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A virus-induced gene-silencing system for functional genetics in a betalainic species, Amaranthus tricolor (Amaranthaceae).

Adhikary D, Khatri-Chhetri U, Tymm FJM, Murch SJ, Deyholos MK.

Appl Plant Sci. 2019 Feb 7;7(2):e01221. doi: 10.1002/aps3.1221. eCollection 2019 Feb.


VvWRKY30, a grape WRKY transcription factor, plays a positive regulatory role under salinity stress.

Zhu D, Hou L, Xiao P, Guo Y, Deyholos MK, Liu X.

Plant Sci. 2019 Mar;280:132-142. doi: 10.1016/j.plantsci.2018.03.018. Epub 2018 Mar 20.


Chromosome-scale pseudomolecules refined by optical, physical and genetic maps in flax.

You FM, Xiao J, Li P, Yao Z, Jia G, He L, Zhu T, Luo MC, Wang X, Deyholos MK, Cloutier S.

Plant J. 2018 Jul;95(2):371-384. doi: 10.1111/tpj.13944. Epub 2018 May 21.


A Novel NAC-Type Transcription Factor, NAC87, from Oilseed Rape Modulates Reactive Oxygen Species Accumulation and Cell Death.

Yan J, Tong T, Li X, Chen Q, Dai M, Niu F, Yang M, Deyholos MK, Yang B, Jiang YQ.

Plant Cell Physiol. 2018 Feb 1;59(2):290-303. doi: 10.1093/pcp/pcx184.


Induced Mutagenesis in UGT74S1 Gene Leads to Stable New Flax Lines with Altered Secoisolariciresinol Diglucoside (SDG) Profiles.

Fofana B, Ghose K, Somalraju A, McCallum J, Main D, Deyholos MK, Rowland GG, Cloutier S.

Front Plant Sci. 2017 Sep 21;8:1638. doi: 10.3389/fpls.2017.01638. eCollection 2017.


LTR-retrotransposons in plants: Engines of evolution.

Galindo-González L, Mhiri C, Deyholos MK, Grandbastien MA.

Gene. 2017 Aug 30;626:14-25. doi: 10.1016/j.gene.2017.04.051. Epub 2017 May 2. Review.


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.


RNA-seq Transcriptome Response of Flax (Linum usitatissimum L.) to the Pathogenic Fungus Fusarium oxysporum f. sp. lini.

Galindo-González L, Deyholos MK.

Front Plant Sci. 2016 Nov 24;7:1766. eCollection 2016.


Ty1-copia elements reveal diverse insertion sites linked to polymorphisms among flax (Linum usitatissimum L.) accessions.

Galindo-González L, Mhiri C, Grandbastien MA, Deyholos MK.

BMC Genomics. 2016 Dec 7;17(1):1002.


The Amaranth Genome: Genome, Transcriptome, and Physical Map Assembly.

Clouse JW, Adhikary D, Page JT, Ramaraj T, Deyholos MK, Udall JA, Fairbanks DJ, Jellen EN, Maughan PJ.

Plant Genome. 2016 Mar;9(1). doi: 10.3835/plantgenome2015.07.0062. Erratum in: Plant Genome. 2016 Nov;9(3):.


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.


RNASeq Analysis of the Shoot Apex of Flax (Linum usitatissimum) to Identify Phloem Fiber Specification Genes.

Zhang N, Deyholos MK.

Front Plant Sci. 2016 Jun 28;7:950. doi: 10.3389/fpls.2016.00950. eCollection 2016. No abstract available.


Functional characterization of NAC55 transcription factor from oilseed rape (Brassica napus L.) as a novel transcriptional activator modulating reactive oxygen species accumulation and cell death.

Niu F, Wang C, Yan J, Guo X, Wu F, Yang B, Deyholos MK, Jiang YQ.

Plant Mol Biol. 2016 Sep;92(1-2):89-104. doi: 10.1007/s11103-016-0502-7. Epub 2016 Jun 16.


Optimal fertilizer application for Panax notoginseng and effect of soil water on root rot disease and saponin contents.

Xia P, Guo H, Zhao H, Jiao J, Deyholos MK, Yan X, Liu Y, Liang Z.

