GENESPACE tracks regions of interest and gene copy number variation across multiple genomes von Lovell, John T, Sreedasyam, Avinash, Schranz, M Eric, Wilson, Melissa, Carlson, Joseph W, Harkess, Alex, Emms, David, Goodstein, David M, Schmutz, Jeremy

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Phytozome: a comparative platform for green plant genomics von Goodstein, David M., Shu, Shengqiang, Howson, Russell, Neupane, Rochak, Hayes, Richard D., Fazo, Joni, Mitros, Therese, Dirks, William, Hellsten, Uffe, Putnam, Nicholas , Rokhsar, Daniel S.

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The Amphimedon queenslandica genome and the evolution of animal complexity von Srivastava, Mansi, Degnan, Bernard M, Rokhsar, Daniel S, Simakov, Oleg, Chapman, Jarrod, Fahey, Bryony, Gauthier, Marie E. A, Mitros, Therese, Richards, Gemma S, Conaco, Cecilia, Dacre, Michael, Hellsten, Uffe, Larroux, Claire, Putnam, Nicholas H, Stanke, Mario, Adamska, Maja, Darling, Aaron, Degnan, Sandie M, Oakley, Todd H, Plachetzki, David C, Zhai, Yufeng, Adamski, Marcin, Calcino, Andrew, Cummins, Scott F, Goodstein, David M, Harris, Christina, Jackson, Daniel J, Leys, Sally P, Shu, Shengqiang, Woodcroft, Ben J, Vervoort, Michel, Kosik, Kenneth S, Manning, Gerard

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The Kalanchoë genome provides insights into convergent evolution and building blocks of crassulacean acid metabolism von Yang, Xiaohan, Hu, Rongbin, Yin, Hengfu, Jenkins, Jerry, Shu, Shengqiang, Tang, Haibao, Liu, Degao, Weighill, Deborah A., Cheol Yim, Won, Ha, Jungmin, Heyduk, Karolina, Goodstein, David M., Guo, Hao-Bo, Moseley, Robert C., Fitzek, Elisabeth, Jawdy, Sara, Zhang, Zhihao, Xie, Meng, Hartwell, James, Grimwood, Jane, Abraham, Paul E., Mewalal, Ritesh, Beltrán, Juan D., Boxall, Susanna F., Dever, Louisa V., Palla, Kaitlin J., Albion, Rebecca, Garcia, Travis, Mayer, Jesse A., Don Lim, Sung, Man Wai, Ching, Peluso, Paul, Van Buren, Robert, De Paoli, Henrique Cestari, Borland, Anne M., Guo, Hong, Chen, Jin-Gui, Muchero, Wellington, Yin, Yanbin, Jacobson, Daniel A., Tschaplinski, Timothy J., Hettich, Robert L., Ming, Ray, Winter, Klaus, Leebens-Mack, James H., Smith, J. Andrew C., Cushman, John C., Schmutz, Jeremy, Tuskan, Gerald A.

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A view of the pan‐genome of domesticated Cowpea (Vigna unguiculata [L.] Walp.) von Liang, Qihua, Muñoz‐Amatriaín, María, Shu, Shengqiang, Lo, Sassoum, Wu, Xinyi, Carlson, Joseph W., Davidson, Patrick, Goodstein, David M., Phillips, Jeremy, Janis, Nadia M., Lee, Elaine J., Liang, Chenxi, Morrell, Peter L., Farmer, Andrew D., Xu, Pei, Close, Timothy J., Lonardi, Stefano

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JBrowse: a dynamic web platform for genome visualization and analysis von Buels, Robert, Yao, Eric, Diesh, Colin M, Hayes, Richard D, Munoz-Torres, Monica, Helt, Gregg, Goodstein, David M, Elsik, Christine G, Lewis, Suzanna E, Stein, Lincoln, Holmes, Ian H

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The Chlamydomonas Genome Project, version 6: Reference assemblies for mating-type plus and minus strains reveal extensive structural mutation in the laboratory von Craig, Rory J, Gallaher, Sean D, Shu, Shengqiang, Salomé, Patrice A, Jenkins, Jerry W, Blaby-Haas, Crysten E, Purvine, Samuel O, O'Donnell, Samuel, Barry, Kerrie, Grimwood, Jane, Strenkert, Daniela, Kropat, Janette, Daum, Chris, Yoshinaga, Yuko, Goodstein, David M, Vallon, Olivier, Schmutz, Jeremy, Merchant, Sabeeha S

