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3. One thousand plant transcriptomes and the phylogenomics of green plants

Author

Leebens-Mack, James H., Barker, Michael S., Carpenter, Eric J., Deyholos, Michael K., Gitzendanner, Matthew A., Graham, Sean W., Grosse, Ivo, Li, Zheng, Melkonian, Michael, Mirarab, Siavash, Porsch, Martin, Quint, Marcel, Rensing, Stefan A., Soltis, Douglas E., Soltis, Pamela S., Stevenson, Dennis W., Ullrich, Kristian K., Wickett, Norman J., DeGironimo, Lisa, Edger, Patrick P., Jordon-Thaden, Ingrid E., Joya, Steve, Liu, Tao, Melkonian, Barbara, Miles, Nicholas W., Pokorny, Lisa, Quigley, Charlotte, Thomas, Philip, Villarreal, Juan Carlos, Augustin, Megan M., Barrett, Matthew D., Baucom, Regina S., Beerling, David J., Benstein, Ruben Maximilian, Biffin, Ed, Brockington, Samuel F., Burge, Dylan O., Burris, Jason N., Burris, Kellie P., Burtet-Sarramegna, Valerie, Caicedo, Ana L., Cannon, Steven B., Cebi, Zehra, Chang, Ying, Chater, Caspar, Cheeseman, John M., Chen, Tao, Clarke, Neil D., Clayton, Harmony, Covshoff, Sarah, Crandall-Stotler, Barbara J., Cross, Hugh, dePamphilis, Claude W., Der, Joshua P., Determann, Ron, Dickson, Rowan C., Di Stilio, Veronica S., Ellis, Shona, Fast, Eva, Feja, Nicole, Field, Katie J., Filatov, Dmitry A., Finnegan, Patrick M., Floyd, Sandra K., Fogliani, Bruno, Garcia, Nicolas, Gateble, Gildas, Godden, Grant T., Goh, Falicia (Qi Yun), Greiner, Stephan, Harkess, Alex, Heaney, James Mike, Helliwell, Katherine E., Heyduk, Karolina, Hibberd, Julian M., Hodel, Richard G. J., Hollingsworth, Peter M., Johnson, Marc T. J., Jost, Ricarda, Joyce, Blake, Kapralov, Maxim V., Kazamia, Elena, Kellogg, Elizabeth A., Koch, Marcus A., Von Konrat, Matt, Konyves, Kalman, Kutchan, Toni M., Lam, Vivienne, Larsson, Anders, Leitch, Andrew R., Lentz, Roswitha, Li, Fay-Wei, Lowe, Andrew J., Ludwig, Martha, Manos, Paul S., Mavrodiev, Evgeny, McCormick, Melissa K., McKain, Michael, McLellan, Tracy, McNeal, Joel R., Miller, Richard E., Nelson, Matthew N., Peng, Yanhui, Ralph, Paula, Real, Daniel, Riggins, Chance W., Ruhsam, Markus, Sage, Rowan F., Sakai, Ann K., Scascitella, Moira, Schilling, Edward E., Schlosser, Eva-Marie, Sederoff, Heike, Servick, Stein, Sessa, Emily B., Shaw, A. Jonathan, Shaw, Shane W., Sigel, Erin M., Skema, Cynthia, Smith, Alison G., Smithson, Ann, Stewart, C. Neal, Jr., Stinchcombe, John R., Szovenyi, Peter, Tate, Jennifer A., Tiebel, Helga, Trapnell, Dorset, Villegente, Matthieu, Wang, Chun-Neng, Weller, Stephen G., Wenzel, Michael, Weststrand, Stina, Westwood, James H., Whigham, Dennis F., Wu, Shuangxiu, Wulff, Adrien S., Yang, Yu, Zhu, Dan, Zhuang, Cuili, Zuidof, Jennifer, Chase, Mark W., Pires, J. Chris, Rothfels, Carl J., Yu, Jun, Chen, Cui, Chen, Li, Cheng, Shifeng, Li, Juanjuan, Li, Ran, Li, Xia, Lu, Haorong, Ou, Yanxiang, Sun, Xiao, Tan, Xuemei, Tang, Jingbo, Tian, Zhijian, Wang, Feng, Wang, Jun, Wei, Xiaofeng, Xu, Xun, Yan, Zhixiang, Yang, Fan, Zhong, Xiaoni, Zhou, Feiyu, Zhu, Ying, Zhang, Yong, Ayyampalayam, Saravanaraj, Barkman, Todd J., Nguyen, Nam-Phuong, Matasci, Naim, Nelson, David R., Sayyari, Erfan, Wafula, Eric K., Walls, Ramona L., Warnow, Tandy, An, Hong, Arrigo, Nils, Baniaga, Anthony E., Galuska, Sally, Jorgensen, Stacy A., Kidder, Thomas I., Kong, Hanghui, Lu-Irving, Patricia, Marx, Hannah E., Qi, Xinshuai, Reardon, Chris R., Sutherland, Brittany L., Tiley, George P., Welles, Shana