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Items: 39

1.

Widespread co-occurrence of multiple ploidy levels in fragile ferns (Cystopteris fragilis complex; Cystopteridaceae) probably stems from similar ecology of cytotypes, their efficient dispersal and inter-ploidy hybridization.

Hanušová K, Certner M, Urfus T, Koutecký P, Košnar J, Rothfels CJ, Jarolímová V, Ptácek J, Ekrt L.

Ann Bot. 2018 Dec 12. doi: 10.1093/aob/mcy219. [Epub ahead of print]

PMID:
30541055
2.

Target sequence capture of nuclear-encoded genes for phylogenetic analysis in ferns.

Wolf PG, Robison TA, Johnson MG, Sundue MA, Testo WL, Rothfels CJ.

Appl Plant Sci. 2018 May 17;6(5):e01148. doi: 10.1002/aps3.1148. eCollection 2018 May.

3.

Fern genomes elucidate land plant evolution and cyanobacterial symbioses.

Li FW, Brouwer P, Carretero-Paulet L, Cheng S, de Vries J, Delaux PM, Eily A, Koppers N, Kuo LY, Li Z, Simenc M, Small I, Wafula E, Angarita S, Barker MS, Bräutigam A, dePamphilis C, Gould S, Hosmani PS, Huang YM, Huettel B, Kato Y, Liu X, Maere S, McDowell R, Mueller LA, Nierop KGJ, Rensing SA, Robison T, Rothfels CJ, Sigel EM, Song Y, Timilsena PR, Van de Peer Y, Wang H, Wilhelmsson PKI, Wolf PG, Xu X, Der JP, Schluepmann H, Wong GK, Pryer KM.

Nat Plants. 2018 Jul;4(7):460-472. doi: 10.1038/s41477-018-0188-8. Epub 2018 Jul 2.

PMID:
29967517
4.

Inferring the evolutionary reduction of corm lobation in Isoëtes using Bayesian model-averaged ancestral state reconstruction.

Freund FD, Freyman WA, Rothfels CJ.

Am J Bot. 2018 Feb;105(2):275-286. doi: 10.1002/ajb2.1024. Epub 2018 Mar 24.

PMID:
29573405
5.

A novel chloroplast gene reported for flagellate plants.

Song M, Kuo LY, Huiet L, Pryer KM, Rothfels CJ, Li FW.

Am J Bot. 2018 Jan;105(1):117-121. doi: 10.1002/ajb2.1010. Epub 2018 Feb 12.

6.

Rapid allopolyploid radiation of moonwort ferns (Botrychium; Ophioglossaceae) revealed by PacBio sequencing of homologous and homeologous nuclear regions.

Dauphin B, Grant JR, Farrar DR, Rothfels CJ.

Mol Phylogenet Evol. 2018 Mar;120:342-353. doi: 10.1016/j.ympev.2017.11.025. Epub 2017 Dec 11.

PMID:
29242164
7.

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.

8.

End of an enigma: Aenigmopteris belongs in Tectaria (Tectariaceae: Polypodiopsida).

Chen CW, Rothfels CJ, Mustapeng AMA, Gubilil M, Karger DN, Kessler M, Huang YM.

J Plant Res. 2018 Jan;131(1):67-76. doi: 10.1007/s10265-017-0966-9. Epub 2017 Jul 24.

PMID:
28741041
9.

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.

10.

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.

11.

Evolutionary Analysis of the LAFL Genes Involved in the Land Plant Seed Maturation Program.

Han JD, Li X, Jiang CK, Wong GK, Rothfels CJ, Rao GY.

Front Plant Sci. 2017 Apr 4;8:439. doi: 10.3389/fpls.2017.00439. eCollection 2017.

12.

Super-resolution ribosome profiling reveals unannotated translation events in Arabidopsis.

Hsu PY, Calviello L, Wu HL, Li FW, Rothfels CJ, Ohler U, Benfey PN.

Proc Natl Acad Sci U S A. 2016 Nov 8;113(45):E7126-E7135. doi: 10.1073/pnas.1614788113. Epub 2016 Oct 21.

13.

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.

14.

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.

PMID:
27789157
15.

Transcriptome sequencing reveals genome-wide variation in molecular evolutionary rate among ferns.

Grusz AL, Rothfels CJ, Schuettpelz E.

BMC Genomics. 2016 Aug 30;17:692. doi: 10.1186/s12864-016-3034-2.

16.

Next-generation polyploid phylogenetics: rapid resolution of hybrid polyploid complexes using PacBio single-molecule sequencing.

Rothfels CJ, Pryer KM, Li FW.

New Phytol. 2017 Jan;213(1):413-429. doi: 10.1111/nph.14111. Epub 2016 Jul 27.

17.

Genes Translocated into the Plastid Inverted Repeat Show Decelerated Substitution Rates and Elevated GC Content.

Li FW, Kuo LY, Pryer KM, Rothfels CJ.

Genome Biol Evol. 2016 Aug 25;8(8):2452-8. doi: 10.1093/gbe/evw167.

18.

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.

19.