J Ginseng Res. 2016 Jan;40(1):38-46. doi: 10.1016/j.jgr.2015.04.003. Epub 2015 Apr 30.


A Plant-Produced Bacteriophage Tailspike Protein for the Control of Salmonella.

Miletic S, Simpson DJ, Szymanski CM, Deyholos MK, Menassa R.

Front Plant Sci. 2016 Jan 8;6:1221. doi: 10.3389/fpls.2015.01221. eCollection 2015.


Development of Microsatellite Markers Derived from Expressed Sequence Tags of Polyporales for Genetic Diversity Analysis of Endangered Polyporus umbellatus.

Zhang Y, Chen Y, Wang R, Zeng A, Deyholos MK, Shu J, Guo H.

Biomed Res Int. 2015;2015:941357. doi: 10.1155/2015/941357. Epub 2015 Jun 3.


Elucidating steroid alkaloid biosynthesis in Veratrum californicum: production of verazine in Sf9 cells.

Augustin MM, Ruzicka DR, Shukla AK, Augustin JM, Starks CM, O'Neil-Johnson M, McKain MR, Evans BS, Barrett MD, Smithson A, Wong GK, Deyholos MK, Edger PP, Pires JC, Leebens-Mack JH, Mann DA, Kutchan TM.

Plant J. 2015 Jun;82(6):991-1003. doi: 10.1111/tpj.12871.


Wild soybean roots depend on specific transcription factors and oxidation reduction related genesin response to alkaline stress.

DuanMu H, Wang Y, Bai X, Cheng S, Deyholos MK, Wong GK, Li D, Zhu D, Li R, Yu Y, Cao L, Chen C, Zhu Y.

Funct Integr Genomics. 2015 Nov;15(6):651-60. doi: 10.1007/s10142-015-0439-y. Epub 2015 Apr 15.


Ion Torrent sequencing as a tool for mutation discovery in the flax (Linum usitatissimum L.) genome.

Galindo-González L, Pinzón-Latorre D, Bergen EA, Jensen DC, Deyholos MK.

Plant Methods. 2015 Mar 14;11:19. doi: 10.1186/s13007-015-0062-x. eCollection 2015.


The location and translocation of ndh genes of chloroplast origin in the Orchidaceae family.

Lin CS, Chen JJ, Huang YT, Chan MT, Daniell H, Chang WJ, Hsu CT, Liao DC, Wu FH, Lin SY, Liao CF, Deyholos MK, Wong GK, Albert VA, Chou ML, Chen CY, Shih MC.

Sci Rep. 2015 Mar 12;5:9040. doi: 10.1038/srep09040.


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.


Calcium mobilization in salicylic acid-induced Salvia miltiorrhiza cell cultures and its effect on the accumulation of rosmarinic acid.

Guo H, Zhu N, Deyholos MK, Liu J, Zhang X, Dong J.

Appl Biochem Biotechnol. 2015 Mar;175(5):2689-702. doi: 10.1007/s12010-014-1459-0. Epub 2015 Jan 6.


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.


Multiple polyploidy events in the early radiation of nodulating and nonnodulating legumes.

Cannon SB, McKain MR, Harkess A, Nelson MN, Dash S, Deyholos MK, Peng Y, Joyce B, Stewart CN Jr, Rolf M, Kutchan T, Tan X, Chen C, Zhang Y, Carpenter E, Wong GK, Doyle JJ, Leebens-Mack J.

Mol Biol Evol. 2015 Jan;32(1):193-210. doi: 10.1093/molbev/msu296. Epub 2014 Oct 27.


Pectinmethylesterases (PME) and pectinmethylesterase inhibitors (PMEI) enriched during phloem fiber development in flax (Linum usitatissimum).

Pinzon-Latorre D, Deyholos MK.

PLoS One. 2014 Aug 14;9(8):e105386. doi: 10.1371/journal.pone.0105386. eCollection 2014.


Chitinase-like (CTL) and cellulose synthase (CESA) gene expression in gelatinous-type cellulosic walls of flax (Linum usitatissimum L.) bast fibers.

Mokshina N, Gorshkova T, Deyholos MK.