R., Yu, Rongpei, Zhan, Shing, Gramzow, Lydia, Theissen, Gunter, Wong, Gane Ka-Shu, Leebens-Mack, James H., Barker, Michael S., Carpenter, Eric J., Deyholos, Michael K., Gitzendanner, Matthew A., Graham, Sean W., Grosse, Ivo, Li, Zheng, Melkonian, Michael, Mirarab, Siavash, Porsch, Martin, Quint, Marcel, Rensing, Stefan A., Soltis, Douglas E., Soltis, Pamela S., Stevenson, Dennis W., Ullrich, Kristian K., Wickett, Norman J., DeGironimo, Lisa, Edger, Patrick P., Jordon-Thaden, Ingrid E., Joya, Steve, Liu, Tao, Melkonian, Barbara, Miles, Nicholas W., Pokorny, Lisa, Quigley, Charlotte, Thomas, Philip, Villarreal, Juan Carlos, Augustin, Megan M., Barrett, Matthew D., Baucom, Regina S., Beerling, David J., Benstein, Ruben Maximilian, Biffin, Ed, Brockington, Samuel F., Burge, Dylan O., Burris, Jason N., Burris, Kellie P., Burtet-Sarramegna, Valerie, Caicedo, Ana L., Cannon, Steven B., Cebi, Zehra, Chang, Ying, Chater, Caspar, Cheeseman, John M., Chen, Tao, Clarke, Neil D., Clayton, Harmony, Covshoff, Sarah, Crandall-Stotler, Barbara J., Cross, Hugh, dePamphilis, Claude W., Der, Joshua P., Determann, Ron, Dickson, Rowan C., Di Stilio, Veronica S., Ellis, Shona, Fast, Eva, Feja, Nicole, Field, Katie J., Filatov, Dmitry A., Finnegan, Patrick M., Floyd, Sandra K., Fogliani, Bruno, Garcia, Nicolas, Gateble, Gildas, Godden, Grant T., Goh, Falicia (Qi Yun), Greiner, Stephan, Harkess, Alex, Heaney, James Mike, Helliwell, Katherine E., Heyduk, Karolina, Hibberd, Julian M., Hodel, Richard G. J., Hollingsworth, Peter M., Johnson, Marc T. J., Jost, Ricarda, Joyce, Blake, Kapralov, Maxim V., Kazamia, Elena, Kellogg, Elizabeth A., Koch, Marcus A., Von Konrat, Matt, Konyves, Kalman, Kutchan, Toni M., Lam, Vivienne, Larsson, Anders, Leitch, Andrew R., Lentz, Roswitha, Li, Fay-Wei, Lowe, Andrew J., Ludwig, Martha, Manos, Paul S., Mavrodiev, Evgeny, McCormick, Melissa K., McKain, Michael, McLellan, Tracy, McNeal, Joel R., Miller, Richard E., Nelson, Matthew N., Peng, Yanhui, Ralph, Paula, Real, Daniel, Riggins, Chance W., Ruhsam, Markus, Sage, Rowan F., Sakai, Ann K., Scascitella, Moira, Schilling, Edward E., Schlosser, Eva-Marie, Sederoff, Heike, Servick, Stein, Sessa, Emily B., Shaw, A. Jonathan, Shaw, Shane W., Sigel, Erin M., Skema, Cynthia, Smith, Alison G., Smithson, Ann, Stewart, C. Neal, Jr., Stinchcombe, John R., Szovenyi, Peter, Tate, Jennifer A., Tiebel, Helga, Trapnell, Dorset, Villegente, Matthieu, Wang, Chun-Neng, Weller, Stephen G., Wenzel, Michael, Weststrand, Stina, Westwood, James H., Whigham, Dennis F., Wu, Shuangxiu, Wulff, Adrien S., Yang, Yu, Zhu, Dan, Zhuang, Cuili, Zuidof, Jennifer, Chase, Mark W., Pires, J. Chris, Rothfels, Carl J., Yu, Jun, Chen, Cui, Chen, Li, Cheng, Shifeng, Li, Juanjuan, Li, Ran, Li, Xia, Lu, Haorong, Ou, Yanxiang, Sun, Xiao, Tan, Xuemei, Tang, Jingbo, Tian, Zhijian, Wang, Feng, Wang, Jun, Wei, Xiaofeng, Xu, Xun, Yan, Zhixiang, Yang, Fan, Zhong, Xiaoni, Zhou, Feiyu, Zhu, Ying, Zhang, Yong, Ayyampalayam, Saravanaraj, Barkman, Todd J., Nguyen, Nam-Phuong, Matasci, Naim, Nelson, David R., Sayyari, Erfan, Wafula, Eric K., Walls, Ramona L., Warnow, Tandy, An, Hong, Arrigo, Nils, Baniaga, Anthony E., Galuska, Sally, Jorgensen, Stacy A., Kidder, Thomas I., Kong, Hanghui, Lu-Irving, Patricia, Marx, Hannah E., Qi, Xinshuai, Reardon, Chris R., Sutherland, Brittany L., Tiley, George P., Welles, Shana R., Yu, Rongpei, Zhan, Shing, Gramzow, Lydia, Theissen, Gunter, and Wong, Gane Ka-Shu

