GetOrganelle: a fast and versatile toolkit for accurate de novo assembly of organelle genomes von Jin, Jian-Jun, Yu, Wen-Bin, Yang, Jun-Bo, Song, Yu, dePamphilis, Claude W., Yi, Ting-Shuang, Li, De-Zhu

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MicroRNAs from the parasitic plant Cuscuta campestris target host messenger RNAs von Shahid, Saima, Kim, Gunjune, Johnson, Nathan R., Wafula, Eric, Wang, Feng, Coruh, Ceyda, Bernal-Galeano, Vivian, Phifer, Tamia, dePamphilis, Claude W., Westwood, James H., Axtell, Michael J.

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The evolution of the plastid chromosome in land plants: gene content, gene order, gene function von Wicke, Susann, Schneeweiss, Gerald M., dePamphilis, Claude W., Müller, Kai F., Quandt, Dietmar

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Genomic-scale exchange of mRNA between a parasitic plant and its hosts von Kim, Gunjune, LeBlanc, Megan L., Wafula, Eric K., dePamphilis, Claude W., Westwood, James H.

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Mechanistic model of evolutionary rate variation en route to a nonphotosynthetic lifestyle in plants von Wicke, Susann, Müller, Kai F., dePamphilis, Claude W., Quandt, Dietmar, Bellot, Sidonie, Schneeweiss, Gerald M.

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Local Auxin Biosynthesis Mediated by a YUCCA Flavin Monooxygenase Regulates Haustorium Development in the Parasitic Plant Phtheirospermum japonicum von Ishida, Juliane K., Wakatake, Takanori, Yoshida, Satoko, Takebayashi, Yumiko, Kasahara, Hiroyuki, Wafula, Eric, de Pamphilis, Claude W., Namba, Shigetou, Shirasu, Ken

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RNA viruses in hymenopteran pollinators: evidence of inter-Taxa virus transmission via pollen and potential impact on non-Apis hymenopteran species von Singh, Rajwinder, Levitt, Abby L, Rajotte, Edwin G, Holmes, Edward C, Ostiguy, Nancy, Vanengelsdorp, Dennis, Lipkin, W Ian, Depamphilis, Claude W, Toth, Amy L, Cox-Foster, Diana L

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Genomics of sorghum local adaptation to a parasitic plant von Bellis, Emily S., Kelly, Elizabeth A., Lorts, Claire M., Gao, Huirong, DeLeo, Victoria L., Rouhan, Germinal, Budden, Andrew, Bhaskara, Govinal B., Hu, Zhenbin, Muscarella, Robert, Timko, Michael P., Nebie, Baloua, Runo, Steven M., Chilcoat, N. Doane, Juenger, Thomas E., Morris, Geoffrey P., dePamphilis, Claude W., Lasky, Jesse R.

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Single-copy nuclear genes place haustorial Hydnoraceae within piperales and reveal a cretaceous origin of multiple parasitic angiosperm lineages von Naumann, Julia, Salomo, Karsten, Der, Joshua P, Wafula, Eric K, Bolin, Jay F, Maass, Erika, Frenzke, Lena, Samain, Marie-Stéphanie, Neinhuis, Christoph, dePamphilis, Claude W, Wanke, Stefan

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PlantTribes2: Tools for comparative gene family analysis in plant genomics von Wafula, Eric K, Zhang, Huiting, Von Kuster, Gregory, Leebens-Mack, James H, Honaas, Loren A, dePamphilis, Claude W

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Selecting Superior De Novo Transcriptome Assemblies: Lessons Learned by Leveraging the Best Plant Genome von Honaas, Loren A, Wafula, Eric K, Wickett, Norman J, Der, Joshua P, Zhang, Yeting, Edger, Patrick P, Altman, Naomi S, Pires, J Chris, Leebens-Mack, James H, dePamphilis, Claude W

