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6. Genetic inference of orchid colonization of a Costa Rican lava flow.

Author

Trapnell, Dorset W. and Hamrick, J. L.

Subjects
LAVA flows, ORCHIDS, COLONIZATION (Ecology), PLANT dispersal, PLANT populations, PLANT colonization
Abstract

Copyright of Biotropica is the property of Wiley-Blackwell and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)

Published
2023
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15. Genetic inference of orchid population dynamics on differentaged lava flows in Costa Rica.

Author

Trapnell, Dorset W. and Hamrick, James L.

Subjects
LAVA flows, POPULATION dynamics, ORCHIDS, COLONIZATION (Ecology), POPULATION genetics, COMPETITION (Biology), HABITATS
Abstract

Colonization is a fundamental ecological process that is important for the persistence of species, particularly when a changing environment necessitates range shifts. Vacant habitats available for colonization often arise from landscape disturbance. Colonization and population expansion processes can be inferred by examining the levels and spatial distribution of genetic variation of plant populations with known disturbance histories. Samples (N = 690) of the terrestrial orchid, Epidendrum radicans, were collected from five lava flow sites on the slopes of Volcán Arenal in Costa Rica that last experienced major eruptions in 1968 and 1992. Individuals were also sampled (N = 188) from four regional populations. Samples were characterized using 15 nuclear genetic markers and analyzed using population genetics statistics. Genetic diversity within sites was moderate (He = 0.092–0.192). Contrary to expectation, diversity tended to be lower on the older lava flows (0.131 vs. 0.172) which may reflect their more sheltered topography that restricted pollen/seed immigration, and/or greater intra- and interspecific competition. Genetic diversity measures indicate that the lava flows were colonized by numerous individuals that likely originated from multiple sources while spatial genetic structure (SGS) statistics indicate that most recruitment in the study sites subsequent to colonization resulted from in situ reproduction and localized seed deposition. Younger sites had significantly greater SGS over larger distances which reflects fewer reproductive events, and less spatial and temporal overlap of seed shadows relative to the older sites. Clones were also generally smaller on the younger sites (≤3 m vs. ≤8 m). [ABSTRACT FROM AUTHOR]

Published
2023
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22. Floral display and mating patterns within populations of the neotropical epiphytic orchid, Laelia rubescens (Orchidaceae)

Author

Trapnell, Dorset W. and Hamrick, J.L.

Subjects
Orchids -- Genetic aspects, Pollination -- Research, Plant population genetics -- Research, Biological sciences
Abstract

Pollinator behavior plays a central role in determining patterns of pollen-mediated gene movement in zoophilous angiosperms. A species' floral display can strongly influence the behavior of its pollinators and thereby affect its evolutionary pathway. We used paternity analysis to directly measure and describe mating patterns within 15 populations of the epiphytic orchid, Laelia rubescens, in Costa Rican dry forest. Strict correlated mating by orchids allows inference of the precise multilocus diploid genotype of the pollen parents. Our data show that mean effective population sizes were small (11.2 in 1999 and 11.8 in 2000) relative to the number of flowering genets (63 and 56, respectively). Fewer genets were reproductively successful as females than males. The relationship between reproductive success (RS) and floral display within three cluster size classes was consistent between years, with large (>30 inflorescences) and small ([less than or equal to] 10 inflorescences) clusters often having significantly lower RS than expected, while the RS of medium-sized clusters (11-30 inflorescences) often significantly exceeded expectations. Paternity analysis allowed us to take advantage of the pollination biology of L. rubescens to provide unusually detailed insights into mating patterns, pollen-mediated gene movement and RS for populations of this epiphytic orchid, an herbaceous perennial, distributed in three-dimensional space. Key words: Costa Rica; dry forest; effective population size; Orchidaceae; paternity analysis; paternity pool; reproductive success.

Published
2006

27. Are small populations larger than they seem? Genetic insights into patchily distributed populations of Drakaea glyptodon (Orchidaceae).

