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Items: 1 to 20 of 92

1.

Local Auxin Biosynthesis Mediated by a YUCCA Flavin Monooxygenase Regulates Haustorium Development in the Parasitic Plant Phtheirospermum japonicum.

Ishida JK, Wakatake T, Yoshida S, Takebayashi Y, Kasahara H, Wafula E, dePamphilis CW, Namba S, Shirasu K.

Plant Cell. 2016 Jul 6. pii: tpc.00310.2016. [Epub ahead of print]

2.

A Phylogenomic Assessment of Ancient Polyploidy and Genome Evolution across the Poales.

McKain MR, Tang H, McNeal JR, Ayyampalayam S, Davis JI, dePamphilis CW, Givnish TJ, Pires JC, Stevenson DW, Leebens-Mack JH.

Genome Biol Evol. 2016 Apr 21;8(4):1150-64. doi: 10.1093/gbe/evw060.

3.

Detecting and Characterizing the Highly Divergent Plastid Genome of the Nonphotosynthetic Parasitic Plant Hydnora visseri (Hydnoraceae).

Naumann J, Der JP, Wafula EK, Jones SS, Wagner ST, Honaas LA, Ralph PE, Bolin JF, Maass E, Neinhuis C, Wanke S, dePamphilis CW.

Genome Biol Evol. 2016 Jan 6;8(2):345-63. doi: 10.1093/gbe/evv256.

4.

Selecting Superior De Novo Transcriptome Assemblies: Lessons Learned by Leveraging the Best Plant Genome.

Honaas LA, Wafula EK, Wickett NJ, Der JP, Zhang Y, Edger PP, Altman NS, Pires JC, Leebens-Mack JH, dePamphilis CW.

PLoS One. 2016 Jan 5;11(1):e0146062. doi: 10.1371/journal.pone.0146062. eCollection 2016.

5.

The butterfly plant arms-race escalated by gene and genome duplications.

Edger PP, Heidel-Fischer HM, Bekaert M, Rota J, Glöckner G, Platts AE, Heckel DG, Der JP, Wafula EK, Tang M, Hofberger JA, Smithson A, Hall JC, Blanchette M, Bureau TE, Wright SI, dePamphilis CW, Eric Schranz M, Barker MS, Conant GC, Wahlberg N, Vogel H, Pires JC, Wheat CW.

Proc Natl Acad Sci U S A. 2015 Jul 7;112(27):8362-6. doi: 10.1073/pnas.1503926112. Epub 2015 Jun 22.

6.

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.

7.

Comparative transcriptome analyses reveal core parasitism genes and suggest gene duplication and repurposing as sources of structural novelty.

Yang Z, Wafula EK, Honaas LA, Zhang H, Das M, Fernandez-Aparicio M, Huang K, Bandaranayake PC, Wu B, Der JP, Clarke CR, Ralph PE, Landherr L, Altman NS, Timko MP, Yoder JI, Westwood JH, dePamphilis CW.

Mol Biol Evol. 2015 Mar;32(3):767-90. doi: 10.1093/molbev/msu343. Epub 2014 Dec 21.

8.

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.

9.

Plant science. Genomic-scale exchange of mRNA between a parasitic plant and its hosts.

Kim G, LeBlanc ML, Wafula EK, dePamphilis CW, Westwood JH.

Science. 2014 Aug 15;345(6198):808-11. doi: 10.1126/science.1253122.

10.

Transcriptome analysis reveals the same 17 S-locus F-box genes in two haplotypes of the self-incompatibility locus of Petunia inflata.

Williams JS, Der JP, dePamphilis CW, Kao TH.

Plant Cell. 2014 Jul;26(7):2873-88. doi: 10.1105/tpc.114.126920. Epub 2014 Jul 28.

11.

Phylogenetic analysis of pectin-related gene families in Physcomitrella patens and nine other plant species yields evolutionary insights into cell walls.

McCarthy TW, Der JP, Honaas LA, dePamphilis CW, Anderson CT.

BMC Plant Biol. 2014 Mar 26;14:79. doi: 10.1186/1471-2229-14-79.

12.

Assembly and validation of the genome of the nonmodel basal angiosperm Amborella.

Chamala S, Chanderbali AS, Der JP, Lan T, Walts B, Albert VA, dePamphilis CW, Leebens-Mack J, Rounsley S, Schuster SC, Wing RA, Xiao N, Moore R, Soltis PS, Soltis DE, Barbazuk WB.

Science. 2013 Dec 20;342(6165):1516-7. doi: 10.1126/science.1241130.

PMID:
24357320
13.