Abstract

Green plants (Viridiplantae) include around 450,000-500,000 species(1,2) of great diversity and have important roles in terrestrial and aquatic ecosystems. Here, as part of the One Thousand Plant Transcriptomes Initiative, we sequenced the vegetative transcriptomes of 1,124 species that span the diversity of plants in a broad sense (Archaeplastida), including green plants (Viridiplantae), glaucophytes (Glaucophyta) and red algae (Rhodophyta). Our analysis provides a robust phylogenomic framework for examining the evolution of green plants. Most inferred species relationships are well supported across multiple species tree and supermatrix analyses, but discordance among plastid and nuclear gene trees at a few important nodes highlights the complexity of plant genome evolution, including polyploidy, periods of rapid speciation, and extinction. Incomplete sorting of ancestral variation, polyploidization and massive expansions of gene families punctuate the evolutionary history of green plants. Notably, we find that large expansions of gene families preceded the origins of green plants, land plants and vascular plants, whereas whole-genome duplications are inferred to have occurred repeatedly throughout the evolution of flowering plants and ferns. The increasing availability of high-quality plant genome sequences and advances in functional genomics are enabling research on genome evolution across the green tree of life.

Published
2019
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4. One thousand plant transcriptomes and the phylogenomics of green plants

Author

School of Plant and Environmental Sciences, Leebens-Mack, James H., Barker, Michael S., Carpenter, Eric J., Deyholos, Michael K., Gitzendanner, Matthew A., Graham, Sean W., Grosse, Ivo, Li, Zheng, Melkonian, Michael, Mirarab, Siavash, Porsch, Martin, Quint, Marcel, Rensing, Stefan A., Soltis, Douglas E., Soltis, Pamela S., Stevenson, Dennis W., Ullrich, Kristian K., Wickett, Norman J., DeGironimo, Lisa, Edger, Patrick P., Jordon-Thaden, Ingrid E., Joya, Steve, Liu, Tao, Melkonian, Barbara, Miles, Nicholas W., Pokorny, Lisa, Quigley, Charlotte, Thomas, Philip, Villarreal, Juan Carlos, Augustin, Megan M., Barrett, Matthew D., Baucom, Regina S., Beerling, David J., Benstein, Ruben Maximilian, Biffin, Ed, Brockington, Samuel F., Burge, Dylan O., Burris, Jason N., Burris, Kellie P., Burtet-Sarramegna, Valerie, Caicedo, Ana L., Cannon, Steven B., Cebi, Zehra, Chang, Ying, Chater, Caspar, Cheeseman, John M., Chen, Tao, Clarke, Neil D., Clayton, Harmony, Covshoff, Sarah, Crandall-Stotler, Barbara J., Cross, Hugh, dePamphilis, Claude W., Der, Joshua P., Determann, Ron, Dickson, Rowan C., Di Stilio, Veronica S., Ellis, Shona, Fast, Eva, Feja, Nicole, Field, Katie J., Filatov, Dmitry A., Finnegan, Patrick M., Floyd, Sandra K., Fogliani, Bruno, Garcia, Nicolas, Gateble, Gildas, Godden, Grant T., Goh, Falicia (Qi Yun), Greiner, Stephan, Harkess, Alex, Heaney, James Mike, Helliwell, Katherine E., Heyduk, Karolina, Hibberd, Julian M., Hodel, Richard G. J., Hollingsworth, Peter M., Johnson, Marc T. J., Jost, Ricarda, Joyce, Blake, Kapralov, Maxim V., Kazamia, Elena, Kellogg, Elizabeth A., Koch, Marcus A., Von Konrat, Matt, Konyves, Kalman, Kutchan, Toni M., Lam, Vivienne, Larsson, Anders, Leitch, Andrew R., Lentz, Roswitha, Li, Fay-Wei, Lowe, Andrew J., Ludwig, Martha, Manos, Paul S., Mavrodiev, Evgeny, McCormick, Melissa K., McKain, Michael, McLellan, Tracy, McNeal, Joel R., Miller, Richard E., Nelson, Matthew N., Peng, Yanhui, Ralph, Paula E., Real, Daniel, Riggins, Chance W., Ruhsam, Markus, Sage, Rowan F., Sakai, Ann K., Scascitella, Moira, Schilling, Edward E., Schlosser, Eva-Marie, Sederoff, Heike, Servick, Stein, Sessa, Emily B., Shaw, A. Jonathan, Shaw, Shane W., Sigel, Erin M., Skema, Cynthia, Smith, Alison G., Smithson, Ann, Stewart, C. Neal, Jr., Stinchcombe, John R., Szovenyi, Peter, Tate, Jennifer A., Tiebel, Helga, Trapnell, Dorset, Villegente, Matthieu, Wang, Chun-Neng, Weller, Stephen G., Wenzel, Michael, Weststrand, Stina, Westwood, James H., Whigham, Dennis F., Wu, Shuangxiu, Wulff, Adrien S., Yang, Yu, Zhu, Dan, Zhuang, Cuili, Zuidof, Jennifer, Chase, Mark