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FLOWERING LOCUS T duplication coordinates reproductive and vegetative growth in perennial poplar von Hsu, Chuan-Yu, Adams, Joshua P, Kim, Hyejin, No, Kyoungok, Ma, Caiping, Strauss, Steven H, Drnevich, Jenny, Vandervelde, Lindsay, Ellis, Jeffrey D, Rice, Brandon M, Wickett, Norman, Gunter, Lee E, Tuskan, Gerald A, Brunner, Amy M, Page, Grier P, Barakat, Abdelali, Carlson, John E, dePamphilis, Claude W, Luthe, Dawn S, Yuceer, Cetin

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Analysis of 81 genes from 64 plastid genomes resolves relationships in angiosperms and identifies genome-scale evolutionary patterns von Jansen, Robert K, Cai, Zhengqiu, Raubeson, Linda A, Daniell, Henry, dePamphilis, Claude W, Leebens-Mack, James, Müller, Kai F, Guisinger-Bellian, Mary, Haberle, Rosemarie C, Hansen, Anne K, Chumley, Timothy W, Lee, Seung-Bum, Peery, Rhiannon, McNeal, Joel R, Kuehl, Jennifer V, Boore, Jeffrey L

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De novo characterization of the gametophyte transcriptome in bracken fern, Pteridium aquilinum von Der, Joshua P, Barker, Michael S, Wickett, Norman J, dePamphilis, Claude W, Wolf, Paul G

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Transcriptomes of the Parasitic Plant Family Orobanchaceae Reveal Surprising Conservation of Chlorophyll Synthesis von Wickett, Norman J., Honaas, Loren A., Wafula, Eric K., Das, Malay, Huang, Kan, Wu, Biao, Landherr, Lena, Timko, Michael P., Yoder, John, Westwood, James H., dePamphilis, Claude W.

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Identification of shared single copy nuclear genes in Arabidopsis, Populus, Vitis and Oryza and their phylogenetic utility across various taxonomic levels von Duarte, Jill M, Wall, P Kerr, Edger, Patrick P, Landherr, Lena L, Ma, Hong, Pires, J Chris, Leebens-Mack, Jim, dePamphilis, Claude W

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Genome-wide identification of MST, SUT and SWEET family sugar transporters in root parasitic angiosperms and analysis of their expression during host parasitism von Misra, Vikram A, Wafula, Eric K, Wang, Yu, dePamphilis, Claude W, Timko, Michael P

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Patterns of gene duplication in the plant SKP1 gene family in angiosperms: evidence for multiple mechanisms of rapid gene birth von Kong, Hongzhi, Landherr, Lena L., Frohlich, Michael W., Leebens‐Mack, Jim, Ma, Hong, DePamphilis, Claude W.

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Compensatory sequence variation between trans -species small RNAs and their target sites von Johnson, Nathan R, dePamphilis, Claude W, Axtell, Michael J

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Evaluating methods for isolating total RNA and predicting the success of sequencing phylogenetically diverse plant transcriptomes von Johnson, Marc T J, Carpenter, Eric J, Tian, Zhijian, Bruskiewich, Richard, Burris, Jason N, Carrigan, Charlotte T, Chase, Mark W, Clarke, Neil D, Covshoff, Sarah, Depamphilis, Claude W, Edger, Patrick P, Goh, Falicia, Graham, Sean, Greiner, Stephan, Hibberd, Julian M, Jordon-Thaden, Ingrid, Kutchan, Toni M, Leebens-Mack, James, Melkonian, Michael, Miles, Nicholas, Myburg, Henrietta, Patterson, Jordan, Pires, J Chris, Ralph, Paula, Rolf, Megan, Sage, Rowan F, Soltis, Douglas, Soltis, Pamela, Stevenson, Dennis, Stewart, Jr, C Neal, Surek, Barbara, Thomsen, Christina J M, Villarreal, Juan Carlos, Wu, Xiaolei, Zhang, Yong, Deyholos, Michael K, Wong, Gane Ka-Shu

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