Author

Trapnell, Dorset W, Smallwood, Patrick A, Dixon, Kingsley W, and Phillips, Ryan D

Subjects
*ORCHIDS, *MICROSATELLITE repeats, *GENE flow, *GENETIC variation, *FRAGMENTED landscapes, *NUCLEAR structure
Abstract

Many orchids are characterized by small, patchily distributed populations. Resolving how they persist is important for understanding the ecology of this hyper-diverse family, many members of which are of conservation concern. Ten populations of the common terrestrial orchid Drakaea glyptodon from south-western Australia were genotyped with ten nuclear and five plastid simple sequence repeat (SSR) markers. Levels and partitioning of genetic variation and effective population sizes (N e) were estimated. Spatial genetic structure of nuclear diversity, together with plastid data, were used to infer the effective number of seed parents per population. We found high genetic diversity, N e values that generally exceed predictions based on the number of flowering individuals and moderate levels of gene flow. Two populations were founded by less than five colonists suggesting some populations are colonized by few seeds, with growth largely resulting from in situ recruitment. A value of 3.65 for m p / m s indicates that pollinators play a greater role than seed in introducing genetic diversity to populations via gene flow. Our results highlight that D. glyptodon is highly effective at persisting in patchily distributed populations. However, it is important to examine how insights from this common, widespread species transfer to species that are rare and/or occur in fragmented landscapes. [ABSTRACT FROM AUTHOR]

Published
2022
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31. 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
Full Text
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32. 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

33. 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

38. Characterization of microsatellite loci for an Australian epiphytic orchid, Dendrobium calamiforme, using Illumina sequencing1

Author

Trapnell, Dorset W., Beasley, Rochelle R., Lance, Stacey L., Field, Ashley R., and Jones, Kenneth L.

Subjects
Dendrobium calamiforme, genetic diversity, phylogeography, Primer Note, Orchidaceae, Dockrillia calamiformis, simple sequence repeat (SSR) markers
Abstract

Premise of the study: Microsatellite loci were developed for the epiphytic pencil orchid Dendrobium calamiforme for population genetic and phylogeographic investigation of this Australian taxon. Methods and Results: Nineteen microsatellite loci were identified from an Illumina paired-end shotgun library of D. calamiforme. Polymorphism and genetic diversity were assessed in 24 individuals from five populations separated by a maximum distance of ∼80 km. All loci were polymorphic with two to 14 alleles per locus, expected heterozygosity ranging from 0.486 to 0.902, and probability of identity values ranging from 0.018 to 0.380. Conclusions: These novel markers will serve as valuable tools for investigation of levels of genetic diversity as well as patterns of gene flow, genetic structure, and phylogeographic history.

Published
2015

45. Phylogenomic analyses of species relationships in the genus Sabal (Arecaceae) using targeted sequence capture.

Author

HEYDUK, KAROLINA, TRAPNELL, DORSET W., BARRETT, CRAIG F., and LEEBENS-MACK, JIM

Subjects
*SABAL, *PLANT genomes, *PLANT species, *PLANT phylogeny, *PLANT DNA, *RNA probes
Abstract

With the increasing availability of high-throughput sequencing, phylogenetic analyses are no longer constrained by the limited availability of a few loci. Here, we describe a sequence capture methodology, which we used to collect data for analyses of diversification within Sabal (Arecaceae), a palm genus native to the south-eastern USA, Caribbean, Bermuda and Central America. RNA probes were developed and used to enrich DNA samples for putatively low copy nuclear genes and the plastomes for all Sabal species and two outgroup species. Sequence data were generated on an Illumina MiSeq sequencer and target sequences were assembled using custom workflows. Both coalescence and supermatrix analyses of 133 nuclear genes were used to estimate species trees relationships. Plastid genomes were also analysed, yielding generally poor resolution with regard to species relationships. Species relationships described in both nuclear gene and plastome sequences largely reflect the biogeography of the group and, to a lesser extent, previous morphology-based hypotheses. Beyond the biological implications, this research validates a high-throughput methodology for generating a large number of genes for coalescence-based phylogenetic analyses in plant lineages. [ABSTRACT FROM AUTHOR]

Published
2016
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