Genetic Analysis of Physcomitrella patens Identifies ABSCISIC ACID NON-RESPONSIVE, a Regulator of ABA Responses Unique to Basal Land Plants and Required for Desiccation Tolerance.

Stevenson SR, Kamisugi Y, Trinh CH, Schmutz J, Jenkins JW, Grimwood J, Muchero W, Tuskan GA, Rensing SA, Lang D, Reski R, Melkonian M, Rothfels CJ, Li FW, Larsson A, Wong GK, Edwards TA, Cuming AC.

Plant Cell. 2016 Jun;28(6):1310-27. doi: 10.1105/tpc.16.00091. Epub 2016 May 18.

20.

Analyses of transcriptome sequences reveal multiple ancient large-scale duplication events in the ancestor of Sphagnopsida (Bryophyta).

Devos N, Szövényi P, Weston DJ, Rothfels CJ, Johnson MG, Shaw AJ.

New Phytol. 2016 Jul;211(1):300-18. doi: 10.1111/nph.13887. Epub 2016 Feb 22.

21.

Algal ancestor of land plants was preadapted for symbiosis.

Delaux PM, Radhakrishnan GV, Jayaraman D, Cheema J, Malbreil M, Volkening JD, Sekimoto H, Nishiyama T, Melkonian M, Pokorny L, Rothfels CJ, Sederoff HW, Stevenson DW, Surek B, Zhang Y, Sussman MR, Dunand C, Morris RJ, Roux C, Wong GK, Oldroyd GE, Ané JM.

Proc Natl Acad Sci U S A. 2015 Oct 27;112(43):13390-5. doi: 10.1073/pnas.1515426112. Epub 2015 Oct 5.

22.

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.

23.

An Exploration into Fern Genome Space.

Wolf PG, Sessa EB, Marchant DB, Li FW, Rothfels CJ, Sigel EM, Gitzendanner MA, Visger CJ, Banks JA, Soltis DE, Soltis PS, Pryer KM, Der JP.

Genome Biol Evol. 2015 Aug 26;7(9):2533-44. doi: 10.1093/gbe/evv163.

24.

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.

25.

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.

26.

Natural hybridization between genera that diverged from each other approximately 60 million years ago.

Rothfels CJ, Johnson AK, Hovenkamp PH, Swofford DL, Roskam HC, Fraser-Jenkins CR, Windham MD, Pryer KM.

Am Nat. 2015 Mar;185(3):433-42. doi: 10.1086/679662.

PMID:
25674696
27.

Methods for studying polyploid diversification and the dead end hypothesis: a reply to Soltis et al. (2014).

Mayrose I, Zhan SH, Rothfels CJ, Arrigo N, Barker MS, Rieseberg LH, Otto SP.

New Phytol. 2015 Apr;206(1):27-35. doi: 10.1111/nph.13192. Epub 2014 Dec 4. No abstract available.

28.

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.

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.

30.

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.

31.

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.

32.

Stasis and convergence characterize morphological evolution in eupolypod II ferns.

Sundue MA, Rothfels CJ.

Ann Bot. 2014 Jan;113(1):35-54. doi: 10.1093/aob/mct247. Epub 2013 Nov 5.

33.

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.

34.

Accelerated rate of molecular evolution for vittarioid ferns is strong and not driven by selection.

Rothfels CJ, Schuettpelz E.

Syst Biol. 2014 Jan 1;63(1):31-54. doi: 10.1093/sysbio/syt058. Epub 2013 Aug 20.

PMID:
23963353
35.

Unique expression of a sporophytic character on the gametophytes of notholaenid ferns (Pteridaceae).

Johnson AK, Rothfels CJ, Windham MD, Pryer KM.

Am J Bot. 2012 Jun;99(6):1118-24. doi: 10.3732/ajb.1200049. Epub 2012 Apr 28.

36.

Overcoming deep roots, fast rates, and short internodes to resolve the ancient rapid radiation of eupolypod II ferns.

Rothfels CJ, Larsson A, Kuo LY, Korall P, Chiou WL, Pryer KM.

Syst Biol. 2012 May;61(3):490-509. doi: 10.1093/sysbio/sys001. Epub 2012 Jan 4.

PMID:
22223449
37.

rbcL and matK earn two thumbs up as the core DNA barcode for ferns.

Li FW, Kuo LY, Rothfels CJ, Ebihara A, Chiou WL, Windham MD, Pryer KM.

PLoS One. 2011;6(10):e26597. doi: 10.1371/journal.pone.0026597. Epub 2011 Oct 20.

38.

Recently formed polyploid plants diversify at lower rates.

Mayrose I, Zhan SH, Rothfels CJ, Magnuson-Ford K, Barker MS, Rieseberg LH, Otto SP.

Science. 2011 Sep 2;333(6047):1257. doi: 10.1126/science.1207205. Epub 2011 Aug 18.

39.

DNA barcoding exposes a case of mistaken identity in the fern horticultural trade.

Pryer KM, Schuettpelz E, Huiet L, Grusz AL, Rothfels CJ, Avent T, Schwartz D, Windham MD.

Mol Ecol Resour. 2010 Nov;10(6):979-85. doi: 10.1111/j.1755-0998.2010.02858.x.

PMID:
21565107

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