W., Pires, J. Chris, Rothfels, Carl J., Yu, Jun, Chen, Cui, Chen, Li, Cheng, Shifeng, Li, Juanjuan, Li, Ran, Li, Xia, Lu, Haorong, Ou, Yanxiang, Sun, Xiao, Tan, Xuemei, Tang, Jingbo, Tian, Zhijian, Wang, Feng, Wang, Jun, Wei, Xiaofeng, Xu, Xun, Yan, Zhixiang, Yang, Fan, Zhong, Xiaoni, Zhou, Feiyu, Zhu, Ying, Zhang, Yong, Ayyampalayam, Saravanaraj, Barkman, Todd J., Nam-Phuong Nguyen, Matasci, Naim, Nelson, David R., Sayyari, Erfan, Wafula, Eric K., Walls, Ramona L., Warnow, Tandy, An, Hong, Arrigo, Nils, Baniaga, Anthony E., Galuska, Sally, Jorgensen, Stacy A., Kidder, Thomas I., Kong, Hanghui, Lu-Irving, Patricia, Marx, Hannah E., Qi, Xinshuai, Reardon, Chris R., Sutherland, Brittany L., Tiley, George P., Welles, Shana R., Yu, Rongpei, Zhan, Shing, Gramzow, Lydia, Theissen, Gunter, Wong, Gane Ka-Shu, School of Plant and Environmental Sciences, Leebens-Mack, James H., Barker, Michael S., Carpenter, Eric J., Deyholos, Michael K., Gitzendanner, Matthew A., Graham, Sean W., Grosse, Ivo, Li, Zheng, Melkonian, Michael, Mirarab, Siavash, Porsch, Martin, Quint, Marcel, Rensing, Stefan A., Soltis, Douglas E., Soltis, Pamela S., Stevenson, Dennis W., Ullrich, Kristian K., Wickett, Norman J., DeGironimo, Lisa, Edger, Patrick P., Jordon-Thaden, Ingrid E., Joya, Steve, Liu, Tao, Melkonian, Barbara, Miles, Nicholas W., Pokorny, Lisa, Quigley, Charlotte, Thomas, Philip, Villarreal, Juan Carlos, Augustin, Megan M., Barrett, Matthew D., Baucom, Regina S., Beerling, David J., Benstein, Ruben Maximilian, Biffin, Ed, Brockington, Samuel F., Burge, Dylan O., Burris, Jason N., Burris, Kellie P., Burtet-Sarramegna, Valerie, Caicedo, Ana L., Cannon, Steven B., Cebi, Zehra, Chang, Ying, Chater, Caspar, Cheeseman, John M., Chen, Tao, Clarke, Neil D., Clayton, Harmony, Covshoff, Sarah, Crandall-Stotler, Barbara J., Cross, Hugh, dePamphilis, Claude W., Der, Joshua P., Determann, Ron, Dickson, Rowan C., Di Stilio, Veronica S., Ellis, Shona, Fast, Eva, Feja, Nicole, Field, Katie J., Filatov, Dmitry A., Finnegan, Patrick M., Floyd, Sandra K., Fogliani, Bruno, Garcia, Nicolas, Gateble, Gildas, Godden, Grant T., Goh, Falicia (Qi Yun), Greiner, Stephan, Harkess, Alex, Heaney, James Mike, Helliwell, Katherine E., Heyduk, Karolina, Hibberd, Julian M., Hodel, Richard G. J., Hollingsworth, Peter M., Johnson, Marc T. J., Jost, Ricarda, Joyce, Blake, Kapralov, Maxim V., Kazamia, Elena, Kellogg, Elizabeth A., Koch, Marcus A., Von Konrat, Matt, Konyves, Kalman, Kutchan, Toni M., Lam, Vivienne, Larsson, Anders, Leitch, Andrew R., Lentz, Roswitha, Li, Fay-Wei, Lowe, Andrew J., Ludwig, Martha, Manos, Paul S., Mavrodiev, Evgeny, McCormick, Melissa K., McKain, Michael, McLellan, Tracy, McNeal, Joel R., Miller, Richard E., Nelson, Matthew N., Peng, Yanhui, Ralph, Paula E., Real, Daniel, Riggins, Chance W., Ruhsam, Markus, Sage, Rowan F., Sakai, Ann K., Scascitella, Moira, Schilling, Edward E., Schlosser, Eva-Marie, Sederoff, Heike, Servick, Stein, Sessa, Emily B., Shaw, A. Jonathan, Shaw, Shane W., Sigel, Erin M., Skema, Cynthia, Smith, Alison G., Smithson, Ann, Stewart, C. Neal, Jr., Stinchcombe, John R., Szovenyi, Peter, Tate, Jennifer A., Tiebel, Helga, Trapnell, Dorset, Villegente, Matthieu, Wang, Chun-Neng, Weller, Stephen G., Wenzel, Michael, Weststrand, Stina, Westwood, James H., Whigham, Dennis F., Wu, Shuangxiu, Wulff, Adrien S., Yang, Yu, Zhu, Dan, Zhuang, Cuili, Zuidof, Jennifer, Chase, Mark W., Pires, J. Chris, Rothfels, Carl J., Yu, Jun, Chen, Cui, Chen, Li, Cheng, Shifeng, Li, Juanjuan, Li, Ran, Li, Xia, Lu, Haorong, Ou, Yanxiang, Sun, Xiao, Tan, Xuemei, Tang, Jingbo, Tian, Zhijian, Wang, Feng, Wang, Jun, Wei, Xiaofeng, Xu, Xun, Yan, Zhixiang, Yang, Fan, Zhong, Xiaoni, Zhou, Feiyu, Zhu, Ying, Zhang, Yong, Ayyampalayam, Saravanaraj, Barkman, Todd J., Nam-Phuong Nguyen, Matasci, Naim, Nelson, David R., Sayyari, Erfan, Wafula, Eric K., Walls, Ramona L., Warnow, Tandy, An, Hong, Arrigo, Nils, Baniaga, Anthony E., Galuska, Sally, Jorgensen, Stacy A., Kidder, Thomas I., Kong, Hanghui, Lu-Irving, Patricia, Marx, Hannah E., Qi, Xinshuai, Reardon, Chris R., Sutherland, Brittany L., Tiley, George P., Welles, Shana R., Yu, Rongpei, Zhan, Shing, Gramzow, Lydia, Theissen, Gunter, and Wong, Gane Ka-Shu