PLoS One. 2014 Jun 11;9(2):e97949. doi: 10.1371/journal.pone.0097949. eCollection 2014.


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.


Identification, expression and interaction analyses of calcium-dependent protein kinase (CPK) genes in canola (Brassica napus L.).

Zhang H, Liu WZ, Zhang Y, Deng M, Niu F, Yang B, Wang X, Wang B, Liang W, Deyholos MK, Jiang YQ.

BMC Genomics. 2014 Mar 19;15:211. doi: 10.1186/1471-2164-15-211.


Identification and functional analysis of mitogen-activated protein kinase kinase kinase (MAPKKK) genes in canola (Brassica napus L.).

Sun Y, Wang C, Yang B, Wu F, Hao X, Liang W, Niu F, Yan J, Zhang H, Wang B, Deyholos MK, Jiang YQ.

J Exp Bot. 2014 May;65(8):2171-88. doi: 10.1093/jxb/eru092. Epub 2014 Mar 6.


Differential expression of miRNAs in Brassica napus root following infection with Plasmodiophora brassicae.

Verma SS, Rahman MH, Deyholos MK, Basu U, Kav NN.

PLoS One. 2014 Jan 31;9(1):e86648. doi: 10.1371/journal.pone.0086648. eCollection 2014.


Identification and characterization of CBL and CIPK gene families in canola (Brassica napus L.).

Zhang H, Yang B, Liu WZ, Li H, Wang L, Wang B, Deng M, Liang W, Deyholos MK, Jiang YQ.

BMC Plant Biol. 2014 Jan 7;14:8. doi: 10.1186/1471-2229-14-8.


Phylogenetic pinpointing of a paleopolyploidy event within the flax genus (Linum) using transcriptomics.

Sveinsson S, McDill J, Wong GK, Li J, Li X, Deyholos MK, Cronk QC.

Ann Bot. 2014 Apr;113(5):753-61. doi: 10.1093/aob/mct306. Epub 2013 Dec 30.


Ecological implications of single and mixed nitrogen nutrition in Arabidopsis thaliana.

McNickle GG, Deyholos MK, Cahill JF Jr.

BMC Ecol. 2013 Jul 23;13:28. doi: 10.1186/1472-6785-13-28.


Identification and analysis of MKK and MPK gene families in canola (Brassica napus L.).

Liang W, Yang B, Yu BJ, Zhou Z, Li C, Jia M, Sun Y, Zhang Y, Wu F, Zhang H, Wang B, Deyholos MK, Jiang YQ.

BMC Genomics. 2013 Jun 11;14:392. doi: 10.1186/1471-2164-14-392.


Genomic and expression analysis of the flax (Linum usitatissimum) family of glycosyl hydrolase 35 genes.

Hobson N, Deyholos MK.

BMC Genomics. 2013 May 23;14:344. doi: 10.1186/1471-2164-14-344.


LuFLA1PRO and LuBGAL1PRO promote gene expression in the phloem fibres of flax (Linum usitatissimum).

Hobson N, Deyholos MK.

Plant Cell Rep. 2013 Apr;32(4):517-28. doi: 10.1007/s00299-013-1383-8. Epub 2013 Jan 18.


Evaluating methods for isolating total RNA and predicting the success of sequencing phylogenetically diverse plant transcriptomes.

Johnson MT, Carpenter EJ, Tian Z, Bruskiewich R, Burris JN, Carrigan CT, Chase MW, Clarke ND, Covshoff S, Depamphilis CW, Edger PP, Goh F, Graham S, Greiner S, Hibberd JM, Jordon-Thaden I, Kutchan TM, Leebens-Mack J, Melkonian M, Miles N, Myburg H, Patterson J, Pires JC, Ralph P, Rolf M, Sage RF, Soltis D, Soltis P, Stevenson D, Stewart CN Jr, Surek B, Thomsen CJ, Villarreal JC, Wu X, Zhang Y, Deyholos MK, Wong GK.

PLoS One. 2012;7(11):e50226. doi: 10.1371/journal.pone.0050226. Epub 2012 Nov 21.


