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A genome triplication associated with early diversification of the core eudicots

Jiao, Yuannian; Leebens-Mack, Jim; Ayyampalayam, Saravanaraj; Bowers, John E; McKain, Michael R; McNeal, Joel; Rolf, Megan; Ruzicka, Daniel R; Wafula, Eric; Wickett, Norman J; Wu, Xiaolei; Zhang, Yong; Wang, Jun; Zhang, Yeting; Carpenter, Eric J; Deyholos, Michael K; Kutchan, Toni M; Chanderbali, Andre S; Soltis, Pamela S; Stevenson, Dennis W; McCombie, Richard; Pires, J C; Wong, Gane KS; Soltis, Douglas E; dePamphilis, Claude W (2012-01-26)

Abstract Background Although it is agreed that a major polyploidy event, gamma, occurred within the eudicots, the phylogenetic placement of the event remains unclear. Results To determine when this polyploidization ...

Data access for the 1,000 Plants (1KP) project

Matasci, Naim; Hung, Ling-Hong; Yan, Zhixiang; Carpenter, Eric J; Wickett, Norman J; Mirarab, Siavash; Nguyen, Nam; Warnow, Tandy; Ayyampalayam, Saravanaraj; Barker, Michael; Burleigh, J G; Gitzendanner, Matthew A; Wafula, Eric; Der, Joshua P; dePamphilis, Claude W; Roure, Béatrice; Philippe, Hervé; Ruhfel, Brad R; Miles, Nicholas W; Graham, Sean W; Mathews, Sarah; Surek, Barbara; Melkonian, Michael; Soltis, Douglas E; Soltis, Pamela S; Rothfels, Carl; Pokorny, Lisa; Shaw, Jonathan A; DeGironimo, Lisa; Stevenson, Dennis W; Villarreal, Juan C; Chen, Tao; Kutchan, Toni M; Rolf, Megan; Baucom, Regina S; Deyholos, Michael K; Samudrala, Ram; Tian, Zhijian; Wu, Xiaolei; Sun, Xiao; Zhang, Yong; Wang, Jun; Leebens-Mack, Jim; Wong, Gane K (2014-10-27)

Abstract The 1,000 plants (1KP) project is an international multi-disciplinary consortium that has generated transcriptome data from over 1,000 plant species, with exemplars for all of the major lineages ...

A physical map for the Amborella trichopoda genome sheds light on the evolution of angiosperm genome structure

Zuccolo, Andrea; Bowers, John E; Estill, James C; Xiong, Zhiyong; Luo, Meizhong; Sebastian, Aswathy; Goicoechea, José L; Collura, Kristi; Yu, Yeisoo; Jiao, Yuannian; Duarte, Jill; Tang, Haibao; Ayyampalayam, Saravanaraj; Rounsley, Steve; Kudrna, Dave; Paterson, Andrew H; Pires, J C; Chanderbali, Andre; Soltis, Douglas E; Chamala, Srikar; Barbazuk, Brad; Soltis, Pamela S; Albert, Victor A; Ma, Hong; Mandoli, Dina; Banks, Jody; Carlson, John E; Tomkins, Jeffrey; dePamphilis, Claude W; Wing, Rod A; Leebens-Mack, Jim (2011-05-27)

Abstract Background Recent phylogenetic analyses have identified Amborella trichopoda, an understory tree species endemic to the forests of New Caledonia, as sister to a clade including all other known flowering plant ...

Comparison of next generation sequencing technologies for transcriptome characterization

Wall, P Kerr; Leebens-Mack, Jim; Chanderbali, André S; Barakat, Abdelali; Wolcott, Erik; Liang, Haiying; Landherr, Lena; Tomsho, Lynn P; Hu, Yi; Carlson, John E; Ma, Hong; Schuster, Stephan C; Soltis, Douglas E; Soltis, Pamela S; Altman, Naomi; dePamphilis, Claude W (2009-08-01)

Abstract Background We have developed a simulation approach to help determine the optimal mixture of sequencing methods for most ...