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Items: 30

1.

Hyb-Seq for Flowering Plant Systematics.

Dodsworth S, Pokorny L, Johnson MG, Kim JT, Maurin O, Wickett NJ, Forest F, Baker WJ.

Trends Plant Sci. 2019 Oct;24(10):887-891. doi: 10.1016/j.tplants.2019.07.011. Epub 2019 Aug 30.

PMID:
31477409
2.

Phylogeny, host use, and diversification in the moth family Momphidae (Lepidoptera: Gelechioidea).

Bruzzese DJ, Wagner DL, Harrison T, Jogesh T, Overson RP, Wickett NJ, Raguso RA, Skogen KA.

PLoS One. 2019 Jun 6;14(6):e0207833. doi: 10.1371/journal.pone.0207833. eCollection 2019.

3.

Resolution of the ordinal phylogeny of mosses using targeted exons from organellar and nuclear genomes.

Liu Y, Johnson MG, Cox CJ, Medina R, Devos N, Vanderpoorten A, Hedenäs L, Bell NE, Shevock JR, Aguero B, Quandt D, Wickett NJ, Shaw AJ, Goffinet B.

Nat Commun. 2019 Apr 2;10(1):1485. doi: 10.1038/s41467-019-09454-w.

4.

A Universal Probe Set for Targeted Sequencing of 353 Nuclear Genes from Any Flowering Plant Designed Using k-Medoids Clustering.

Johnson MG, Pokorny L, Dodsworth S, Botigué LR, Cowan RS, Devault A, Eiserhardt WL, Epitawalage N, Forest F, Kim JT, Leebens-Mack JH, Leitch IJ, Maurin O, Soltis DE, Soltis PS, Wong GK, Baker WJ, Wickett NJ.

Syst Biol. 2019 Jul 1;68(4):594-606. doi: 10.1093/sysbio/syy086.

5.

Bridging the micro- and macroevolutionary levels in phylogenomics: Hyb-Seq solves relationships from populations to species and above.

Villaverde T, Pokorny L, Olsson S, Rincón-Barrado M, Johnson MG, Gardner EM, Wickett NJ, Molero J, Riina R, Sanmartín I.

New Phytol. 2018 Oct;220(2):636-650. doi: 10.1111/nph.15312. Epub 2018 Jul 17.

6.

A transcriptome screen for positive selection in domesticated breadfruit and its wild relatives (Artocarpus spp.).

Laricchia KM, Johnson MG, Ragone D, Williams EW, Zerega NJC, Wickett NJ.

Am J Bot. 2018 May;105(5):915-926. doi: 10.1002/ajb2.1095. Epub 2018 Jun 8.

7.

Recurrent Loss, Horizontal Transfer, and the Obscure Origins of Mitochondrial Introns in Diatoms (Bacillariophyta).

Guillory WX, Onyshchenko A, Ruck EC, Parks M, Nakov T, Wickett NJ, Alverson AJ.

Genome Biol Evol. 2018 Jun 1;10(6):1504-1515. doi: 10.1093/gbe/evy103.

8.

Allele phasing has minimal impact on phylogenetic reconstruction from targeted nuclear gene sequences in a case study of Artocarpus.

Kates HR, Johnson MG, Gardner EM, Zerega NJC, Wickett NJ.

Am J Bot. 2018 Mar;105(3):404-416. doi: 10.1002/ajb2.1068. Epub 2018 May 5.

9.

Phylogenomics reveals an extensive history of genome duplication in diatoms (Bacillariophyta).

Parks MB, Nakov T, Ruck EC, Wickett NJ, Alverson AJ.

Am J Bot. 2018 Mar;105(3):330-347. doi: 10.1002/ajb2.1056. Epub 2018 Apr 17.

10.

Signal, Uncertainty, and Conflict in Phylogenomic Data for a Diverse Lineage of Microbial Eukaryotes (Diatoms, Bacillariophyta).

Parks MB, Wickett NJ, Alverson AJ.

Mol Biol Evol. 2018 Jan 1;35(1):80-93. doi: 10.1093/molbev/msx268.

11.

HybPiper: Extracting coding sequence and introns for phylogenetics from high-throughput sequencing reads using target enrichment.

Johnson MG, Gardner EM, Liu Y, Medina R, Goffinet B, Shaw AJ, Zerega NJ, Wickett NJ.

Appl Plant Sci. 2016 Jul 12;4(7). pii: apps.1600016. doi: 10.3732/apps.1600016. eCollection 2016 Jul.