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The high-quality draft genome of peach (Prunus persica) identifies unique patterns of genetic diversity, domestication and genome evolution von Verde, Ignazio, Abbott, Albert G, Scalabrin, Simone, Jung, Sook, Shu, Shengqiang, Marroni, Fabio, Zhebentyayeva, Tatyana, Dettori, Maria Teresa, Grimwood, Jane, Cattonaro, Federica, Zuccolo, Andrea, Rossini, Laura, Jenkins, Jerry, Vendramin, Elisa, Meisel, Lee A, Decroocq, Veronique, Sosinski, Bryon, Prochnik, Simon, Mitros, Therese, Policriti, Alberto, Cipriani, Guido, Dondini, Luca, Ficklin, Stephen, Goodstein, David M, Xuan, Pengfei, Fabbro, Cristian Del, Aramini, Valeria, Copetti, Dario, Gonzalez, Susana, Horner, David S, Falchi, Rachele, Lucas, Susan, Mica, Erica, Maldonado, Jonathan, Lazzari, Barbara, Bielenberg, Douglas, Pirona, Raul, Miculan, Mara, Barakat, Abdelali, Testolin, Raffaele, Stella, Alessandra, Tartarini, Stefano, Tonutti, Pietro, Arús, Pere, Orellana, Ariel, Wells, Christina, Main, Dorrie, Vizzotto, Giannina, Silva, Herman, Salamini, Francesco, Schmutz, Jeremy, Morgante, Michele, Rokhsar, Daniel S

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A reference genome for common bean and genome-wide analysis of dual domestications von Schmutz, Jeremy, McClean, Phillip E, Mamidi, Sujan, Wu, G Albert, Cannon, Steven B, Grimwood, Jane, Jenkins, Jerry, Shu, Shengqiang, Song, Qijian, Chavarro, Carolina, Torres-Torres, Mirayda, Geffroy, Valerie, Moghaddam, Samira Mafi, Gao, Dongying, Abernathy, Brian, Barry, Kerrie, Blair, Matthew, Brick, Mark A, Chovatia, Mansi, Gepts, Paul, Goodstein, David M, Gonzales, Michael, Hellsten, Uffe, Hyten, David L, Jia, Gaofeng, Kelly, James D, Kudrna, Dave, Lee, Rian, Richard, Manon M S, Miklas, Phillip N, Osorno, Juan M, Rodrigues, Josiane, Thareau, Vincent, Urrea, Carlos A, Wang, Mei, Yu, Yeisoo, Zhang, Ming, Wing, Rod A, Cregan, Perry B, Rokhsar, Daniel S, Jackson, Scott A

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Construction and comparison of three reference‐quality genome assemblies for soybean von Valliyodan, Babu, Cannon, Steven B., Bayer, Philipp E., Shu, Shengqiang, Brown, Anne V., Ren, Longhui, Jenkins, Jerry, Chung, Claire Y.‐L., Chan, Ting‐Fung, Daum, Christopher G., Plott, Christopher, Hastie, Alex, Baruch, Kobi, Barry, Kerrie W., Huang, Wei, Patil, Gunvant, Varshney, Rajeev K., Hu, Haifei, Batley, Jacqueline, Yuan, Yuxuan, Song, Qijian, Stupar, Robert M., Goodstein, David M., Stacey, Gary, Lam, Hon‐Ming, Jackson, Scott A., Schmutz, Jeremy, Grimwood, Jane, Edwards, David, Nguyen, Henry T.

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Multiple origins, one evolutionary trajectory: gradual evolution characterizes distinct lineages of allotetraploid Brachypodium von Scarlett, Virginia T, Lovell, John T, Shao, Mingqin, Phillips, Jeremy, Shu, Shengqiang, Lusinska, Joanna, Goodstein, David M, Jenkins, Jerry, Grimwood, Jane, Barry, Kerrie, Chalhoub, Boulos, Schmutz, Jeremy, Hasterok, Robert, Catalán, Pilar, Vogel, John P

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Genome sequence and evolution of Betula platyphylla von Chen, Su, Wang, Yucheng, Yu, Lili, Zheng, Tao, Wang, Sui, Yue, Zhen, Jiang, Jing, Kumari, Sapna, Zheng, Chunfang, Tang, Haibao, Li, Jun, Li, Yuqi, Chen, Jiongjiong, Zhang, Wenbo, Kuang, Hanhui, Robertson, Jon S., Zhao, Patrick X., Li, Huiyu, Shu, Shengqiang, Yordanov, Yordan S., Huang, Haijiao, Goodstein, David M., Gai, Ying, Qi, Qi, Min, JiuMeng, Xu, ChunYan, Wang, SongBo, Qu, Guan-Zheng, Paterson, Andrew H., Sankoff, David, Wei, Hairong, Liu, Guifeng, Yang, Chuanping