Horizontal transfer of entire genomes via mitochondrial fusion in the angiosperm Amborella.

Rice DW, Alverson AJ, Richardson AO, Young GJ, Sanchez-Puerta MV, Munzinger J, Barry K, Boore JL, Zhang Y, dePamphilis CW, Knox EB, Palmer JD.

Science. 2013 Dec 20;342(6165):1468-73. doi: 10.1126/science.1246275.

PMID:
24357311
14.

Disproportional plastome-wide increase of substitution rates and relaxed purifying selection in genes of carnivorous Lentibulariaceae.

Wicke S, Schäferhoff B, dePamphilis CW, Müller KF.

Mol Biol Evol. 2014 Mar;31(3):529-45. doi: 10.1093/molbev/mst261. Epub 2013 Dec 15.

15.

Single-copy nuclear genes place haustorial Hydnoraceae within piperales and reveal a cretaceous origin of multiple parasitic angiosperm lineages.

Naumann J, Salomo K, Der JP, Wafula EK, Bolin JF, Maass E, Frenzke L, Samain MS, Neinhuis C, dePamphilis CW, Wanke S.

PLoS One. 2013 Nov 12;8(11):e79204. doi: 10.1371/journal.pone.0079204. eCollection 2013.

16.

Genome of the long-living sacred lotus (Nelumbo nucifera Gaertn.).

Ming R, VanBuren R, Liu Y, Yang M, Han Y, Li LT, Zhang Q, Kim MJ, Schatz MC, Campbell M, Li J, Bowers JE, Tang H, Lyons E, Ferguson AA, Narzisi G, Nelson DR, Blaby-Haas CE, Gschwend AR, Jiao Y, Der JP, Zeng F, Han J, Min XJ, Hudson KA, Singh R, Grennan AK, Karpowicz SJ, Watling JR, Ito K, Robinson SA, Hudson ME, Yu Q, Mockler TC, Carroll A, Zheng Y, Sunkar R, Jia R, Chen N, Arro J, Wai CM, Wafula E, Spence A, Han Y, Xu L, Zhang J, Peery R, Haus MJ, Xiong W, Walsh JA, Wu J, Wang ML, Zhu YJ, Paull RE, Britt AB, Du C, Downie SR, Schuler MA, Michael TP, Long SP, Ort DR, Schopf JW, Gang DR, Jiang N, Yandell M, dePamphilis CW, Merchant SS, Paterson AH, Buchanan BB, Li S, Shen-Miller J.

Genome Biol. 2013 May 10;14(5):R41. doi: 10.1186/gb-2013-14-5-r41.

17.

Evolution of a horizontally acquired legume gene, albumin 1, in the parasitic plant Phelipanche aegyptiaca and related species.

Zhang Y, Fernandez-Aparicio M, Wafula EK, Das M, Jiao Y, Wickett NJ, Honaas LA, Ralph PE, Wojciechowski MF, Timko MP, Yoder JI, Westwood JH, Depamphilis CW.

BMC Evol Biol. 2013 Feb 20;13:48. doi: 10.1186/1471-2148-13-48.

18.

Characterization of the basal angiosperm Aristolochia fimbriata: a potential experimental system for genetic studies.

Bliss BJ, Wanke S, Barakat A, Ayyampalayam S, Wickett N, Wall PK, Jiao Y, Landherr L, Ralph PE, Hu Y, Neinhuis C, Leebens-Mack J, Arumuganathan K, Clifton SW, Maximova SN, Ma H, dePamphilis CW.

BMC Plant Biol. 2013 Jan 24;13:13. doi: 10.1186/1471-2229-13-13.

19.

Functional genomics of a generalist parasitic plant: laser microdissection of host-parasite interface reveals host-specific patterns of parasite gene expression.

Honaas LA, Wafula EK, Yang Z, Der JP, Wickett NJ, Altman NS, Taylor CG, Yoder JI, Timko MP, Westwood JH, dePamphilis CW.

BMC Plant Biol. 2013 Jan 9;13:9. doi: 10.1186/1471-2229-13-9.

20.

Application of qRT-PCR and RNA-Seq analysis for the identification of housekeeping genes useful for normalization of gene expression values during Striga hermonthica development.

Fernández-Aparicio M, Huang K, Wafula EK, Honaas LA, Wickett NJ, Timko MP, Depamphilis CW, Yoder JI, Westwood JH.

Mol Biol Rep. 2013 Apr;40(4):3395-407. doi: 10.1007/s11033-012-2417-y. Epub 2012 Dec 28.

PMID:
23271128
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