Identification, characterization and distribution of transposable elements in the flax (Linum usitatissimum L.) genome.

González LG, Deyholos MK.

BMC Genomics. 2012 Nov 21;13:644. doi: 10.1186/1471-2164-13-644.


Over-expression of a novel JAZ family gene from Glycine soja, increases salt and alkali stress tolerance.

Zhu D, Cai H, Luo X, Bai X, Deyholos MK, Chen Q, Chen C, Ji W, Zhu Y.

Biochem Biophys Res Commun. 2012 Sep 21;426(2):273-9. doi: 10.1016/j.bbrc.2012.08.086. Epub 2012 Aug 25.


Modeling the yew tree tubulin and a comparison of its interaction with paclitaxel to human tubulin.

Tuszynski JA, Craddock TJ, Mane JY, Barakat K, Tseng CY, Gajewski M, Winter P, Alisaraie L, Patterson J, Carpenter E, Wang W, Deyholos MK, Li L, Sun X, Zhang Y, Wong GK.

Pharm Res. 2012 Nov;29(11):3007-21. doi: 10.1007/s11095-012-0829-y. Epub 2012 Jul 26.


The genome of flax (Linum usitatissimum) assembled de novo from short shotgun sequence reads.

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.

Plant J. 2012 Nov;72(3):461-73. doi: 10.1111/j.1365-313X.2012.05093.x. Epub 2012 Aug 14.


A genome triplication associated with early diversification of the core eudicots.

Jiao Y, Leebens-Mack J, Ayyampalayam S, Bowers JE, McKain MR, McNeal J, Rolf M, Ruzicka DR, Wafula E, Wickett NJ, Wu X, Zhang Y, Wang J, Zhang Y, Carpenter EJ, Deyholos MK, Kutchan TM, Chanderbali AS, Soltis PS, Stevenson DW, McCombie R, Pires JC, Wong GK, Soltis DE, Depamphilis CW.

Genome Biol. 2012 Jan 26;13(1):R3. doi: 10.1186/gb-2012-13-1-r3.


Two wheat (Triticum aestivum) pathogenesis-related 10 (PR-10) transcripts with distinct patterns of abundance in different organs.

Mohammadi M, Srivastava S, Hall JC, Kav NN, Deyholos MK.

Mol Biotechnol. 2012 Jun;51(2):103-8. doi: 10.1007/s12033-011-9441-3.


Development of cellulosic secondary walls in flax fibers requires beta-galactosidase.

Roach MJ, Mokshina NY, Badhan A, Snegireva AV, Hobson N, Deyholos MK, Gorshkova TA.

Plant Physiol. 2011 Jul;156(3):1351-63. doi: 10.1104/pp.111.172676. Epub 2011 May 19.


PELPK1 (At5g09530) contains a unique pentapeptide repeat and is a positive regulator of germination in Arabidopsis thaliana.

Rashid A, Deyholos MK.

Plant Cell Rep. 2011 Sep;30(9):1735-45. doi: 10.1007/s00299-011-1081-3. Epub 2011 May 11.


Exploration of inhibitors for diaminopimelate aminotransferase.

Fan C, Clay MD, Deyholos MK, Vederas JC.

Bioorg Med Chem. 2010 Mar 15;18(6):2141-2151. doi: 10.1016/j.bmc.2010.02.001. Epub 2010 Feb 6.


Transcriptome analysis of secondary-wall-enriched seed coat tissues of canola (Brassica napus L.).

Jiang Y, Deyholos MK.

Plant Cell Rep. 2010 Apr;29(4):327-42. doi: 10.1007/s00299-010-0824-x. Epub 2010 Feb 10.


Making the most of drought and salinity transcriptomics.

Deyholos MK.

Plant Cell Environ. 2010 Apr;33(4):648-54. doi: 10.1111/j.1365-3040.2009.02092.x. Epub 2009 Nov 25. Review.


Functional characterization of the Arabidopsis bHLH92 transcription factor in abiotic stress.

Jiang Y, Yang B, Deyholos MK.

Mol Genet Genomics. 2009 Nov;282(5):503-16. doi: 10.1007/s00438-009-0481-3. Epub 2009 Sep 17.


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