Abstract

Green plants (Viridiplantae) include around 450,000-500,000 species(1,2) of great diversity and have important roles in terrestrial and aquatic ecosystems. Here, as part of the One Thousand Plant Transcriptomes Initiative, we sequenced the vegetative transcriptomes of 1,124 species that span the diversity of plants in a broad sense (Archaeplastida), including green plants (Viridiplantae), glaucophytes (Glaucophyta) and red algae (Rhodophyta). Our analysis provides a robust phylogenomic framework for examining the evolution of green plants. Most inferred species relationships are well supported across multiple species tree and supermatrix analyses, but discordance among plastid and nuclear gene trees at a few important nodes highlights the complexity of plant genome evolution, including polyploidy, periods of rapid speciation, and extinction. Incomplete sorting of ancestral variation, polyploidization and massive expansions of gene families punctuate the evolutionary history of green plants. Notably, we find that large expansions of gene families preceded the origins of green plants, land plants and vascular plants, whereas whole-genome duplications are inferred to have occurred repeatedly throughout the evolution of flowering plants and ferns. The increasing availability of high-quality plant genome sequences and advances in functional genomics are enabling research on genome evolution across the green tree of life.

Published
2019

5. One thousand plant transcriptomes and the phylogenomics of green plants

Author

National Key Research and Development Program (China), Ministry of Science and Technology of the People's Republic of China, Leebens-Mack, James H., Barker, M. S., Carpenter, Eric J., Deyholos, Michael K., Gitzendanner, Matthew A., Graham, Sean W., Grosse,Ivo, Li, Zheng, Melkonian, Michael, Mirarab, Siavash, Porsch, Martin, Nelson, Matthew N., Peng, Yanhui, Ralph, Paula, Real, Daniel, Riggins, Chance W., Ruhsam, Markus, Sage, Rowan F., Sakai, Ann K., Scascitella, Moira, Schilling, Edward E., Quint, Marcel, Schlösser, Eva-Marie, Sederoff, Heike, Servick, Stein, Sessa, Emily B., Shaw, Jonathan, Shane W., Sigel, Erin M., Skema, Cynthia, Smith, Alison G., Smithson, Ann, Rensing, Stefan A., Stewart Jr, Neal, Stinchcombe, John R., Szövényi, Peter, Tate, Jennifer A., Tiebel, Helga, Trapnell, Dorset, Villegente, Matthieu, Wang, Chun-Neng, Weller, Stephen G., Wenzel, Michael, Soltis, Douglas E., Weststrand, Stina, Westwood, James H., Whigham, Dennis F., Wu, Shuangxiu, Wulff , Adrien S., Yang, Yu, Zhu, Dan, Zhuang, Cuili, Zuidof, Jennifer, Pires, J. Chris, Soltis, Pamela S., Chase, Mark W., Rothfels, Carl J., Yu, Jun, Chen, Cui, Chen, Li, Cheng, Shifeng, Li, Juanjuan, Li, Ran, Li, Xia, Lu, Haorong, Stevenson, Dennis W., Ou, Yanxiang, Sun, Xiao, Tan, Xuemei, Tang, Jingbo, Tian, Zhijian, Wang, Feng, Wang, Jun, Wei, Xiaofeng, Xu, Xun, Yan, Zhixiang, Ullrich, Kristian K., Yang, Fan, Zhong, Xiaoni, Zhou, Feiyu, Zhu, Ying, Zhang, Yong, Ayyampalayam, Saravanaraj, Barkman, Todd J., Nguyen, Nam-phuong, Matasci, Naim, Nelson, David R., Wickett, Norman J., Sayyari, Erfan, Wafula, Eric K., Walls, Ramona L., Warnow, Tandy, An, Hong, Arrigo, Nils, Baniaga, Anthony E., Galuska, Sally, Jorgensen, Stacy A., Kidder, Thomas I., DeGironimo, Lisa, Kong, Hanghui, Lu-Irving, Patricia, Marx, Hannah E., Qi, Xinshuai, Reardon, Chris R., Sutherland, Brittany L., Tiley, George P., Welles, Shana R., Yu, Rongpei, Zhan, Shing, Edger, Patrick P., Gramzow, Lydia, Theißen, Günter, Wong, Gane Ka-Shu, Jordon-Thaden, Ingrid E., Joya. Steve, Melkonian, Barbara, Miles, Nicholas W., Pokorny, Lisa, Quigley, Charlotte, Thomas, Philip, Villarreal, Juan Carlos, Augustin, Megan M., Barrett, Matthew D., Baucom, Regina S., Beerling, David J., Benstein, Ruben Maximilian, Biffin, Ed, Brockington, Samuel F., Burge, Dylan O., Burris, Jason N., Burris, Kellie P., Burtet-Sarramegna, Valérie, Caicedo, Ana L., Cannon, Steven B., Çebi, Zehra, Chang, Ying, Chater, Caspar, Cheeseman, John M., Chen, Tao, Clarke, Neil D., Clayton, Harmony, Covshoff, Sarah, Crandall-Stotler, Barbara J., Cross, Hugh, dePamphilis,Claude W., Der, Joshua P., Determann, Ron, Dickson, Rowan C., Di Stilio, Verónica