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The reference genome and abiotic stress responses of the model perennial grass Brachypodium sylvaticum von Lei, Li, Gordon, Sean P, Liu, Lifeng, Sade, Nir, Lovell, John T, Rubio Wilhelmi, Maria Del Mar, Singan, Vasanth, Sreedasyam, Avinash, Hestrin, Rachel, Phillips, Jeremy, Hernandez, Bryan T, Barry, Kerrie, Shu, Shengqiang, Jenkins, Jerry, Schmutz, Jeremy, Goodstein, David M, Thilmony, Roger, Blumwald, Eduardo, Vogel, John P

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The genome of Eucalyptus grandis von Myburg, Alexander A., Grattapaglia, Dario, Tuskan, Gerald A., Hellsten, Uffe, Hayes, Richard D., Grimwood, Jane, Jenkins, Jerry, Lindquist, Erika, Tice, Hope, Bauer, Diane, Goodstein, David M., Dubchak, Inna, Poliakov, Alexandre, Mizrachi, Eshchar, Kullan, Anand R. K., Hussey, Steven G., Pinard, Desre, van der Merwe, Karen, Singh, Pooja, van Jaarsveld, Ida, Silva-Junior, Orzenil B., Togawa, Roberto C., Pappas, Marilia R., Faria, Danielle A., Sansaloni, Carolina P., Petroli, Cesar D., Yang, Xiaohan, Ranjan, Priya, Tschaplinski, Timothy J., Ye, Chu-Yu, Li, Ting, Sterck, Lieven, Vanneste, Kevin, Murat, Florent, Soler, Marçal, Clemente, Hélène San, Saidi, Naijib, Cassan-Wang, Hua, Dunand, Christophe, Hefer, Charles A., Bornberg-Bauer, Erich, Kersting, Anna R., Vining, Kelly, Amarasinghe, Vindhya, Ranik, Martin, Naithani, Sushma, Elser, Justin, Boyd, Alexander E., Liston, Aaron, Spatafora, Joseph W., Dharmwardhana, Palitha, Raja, Rajani, Sullivan, Christopher, Romanel, Elisson, Alves-Ferreira, Marcio, Külheim, Carsten, Foley, William, Carocha, Victor, Paiva, Jorge, Kudrna, David, Brommonschenkel, Sergio H., Pasquali, Giancarlo, Byrne, Margaret, Rigault, Philippe, Tibbits, Josquin, Spokevicius, Antanas, Jones, Rebecca C., Steane, Dorothy A., Vaillancourt, René E., Potts, Brad M., Joubert, Fourie, Barry, Kerrie, Pappas, Georgios J., Strauss, Steven H., Jaiswal, Pankaj, Grima-Pettenati, Jacqueline, Salse, Jérôme, Van de Peer, Yves, Rokhsar, Daniel S., Schmutz, Jeremy

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The Draft Genome of Ciona intestinalis: Insights into Chordate and Vertebrate Origins von Dehal, Paramvir, Satou, Yutaka, Campbell, Robert K., Chapman, Jarrod, Degnan, Bernard, de Tomaso, Anthony, Davidson, Brad, Di Gregorio, Anna, Gelpke, Maarten, Goodstein, David M., Harafuji, Naoe, Kenneth E. M. Hastings, Ho, Isaac, Hotta, Kohji, Huang, Wayne, Kawashima, Takeshi, Lemaire, Patrick, Martinez, Diego, Meinertzhagen, Ian A., Necula, Simona, Nonaka, Masaru, Putnam, Nik, Rash, Sam, Saiga, Hidetoshi, Satake, Masanobu, Terry, Astrid, Yamada, Lixy, Wang, Hong-Gang, Awazu, Satoko, Azumi, Kaoru, Boore, Jeffrey, Branno, Margherita, Chin-bow, Stephen, DeSantis, Rosaria, Doyle, Sharon, Francino, Pilar, Keys, David N., Haga, Shinobu, Hayashi, Hiroko, Hino, Kyosuke, Imai, Kaoru S., Inaba, Kazuo, Kano, Shungo, Kobayashi, Kenji, Kobayashi, Mari, Lee, Byung-In, Makabe, Kazuhiro W., Manohar, Chitra, Matassi, Giorgio, Medina, Monica, Mochizuki, Yasuaki, Mount, Steve, Morishita, Tomomi, Miura, Sachiko, Nakayama, Akie, Nishizaka, Satoko, Nomoto, Hisayo, Ohta, Fumiko, Oishi, Kazuko, Rigoutsos, Isidore, Sano, Masako, Sasaki, Akane, Sasakura, Yasunori, Shoguchi, Eiichi, Tadasu Shin-i, Spagnuolo, Antoinetta, Stainier, Didier, Suzuki, Miho M., Tassy, Olivier, Takatori, Naohito, Tokuoka, Miki, Yagi, Kasumi, Yoshizaki, Fumiko, Wada, Shuichi, Zhang, Cindy, Hyatt, P. Douglas, Larimer, Frank, Detter, Chris, Doggett, Norman, Glavina, Tijana, Hawkins, Trevor, Richardson, Paul, Lucas, Susan, Kohara, Yuji, Levine, Michael, Satoh, Nori, Rokhsar, Daniel S.