12.

Low-coverage, whole-genome sequencing of Artocarpus camansi (Moraceae) for phylogenetic marker development and gene discovery.

Gardner EM, Johnson MG, Ragone D, Wickett NJ, Zerega NJ.

Appl Plant Sci. 2016 Jul 13;4(7). pii: apps.1600017. doi: 10.3732/apps.1600017. eCollection 2016 Jul.

13.

A phylotranscriptomic analysis of gene family expansion and evolution in the largest order of pleurocarpous mosses (Hypnales, Bryophyta).

Johnson MG, Malley C, Goffinet B, Shaw AJ, Wickett NJ.

Mol Phylogenet Evol. 2016 May;98:29-40. doi: 10.1016/j.ympev.2016.01.008. Epub 2016 Jan 23.

PMID:
26811877
14.

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.

15.

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.

16.

Transcriptomic Insights into the Life History of Bolidophytes, the Sister Lineage to Diatoms.

Kessenich CR, Ruck EC, Schurko AM, Wickett NJ, Alverson AJ.

J Phycol. 2014 Dec;50(6):977-83. doi: 10.1111/jpy.12222. Epub 2014 Sep 3.

PMID:
26988780
17.

Examining the efficacy of a genotyping-by-sequencing technique for population genetic analysis of the mushroom Laccaria bicolor and evaluating whether a reference genome is necessary to assess homology.

Wilson AW, Wickett NJ, Grabowski P, Fant J, Borevitz J, Mueller GM.

Mycologia. 2015 Jan-Feb;107(1):217-26. doi: 10.3852/13-278. Epub 2014 Oct 31.

18.

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.

19.

Mechanisms of functional and physical genome reduction in photosynthetic and nonphotosynthetic parasitic plants of the broomrape family.

Wicke S, Müller KF, de Pamphilis CW, Quandt D, Wickett NJ, Zhang Y, Renner SS, Schneeweiss GM.

Plant Cell. 2013 Oct;25(10):3711-25. doi: 10.1105/tpc.113.113373. Epub 2013 Oct 18.

20.

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.

21.

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.

22.

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
23.

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.

24.

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.

25.

Frequent pseudogenization and loss of the plastid-encoded sulfate-transport gene cysA throughout the evolution of liverworts.

Wickett NJ, Forrest LL, Budke JM, Shaw B, Goffinet B.

Am J Bot. 2011 Aug;98(8):1263-75. doi: 10.3732/ajb.1100010.

26.

Ancestral polyploidy in seed plants and angiosperms.

Jiao Y, Wickett NJ, Ayyampalayam S, Chanderbali AS, Landherr L, Ralph PE, Tomsho LP, Hu Y, Liang H, Soltis PS, Soltis DE, Clifton SW, Schlarbaum SE, Schuster SC, Ma H, Leebens-Mack J, dePamphilis CW.

Nature. 2011 May 5;473(7345):97-100. doi: 10.1038/nature09916. Epub 2011 Apr 10.

PMID:
21478875
27.

De novo characterization of the gametophyte transcriptome in bracken fern, Pteridium aquilinum.

Der JP, Barker MS, Wickett NJ, dePamphilis CW, Wolf PG.

BMC Genomics. 2011 Feb 8;12:99. doi: 10.1186/1471-2164-12-99.

28.

Distribution and evolution of pseudogenes, gene losses, and a gene rearrangement in the plastid genome of the nonphotosynthetic liverwort, Aneura mirabilis (Metzgeriales, Jungermanniopsida).

Wickett NJ, Fan Y, Lewis PO, Goffinet B.

J Mol Evol. 2008 Jul;67(1):111-22. doi: 10.1007/s00239-008-9133-1. Epub 2008 Jul 2.

PMID:
18594897
29.

Functional gene losses occur with minimal size reduction in the plastid genome of the parasitic liverwort Aneura mirabilis.

Wickett NJ, Zhang Y, Hansen SK, Roper JM, Kuehl JV, Plock SA, Wolf PG, DePamphilis CW, Boore JL, Goffinet B.

Mol Biol Evol. 2008 Feb;25(2):393-401. Epub 2007 Dec 1.

PMID:
18056074
30.

Distribution and phylogenetic significance of the 71-kb inversion in the plastid genome in Funariidae (Bryophyta).

Goffinet B, Wickett NJ, Werner O, Ros RM, Shaw AJ, Cox CJ.

Ann Bot. 2007 Apr;99(4):747-53. Epub 2007 Mar 2.

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