S., Ellis, Shona, Fast, Eva, Feja, Nicole, Field, Katie J., Filatov, Dmitry A., Finnegan, Patrick M., Floyd, Sandra K., Fogliani, Bruno, García, Nicolás, Gâteblé, Gildas, Godden, Grant T., Goh, Falicia (Qi Yun), Greiner, Stephan, Harkess, Alex, Heaney, James Mike, Helliwell, Katherine E., Heyduk, Karolina, Hibberd, Julian M., Hodel, Richard G. J., Hollingsworth, Peter M., Johnson, Marc T. J., Jost, Ricarda, Joyce, Blake, Kapralov, Maxim V., Kazamia, Elena, Kellogg, Elizabeth A., Koch, Marcus A., Konrat, Matt von, Könyves, Kálmán, Kutchan, Toni M., Lam, Vivienne, Larsson, Anders, Leitch, Andrew R., Lentz, Roswitha, Li, Fay-Wei, Lowe, Andrew J., Ludwig, Martha, Manos, Paul S., Mavrodiev, Evgeny, McCormick, Melissa K., McKain, Michael, McLellan, Tracy, McNeal, Joel R., Miller, Richard E., National Key Research and Development Program (China), Ministry of Science and Technology of the People's Republic of China, Leebens-Mack, James H., Barker, M. S., Carpenter, Eric J., Deyholos, Michael K., Gitzendanner, Matthew A., Graham, Sean W., Grosse,Ivo, Li, Zheng, Melkonian, Michael, Mirarab, Siavash, Porsch, Martin, Nelson, Matthew N., Peng, Yanhui, Ralph, Paula, Real, Daniel, Riggins, Chance W., Ruhsam, Markus, Sage, Rowan F., Sakai, Ann K., Scascitella, Moira, Schilling, Edward E., Quint, Marcel, Schlösser, Eva-Marie, Sederoff, Heike, Servick, Stein, Sessa, Emily B., Shaw, Jonathan, Shane W., Sigel, Erin M., Skema, Cynthia, Smith, Alison G., Smithson, Ann, Rensing, Stefan A., Stewart Jr, Neal, Stinchcombe, John R., Szövényi, Peter, Tate, Jennifer A., Tiebel, Helga, Trapnell, Dorset, Villegente, Matthieu, Wang, Chun-Neng, Weller, Stephen G., Wenzel, Michael, Soltis, Douglas E., Weststrand, Stina, Westwood, James H., Whigham, Dennis F., Wu, Shuangxiu, Wulff , Adrien S., Yang, Yu, Zhu, Dan, Zhuang, Cuili, Zuidof, Jennifer, Pires, J. Chris, Soltis, Pamela S., Chase, Mark W., Rothfels, Carl J., Yu, Jun, Chen, Cui, Chen, Li, Cheng, Shifeng, Li, Juanjuan, Li, Ran, Li, Xia, Lu, Haorong, Stevenson, Dennis W., Ou, Yanxiang, Sun, Xiao, Tan, Xuemei, Tang, Jingbo, Tian, Zhijian, Wang, Feng, Wang, Jun, Wei, Xiaofeng, Xu, Xun, Yan, Zhixiang, Ullrich, Kristian K., Yang, Fan, Zhong, Xiaoni, Zhou, Feiyu, Zhu, Ying, Zhang, Yong, Ayyampalayam, Saravanaraj, Barkman, Todd J., Nguyen, Nam-phuong, Matasci, Naim, Nelson, David R., Wickett, Norman J., Sayyari, Erfan, Wafula, Eric K., Walls, Ramona L., Warnow, Tandy, An, Hong, Arrigo, Nils, Baniaga, Anthony E., Galuska, Sally, Jorgensen, Stacy A., Kidder, Thomas I., DeGironimo, Lisa, Kong, Hanghui, Lu-Irving, Patricia, Marx, Hannah E., Qi, Xinshuai, Reardon, Chris R., Sutherland, Brittany L., Tiley, George P., Welles, Shana R., Yu, Rongpei, Zhan, Shing, Edger, Patrick P., Gramzow, Lydia, Theißen, Günter, Wong, Gane Ka-Shu, Jordon-Thaden, Ingrid E., Joya. Steve, Melkonian, Barbara, Miles, Nicholas W., Pokorny, Lisa, Quigley, Charlotte, Thomas, Philip, Villarreal, Juan Carlos, Augustin, Megan M., Barrett, Matthew D., Baucom, Regina S., Beerling, David J., Benstein, Ruben Maximilian, Biffin, Ed, Brockington, Samuel F., Burge, Dylan O., Burris, Jason N., Burris, Kellie P., Burtet-Sarramegna, Valérie, Caicedo, Ana L., Cannon, Steven B., Çebi, Zehra, Chang, Ying, Chater, Caspar, Cheeseman, John M., Chen, Tao, Clarke, Neil D., Clayton, Harmony, Covshoff, Sarah, Crandall-Stotler, Barbara J., Cross, Hugh, dePamphilis,Claude W., Der, Joshua P., Determann, Ron, Dickson, Rowan C., Di Stilio, Verónica S., Ellis, Shona, Fast, Eva, Feja, Nicole, Field, Katie J., Filatov, Dmitry A., Finnegan, Patrick M., Floyd, Sandra K., Fogliani, Bruno, García, Nicolás, Gâteblé, Gildas, Godden, Grant T., Goh, Falicia (Qi Yun), Greiner, Stephan, Harkess, Alex, Heaney, James Mike, Helliwell, Katherine E., Heyduk, Karolina, Hibberd, Julian M., Hodel, Richard G. J., Hollingsworth, Peter M., Johnson, Marc T. J., Jost, Ricarda, Joyce, Blake, Kapralov, Maxim V., Kazamia, Elena, Kellogg, Elizabeth A., Koch, Marcus A., Konrat, Matt von, Könyves, Kálmán, Kutchan, Toni M., Lam, Vivienne, Larsson, Anders, Leitch, Andrew R., Lentz, Roswitha, Li, Fay-Wei, Lowe, Andrew J., Ludwig, Martha, Manos, Paul S., Mavrodiev, Evgeny, McCormick, Melissa K., McKain, Michael, McLellan, Tracy, McNeal, Joel R., and Miller, Richard E.