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The Chlamydomonas Genome Project, version 6: Reference assemblies for mating-type plus and minus strains reveal extensive structural mutation in the laboratory von Craig, Rory J., Gallaher, Sean D., Shu, Shengqiang, Salomé, Patrice A., Jenkins, Jerry W., Blaby-Haas, Crysten E., Purvine, Samuel O., O’Donnell, Samuel, Barry, Kerrie, Grimwood, Jane, Strenkert, Daniela, Kropat, Janette, Daum, Chris, Yoshinaga, Yuko, Goodstein, David M., Vallon, Olivier, Schmutz, Jeremy, Merchant, Sabeeha S.

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The reference genome and abiotic stress responses of the model perennial grass Brachypodium sylvaticum von Lei, Li, Gordon, Sean P., Liu, Lifeng, Sade, Nir, Lovell, John T., Rubio Wilhelmi, Maria Mar, Singan, Vasanth, Sreedasyam, Avinash, Hestrin, Rachel, Phillips, Jeremy, Hernandez, Bryan T., Barry, Kerrie, Shu, Shengqiang, Jenkins, Jerry, Schmutz, Jeremy, Goodstein, David M., Thilmony, Roger, Blumwald, Eduardo, Vogel, John P.

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A view of the pan-genome of domesticated Cowpea (Vigna unguiculata [L.] Walp.) von Liang, Qihua, Muñoz‐Amatriaín, María, Shu, Shengqiang, Lo, Sassoum, Wu, Xinyi, Carlson, Joseph W., Davidson, Patrick, Goodstein, David M., Phillips, Jeremy, Janis, Nadia M., Lee, Elaine J., Liang, Chenxi, Morrell, Peter L., Farmer, Andrew D., Xu, Pei, Close, Timothy J., Lonardi, Stefano

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The genome of Eucalyptus grandis von Myburg, Alexander A, Grattapaglia, Dario, Tuskan, Gerald A, Hellsten, Uffe, Hayes, Richard D, Grimwood, Jane, Jenkins, Jerry, Lindquist, Erika, Tice, Hope, Bauer, Diane, Goodstein, David M, Dubchak, Inna, Poliakov, Alexandre, Mizrachi, Eshchar, Kullan, Anand RK, Hussey, Steven G, Pinard, Desre, Van der Merwe, Karen, Singh, Pooja, Van Jaarsveld, Ida, Silva, Orzenil B, Togawa, Roberto C, Pappas, Marilia R, Faria, Danielle A, Sansaloni, Carolina P, Petroli, Cesar D, Yang, Xiaohan, Ranjan, Priya, Tschaplinski, Timothy J, Ye, Chu-Yu, Li, Ting, Sterck, Lieven, Vanneste, Kevin, Murat, Florent, Soler, Maral, San Clemente, Hélène, Saidi, Naijib, Cassan-Wang, Hua, Dunand, Christophe, Hefer, Charles A, Bornberg-Bauer, Erich, Kersting, Anna R, Vining, Kelly, Amarasinghe, Vindhya, Ranik, Martin, Naithani, Sushma, Elser, Justin, Boyd, Alexander E, Liston, Aaron, Spatafora, Joseph W, Dharmwardhana, Palitha, Raja, Rajani, Sullivan, Christopher, Romanel, Elisson, Alves-Ferreira, Marcio, Külheim, Carsten, Foley, William, Carocha, Victor, Paiva, Jorge, Kudrna, David, Brommonschenkel, Sergio H, Pasquali, Giancarlo, Byrne, Margaret, Rigault, Philippe, Tibbits, Josquin, Spokevicius, Antanas, Jones, Rebecca C, Steane, Dorothy A, Vaillancourt, René E, Potts, Brad M, Joubert, Fourie, Barry, Kerrie, Pappas Jr, Georgios J, Strauss, Steven H, Jaiswal, Pankaj, Grima-Pettenati, Jacqueline, Salse, Jérôme, Van de Peer, Yves, Rokhsar, Daniel S, Schmutz, Jeremy

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Supplemental Material for Lei et al., 2023 von Lei, Li, Gordon, Sean P., Liu, Lifeng, Sade, Nir, Lovell, John T., Wilhelmi, Maria Del Mar Rubio, Singan, Vasanth, Sreedasyam, Avinash, Hestrin, Rachel, Phillips, Jeremy, Hernandez, Bryan T., Barry, Kerrie, Shu, Shengqiang, Jenkins, Jerry, Schmutz, Jeremy, Goodstein, David M., Thilmony, Roger, Blumwald, Eduardo, Vogel, John P.

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