-0998.12375. Epub 2015 Feb 15.


Phylotranscriptomic analysis of the origin and early diversification of land plants.

Wickett NJ, Mirarab S, Nguyen N, Warnow T, Carpenter E, Matasci N, Ayyampalayam S, Barker MS, Burleigh JG, Gitzendanner MA, Ruhfel BR, Wafula E, Der JP, Graham SW, Mathews S, Melkonian M, Soltis DE, Soltis PS, Miles NW, Rothfels CJ, Pokorny L, Shaw AJ, DeGironimo L, Stevenson DW, Surek B, Villarreal JC, Roure B, Philippe H, dePamphilis CW, Chen T, Deyholos MK, Baucom RS, Kutchan TM, Augustin MM, Wang J, Zhang Y, Tian Z, Yan Z, Wu X, Sun X, Wong GK, Leebens-Mack J.

Proc Natl Acad Sci U S A. 2014 Nov 11;111(45):E4859-68. doi: 10.1073/pnas.1323926111. Epub 2014 Oct 29.


Between two fern genomes.

Sessa EB, Banks JA, Barker MS, Der JP, Duffy AM, Graham SW, Hasebe M, Langdale J, Li FW, Marchant DB, Pryer KM, Rothfels CJ, Roux SJ, Salmi ML, Sigel EM, Soltis DE, Soltis PS, Stevenson DW, Wolf PG.

Gigascience. 2014 Sep 25;3:15. doi: 10.1186/2047-217X-3-15. eCollection 2014. Review.


Origin of a novel regulatory module by duplication and degeneration of an ancient plant transcription factor.

Floyd SK, Ryan JG, Conway SJ, Brenner E, Burris KP, Burris JN, Chen T, Edger PP, Graham SW, Leebens-Mack JH, Pires JC, Rothfels CJ, Sigel EM, Stevenson DW, Neal Stewart C Jr, Wong GK, Bowman JL.

Mol Phylogenet Evol. 2014 Dec;81:159-73. doi: 10.1016/j.ympev.2014.06.017. Epub 2014 Sep 27.


Understanding the spectacular failure of DNA barcoding in willows (Salix): does this result from a trans-specific selective sweep?

Percy DM, Argus GW, Cronk QC, Fazekas AJ, Kesanakurti PR, Burgess KS, Husband BC, Newmaster SG, Barrett SC, Graham SW.

Mol Ecol. 2014 Oct;23(19):4737-56. doi: 10.1111/mec.12837. Epub 2014 Jul 15.


Reconstructing the age and historical biogeography of the ancient flowering-plant family Hydatellaceae (Nymphaeales).

Iles WJ, Lee C, Sokoloff DD, Remizowa MV, Yadav SR, Barrett MD, Barrett RL, Macfarlane TD, Rudall PJ, Graham SW.

BMC Evol Biol. 2014 May 13;14:102. doi: 10.1186/1471-2148-14-102.


Paralogous radiations of PIN proteins with multiple origins of noncanonical PIN structure.

Bennett T, Brockington SF, Rothfels C, Graham SW, Stevenson D, Kutchan T, Rolf M, Thomas P, Wong GK, Leyser O, Glover BJ, Harrison CJ.

Mol Biol Evol. 2014 Aug;31(8):2042-60. doi: 10.1093/molbev/msu147. Epub 2014 Apr 23.


Horizontal transfer of an adaptive chimeric photoreceptor from bryophytes to ferns.

Li FW, Villarreal JC, Kelly S, Rothfels CJ, Melkonian M, Frangedakis E, Ruhsam M, Sigel EM, Der JP, Pittermann J, Burge DO, Pokorny L, Larsson A, Chen T, Weststrand S, Thomas P, Carpenter E, Zhang Y, Tian Z, Chen L, Yan Z, Zhu Y, Sun X, Wang J, Stevenson DW, Crandall-Stotler BJ, Shaw AJ, Deyholos MK, Soltis DE, Graham SW, Windham MD, Langdale JA, Wong GK, Mathews S, Pryer KM.

Proc Natl Acad Sci U S A. 2014 May 6;111(18):6672-7. doi: 10.1073/pnas.1319929111. Epub 2014 Apr 14.


Transcriptome-mining for single-copy nuclear markers in ferns.

Rothfels CJ, Larsson A, Li FW, Sigel EM, Huiet L, Burge DO, Ruhsam M, Graham SW, Stevenson DW, Wong GK, Korall P, Pryer KM.

PLoS One. 2013 Oct 8;8(10):e76957. doi: 10.1371/journal.pone.0076957. eCollection 2013.


Molecular phylogenetics of Hydatellaceae (Nymphaeales): sexual-system homoplasy and a new sectional classification.

Iles WJ, Rudall PJ, Sokoloff DD, Remizowa MV, Macfarlane TD, Logacheva MD, Graham SW.

Am J Bot. 2012 Apr;99(4):663-76. doi: 10.3732/ajb.1100524. Epub 2012 Apr 2.


Choosing and using a plant DNA barcode.

Hollingsworth PM, Graham SW, Little DP.

PLoS One. 2011;6(5):e19254. doi: 10.1371/journal.pone.0019254. Epub 2011 May 26. Review.


Reconciling gene and genome duplication events: using multiple nuclear gene families to infer the phylogeny of the aquatic plant family Pontederiaceae.

Ness RW, Graham SW, Barrett SC.

Mol Biol Evol. 2011 Nov;28(11):3009-18. doi: 10.1093/molbev/msr119. Epub 2011 Jun 1.


Utility of a large, multigene plastid data set in inferring higher-order relationships in ferns and relatives (monilophytes).

Rai HS, Graham SW.

Am J Bot. 2010 Sep;97(9):1444-56. doi: 10.3732/ajb.0900305. Epub 2010 Aug 26.


Bryophyte-specific primers for retrieving plastid genes suitable for phylogenetic inference.

Chang Y, Graham SW.

Am J Bot. 2011 May;98(5):e109-13. doi: 10.3732/ajb.1000321.


Spatial patterns of plant diversity below-ground as revealed by DNA barcoding.

Kesanakurti PR, Fazekas AJ, Burgess KS, Percy DM, Newmaster SG, Graham SW, Barrett SC, Hajibabaei M, Husband BC.

Mol Ecol. 2011 Mar;20(6):1289-302. doi: 10.1111/j.1365-294X.2010.04989.x. Epub 2011 Jan 22.


Are plant species inherently harder to discriminate than animal species using DNA barcoding markers?

Fazekas AJ, Kesanakurti PR, Burgess KS, Percy DM, Graham SW, Barrett SC, Newmaster SG, Hajibabaei M, Husband BC.

Mol Ecol Resour. 2009 May;9 Suppl s1:130-9. doi: 10.1111/j.1755-0998.2009.02652.x.


Different gymnosperm outgroups have (mostly) congruent signal regarding the root of flowering plant phylogeny.

Graham SW, Iles WJ.

Am J Bot. 2009 Jan;96(1):216-27. doi: 10.3732/ajb.0800320. Epub 2008 Dec 24.


Introduction to the Darwin special issue: The abominable mystery1.

Stockey RA, Graham SW, Crane PR.

Am J Bot. 2009 Jan;96(1):3-4. doi: 10.3732/ajb.0800402. No abstract available.

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