Abstract

Green plants (Viridiplantae) include around 450,000–500,000 species of great diversity and have important roles in terrestrial and aquatic ecosystems. Here, as part of the One Thousand Plant Transcriptomes Initiative, we sequenced the vegetative transcriptomes of 1,124 species that span the diversity of plants in a broad sense (Archaeplastida), including green plants (Viridiplantae), glaucophytes (Glaucophyta) and red algae (Rhodophyta). Our analysis provides a robust phylogenomic framework for examining the evolution of green plants. Most inferred species relationships are well supported across multiple species tree and supermatrix analyses, but discordance among plastid and nuclear gene trees at a few important nodes highlights the complexity of plant genome evolution, including polyploidy, periods of rapid speciation, and extinction. Incomplete sorting of ancestral variation, polyploidization and massive expansions of gene families punctuate the evolutionary history of green plants. Notably, we find that large expansions of gene families preceded the origins of green plants, land plants and vascular plants, whereas whole-genome duplications are inferred to have occurred repeatedly throughout the evolution of flowering plants and ferns. The increasing availability of high-quality plant genome sequences and advances in functional genomics are enabling research on genome evolution across the green tree of life.

Published
2019

8. Multiple large-scale gene and genome duplications during the evolution of hexapods.

Author

Zheng Li, Tiley, George P., Galuska, Sally R., Reardon, Chris R., Kidder, Thomas I., Rundell, Rebecca J., and Barker, Michael S.

Subjects
GENOMES, POLYPLOIDY, BIOLOGICAL evolution, PHYLOGENY, GENE expression, INSECT genetics, INSECTS
Abstract

Polyploidy or whole genome duplication (WGD) is a major contributor to genome evolution and diversity. Although polyploidy is recognized as an important component of plant evolution, it is generally considered to play a relatively minor role in animal evolution. Ancient polyploidy is found in the ancestry of some animals, especially fishes, but there is little evidence for ancient WGDs in other metazoan lineages. Here we use recently published transcriptomes and genomes from more than 150 species across the insect phylogeny to investigate whether ancient WGDs occurred during the evolution of Hexapoda, the most diverse clade of animals. Using gene age distributions and phylogenomics, we found evidence for 18 ancient WGDs and six other large-scale bursts of gene duplication during insect evolution. These bursts of gene duplication occurred in the history of lineages such as the Lepidoptera, Trichoptera, and Odonata. To further corroborate the nature of these duplications, we evaluated the pattern of gene retention from putative WGDs observed in the gene age distributions. We found a relatively strong signal of convergent gene retention across many of the putative insect WGDs. Considering the phylogenetic breadth and depth of the insect phylogeny, this observation is consistent with polyploidy as we expect dosage balance to drive the parallel retention of genes. Together with recent research on plant evolution, our hexapod results suggest that genome duplications contributed to the evolution of two of the most diverse lineages of eukaryotes on Earth. [ABSTRACT FROM AUTHOR]

Published
2018
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9. One thousand plant transcriptomes and the phylogenomics of green plants

