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Results: 1 to 20 of 87

1.

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.

PMID:
25625010
[PubMed]
Free PMC Article
2.

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.

PMID:
25534030
[PubMed - in process]
Free PMC Article
3.

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.

PMID:
25355905
[PubMed - in process]
Free PMC Article
4.

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.

PMID:
25124438
[PubMed - indexed for MEDLINE]
5.

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.

PMID:
25070642
[PubMed - in process]
6.

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.

PMID:
24666997
[PubMed - indexed for MEDLINE]
Free PMC Article
7.

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
[PubMed - indexed for MEDLINE]
8.

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
[PubMed - indexed for MEDLINE]
9.

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.

PMID:
24344209
[PubMed - indexed for MEDLINE]
Free Article
10.

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.

PMID:
24265760
[PubMed - indexed for MEDLINE]
Free PMC Article
11.

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.

PMID:
23663246
[PubMed - in process]
Free PMC Article
12.

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.

PMID:
23425243
[PubMed - indexed for MEDLINE]
Free PMC Article
13.

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.

PMID:
23347749
[PubMed - indexed for MEDLINE]
Free PMC Article
14.

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.

PMID:
23302495
[PubMed - indexed for MEDLINE]
Free PMC Article
15.

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
[PubMed - indexed for MEDLINE]
16.

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.

PMID:
23185583
[PubMed - indexed for MEDLINE]
Free PMC Article
17.

Phylogenomic analysis of transcriptome data elucidates co-occurrence of a paleopolyploid event and the origin of bimodal karyotypes in Agavoideae (Asparagaceae).

McKain MR, Wickett N, Zhang Y, Ayyampalayam S, McCombie WR, Chase MW, Pires JC, dePamphilis CW, Leebens-Mack J.

Am J Bot. 2012 Feb;99(2):397-406. doi: 10.3732/ajb.1100537. Epub 2012 Feb 1.

PMID:
22301890
[PubMed - indexed for MEDLINE]
Free Article
18.

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.

PMID:
22280555
[PubMed - indexed for MEDLINE]
Free PMC Article
19.

Transcriptomes of the parasitic plant family Orobanchaceae reveal surprising conservation of chlorophyll synthesis.

Wickett NJ, Honaas LA, Wafula EK, Das M, Huang K, Wu B, Landherr L, Timko MP, Yoder J, Westwood JH, dePamphilis CW.

Curr Biol. 2011 Dec 20;21(24):2098-104. doi: 10.1016/j.cub.2011.11.011. Epub 2011 Dec 8.

PMID:
22169535
[PubMed - indexed for MEDLINE]
Free Article
20.

Chasing the hare - evaluating the phylogenetic utility of a nuclear single copy gene region at and below species level within the species rich group Peperomia (Piperaceae).

Naumann J, Symmank L, Samain MS, Müller KF, Neinhuis C, dePamphilis CW, Wanke S.

BMC Evol Biol. 2011 Dec 12;11:357. doi: 10.1186/1471-2148-11-357.

PMID:
22151585
[PubMed - indexed for MEDLINE]
Free PMC Article
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