Author

Leebens-Mack, James H., Barker, Michael S., Carpenter, Eric J., Deyholos, Michael K., Gitzendanner, Matthew A., Graham, Sean W., Grosse, Ivo, Li, Zheng, Melkonian, Michael, Mirarab, Siavash, Porsch, Martin, Quint, Marcel, Rensing, Stefan A., Soltis, Douglas E., Soltis, Pamela S., Stevenson, Dennis W., Ullrich, Kristian K., Wickett, Norman J., DeGironimo, Lisa, Edger, Patrick P., Jordon-Thaden, Ingrid E., Joya, Steve, Liu, Tao, Melkonian, Barbara, Miles, Nicholas W., Pokorny, Lisa, Quigley, Charlotte, Thomas, Philip, Villarreal, Juan Carlos, Augustin, Megan M., Barrett, Matthew D., Baucom, Regina S., Beerling, David J., Benstein, Ruben Maximilian, Biffin, Ed, Brockington, Samuel F., Burge, Dylan O., Burris, Jason N., Burris, Kellie P., Burtet-Sarramegna, Valérie, Caicedo, Ana L., Cannon, Steven B., Çebi, Zehra, Chang, Ying, Chater, Caspar, Cheeseman, John M., Chen, Tao, Clarke, Neil D., Clayton, Harmony, Covshoff, Sarah, Crandall-Stotler, Barbara J., Cross, Hugh, DePamphilis, Claude W., Der, Joshua P., Determann, Ron, Dickson, Rowan C., Di Stilio, Verónica S., Ellis, Shona, Fast, Eva, Feja, Nicole, Field, Katie J., Filatov, Dmitry A., Finnegan, Patrick M., Floyd, Sandra K., Fogliani, Bruno, García, Nicolás, Gâteblé, Gildas, Godden, Grant T., Goh, Falicia (Qi Yun), Greiner, Stephan, Harkess, Alex, Heaney, James Mike, Helliwell, Katherine E., Heyduk, Karolina, Hibberd, Julian M., Hodel, Richard G. J., Hollingsworth, Peter M., Johnson, Marc T. J., Jost, Ricarda, Joyce, Blake, Kapralov, Maxim V., Kazamia, Elena, Kellogg, Elizabeth A., Koch, Marcus A., Von Konrat, Matt, Könyves, Kálmán, Kutchan, Toni M., Lam, Vivienne, Larsson, Anders, Leitch, Andrew R., Lentz, Roswitha, Li, Fay-Wei, Lowe, Andrew J., Ludwig, Martha, Manos, Paul S., Mavrodiev, Evgeny, McCormick, Melissa K., McKain, Michael, McLellan, Tracy, McNeal, Joel R., Miller, Richard E., Nelson, Matthew N., Peng, Yanhui, Ralph, Paula, Real, Daniel, Riggins, Chance W., Ruhsam, Markus, Sage, Rowan F., Sakai, Ann K., Scascitella, Moira, Schilling, Edward E., Schlösser, Eva-Marie, Sederoff, Heike, Servick, Stein, Sessa, Emily B., Shaw, A. Jonathan, Shaw, Shane W., Sigel, Erin M., Skema, Cynthia, Smith, Alison G., Smithson, Ann, Stewart, C. Neal, Stinchcombe, John R., Szövényi, Peter, Tate, Jennifer A., Tiebel, Helga, Trapnell, Dorset, Villegente, Matthieu, Wang, Chun-Neng, Weller, Stephen G., Wenzel, Michael, Weststrand, Stina, Westwood, James H., Whigham, Dennis F., Wu, Shuangxiu, Wulff, Adrien S., Yang, Yu, Zhu, Dan, Zhuang, Cuili, Zuidof, Jennifer, Chase, Mark W., Pires, J. Chris, Rothfels, Carl J., Yu, Jun, Chen, Cui, Chen, Li, Cheng, Shifeng, Li, Juanjuan, Li, Ran, Li, Xia, Lu, Haorong, Ou, Yanxiang, Sun, Xiao, Tan, Xuemei, Tang, Jingbo, Tian, Zhijian, Wang, Feng, Wang, Jun, Wei, Xiaofeng, Xu, Xun, Yan, Zhixiang, Yang, Fan, Zhong, Xiaoni, Zhou, Feiyu, Zhu, Ying, Zhang, Yong, Ayyampalayam, Saravanaraj, Barkman, Todd J., Nguyen, Nam-Phuong, Matasci, Naim, Nelson, David R., Sayyari, Erfan, Wafula, Eric K., Walls, Ramona L., Warnow, Tandy, An, Hong, Arrigo, Nils, Baniaga, Anthony E., Galuska, Sally, Jorgensen, Stacy A., Kidder, Thomas I., Kong, Hanghui, Lu-Irving, Patricia, Marx, Hannah E., Qi, Xinshuai, Reardon, Chris R., Sutherland, Brittany L., Tiley, George P., Welles, Shana R., Yu, Rongpei, Zhan, Shing, Gramzow, Lydia, Theißen, Günter, and Wong, Gane Ka-Shu

Subjects
45/91, 631/181/759/2467, 631/208/212/2306, fungi, article, food and beverages, 631/449/2669, 631/181/735, 15. Life on land, 45/90
Abstract

Green plants (Viridiplantae) include around 450,000–500,000 species1, 2 of great diversity and have important roles in terrestrial and aquatic ecosystems. Here, as part of the One Thousand Plant Transcriptomes Initiative, we sequenced the vegetative transcriptomes of 1,124 species that span the diversity of plants in a broad sense (Archaeplastida), including green plants (Viridiplantae), glaucophytes (Glaucophyta) and red algae (Rhodophyta). Our analysis provides a robust phylogenomic framework for examining the evolution of green plants. Most inferred species relationships are well supported across multiple species tree and supermatrix analyses, but discordance among plastid and nuclear gene trees at a few important nodes highlights the complexity of plant genome evolution, including polyploidy, periods of rapid speciation, and extinction. Incomplete sorting of ancestral variation, polyploidization and massive expansions of gene families punctuate the evolutionary history of green plants. Notably, we find that large expansions of gene families preceded the origins of green plants, land plants and vascular plants, whereas whole-genome duplications are inferred to have occurred repeatedly throughout the evolution of flowering plants and ferns. The increasing availability of high-quality plant genome sequences and advances in functional genomics are enabling research on genome evolution across the green tree of life.

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