The selaginella genome identifies genetic changes associated with the evolution of vascular plants

Jo Ann Banks, Tomoaki Nishiyama, Mitsuyasu Hasebe, John L. Bowman, Michael Gribskov, Claude DePamphilis, Victor A. Albert, Naoki Aono, Tsuyoshi Aoyama, Barbara A. Ambrose, Neil W. Ashton, Michael J. Axtell, Elizabeth Barker, Michael S. Barker, Jeffrey L. Bennetzen, Nicholas D. Bonawitz, Clint Chapple, Chaoyang Cheng, Luiz Gustavo Guedes Correa, Michael DacreJeremy DeBarry, Ingo Dreyer, Marek Elias, Eric M. Engstrom, Mark Estelle, Liang Feng, Cédric Finet, Sandra K. Floyd, Wolf B. Frommer, Tomomichi Fujita, Lydia Gramzow, Michael Gutensohn, Jesper Harholt, Mitsuru Hattori, Alexander Heyl, Tadayoshi Hirai, Yuji Hiwatashi, Masaki Ishikawa, Mineko Iwata, Kenneth G. Karol, Barbara Koehler, Uener Kolukisaoglu, Minoru Kubo, Tetsuya Kurata, Sylvie Lalonde, Kejie Li, Ying Li, Amy Litt, Eric Lyons, Gerard Manning, Takeshi Maruyama, Todd P. Michael, Koji Mikami, Saori Miyazaki, Shin Ichi Morinaga, TakashiMurata, Bernd Mueller-Roeber, David R. Nelson, Mari Obara, Yasuko Oguri, Richard G. Olmstead, Naoko Onodera, Bent Larsen Petersen, Birgit Pils, Michael Prigge, Stefan A. Rensing, Diego Mauricio Riaño-Pachón, Alison W. Roberts, Yoshikatsu Sato, Henrik Vibe Scheller, Burkhard Schulz, Christian Schulz, Eugene V. Shakirov, Nakako Shibagaki, Naoki Shinohara, Dorothy E. Shippen, Iben Sørensen, Ryo Sotooka, Nagisa Sugimoto, Mamoru Sugita, Naomi Sumikawa, Milos Tanurdzic, Günter Theißen, Peter Ulvskov, Sachiko Wakazuki, Jing Ke Weng, William W.G.T. Willats, Daniel Wipf, Paul G. Wolf, Lixing Yang, Andreas D. Zimmer, Qihui Zhu, Therese Mitros, Uffe Hellsten, Dominique Loqué, Robert Otillar, Asaf Salamov, Jeremy Schmutz, Harris Shapiro, Erika Lindquist, Susan Lucas, Daniel Rokhsar, Igor V. Grigoriev

Research output: Contribution to journalArticle

460 Citations (Scopus)

Abstract

Vascular plants appeared ∼410 million years ago, then diverged into several lineages of which only two survive: the euphyllophytes (ferns and seed plants) and the lycophytes. We report here the genome sequence of the lycophyte Selaginella moellendorffii (Selaginella), the first nonseed vascular plant genome reported. By comparing gene content in evolutionarily diverse taxa, we found that the transition from a gametophyte- to a sporophyte-dominated life cycle required far fewer new genes than the transition from a nonseed vascular to a flowering plant, whereas secondary metabolic genes expanded extensively and in parallel in the lycophyte and angiosperm lineages. Selaginella differs in posttranscriptional gene regulation, including small RNA regulation of repetitive elements, an absence of the trans-acting small interfering RNA pathway, and extensive RNA editing of organellar genes.

Original languageEnglish (US)
Pages (from-to)960-963
Number of pages4
JournalScience
Volume332
Issue number6032
DOIs
StatePublished - May 20 2011

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Selaginellaceae
Blood Vessels
Genome
Genes
RNA Editing
Ferns
Plant Genome
Angiosperms
Life Cycle Stages
Small Interfering RNA
Seeds
RNA

All Science Journal Classification (ASJC) codes

  • General

Cite this

Banks, J. A., Nishiyama, T., Hasebe, M., Bowman, J. L., Gribskov, M., DePamphilis, C., ... Grigoriev, I. V. (2011). The selaginella genome identifies genetic changes associated with the evolution of vascular plants. Science, 332(6032), 960-963. https://doi.org/10.1126/science.1203810
Banks, Jo Ann ; Nishiyama, Tomoaki ; Hasebe, Mitsuyasu ; Bowman, John L. ; Gribskov, Michael ; DePamphilis, Claude ; Albert, Victor A. ; Aono, Naoki ; Aoyama, Tsuyoshi ; Ambrose, Barbara A. ; Ashton, Neil W. ; Axtell, Michael J. ; Barker, Elizabeth ; Barker, Michael S. ; Bennetzen, Jeffrey L. ; Bonawitz, Nicholas D. ; Chapple, Clint ; Cheng, Chaoyang ; Correa, Luiz Gustavo Guedes ; Dacre, Michael ; DeBarry, Jeremy ; Dreyer, Ingo ; Elias, Marek ; Engstrom, Eric M. ; Estelle, Mark ; Feng, Liang ; Finet, Cédric ; Floyd, Sandra K. ; Frommer, Wolf B. ; Fujita, Tomomichi ; Gramzow, Lydia ; Gutensohn, Michael ; Harholt, Jesper ; Hattori, Mitsuru ; Heyl, Alexander ; Hirai, Tadayoshi ; Hiwatashi, Yuji ; Ishikawa, Masaki ; Iwata, Mineko ; Karol, Kenneth G. ; Koehler, Barbara ; Kolukisaoglu, Uener ; Kubo, Minoru ; Kurata, Tetsuya ; Lalonde, Sylvie ; Li, Kejie ; Li, Ying ; Litt, Amy ; Lyons, Eric ; Manning, Gerard ; Maruyama, Takeshi ; Michael, Todd P. ; Mikami, Koji ; Miyazaki, Saori ; Morinaga, Shin Ichi ; TakashiMurata ; Mueller-Roeber, Bernd ; Nelson, David R. ; Obara, Mari ; Oguri, Yasuko ; Olmstead, Richard G. ; Onodera, Naoko ; Petersen, Bent Larsen ; Pils, Birgit ; Prigge, Michael ; Rensing, Stefan A. ; Riaño-Pachón, Diego Mauricio ; Roberts, Alison W. ; Sato, Yoshikatsu ; Scheller, Henrik Vibe ; Schulz, Burkhard ; Schulz, Christian ; Shakirov, Eugene V. ; Shibagaki, Nakako ; Shinohara, Naoki ; Shippen, Dorothy E. ; Sørensen, Iben ; Sotooka, Ryo ; Sugimoto, Nagisa ; Sugita, Mamoru ; Sumikawa, Naomi ; Tanurdzic, Milos ; Theißen, Günter ; Ulvskov, Peter ; Wakazuki, Sachiko ; Weng, Jing Ke ; Willats, William W.G.T. ; Wipf, Daniel ; Wolf, Paul G. ; Yang, Lixing ; Zimmer, Andreas D. ; Zhu, Qihui ; Mitros, Therese ; Hellsten, Uffe ; Loqué, Dominique ; Otillar, Robert ; Salamov, Asaf ; Schmutz, Jeremy ; Shapiro, Harris ; Lindquist, Erika ; Lucas, Susan ; Rokhsar, Daniel ; Grigoriev, Igor V. / The selaginella genome identifies genetic changes associated with the evolution of vascular plants. In: Science. 2011 ; Vol. 332, No. 6032. pp. 960-963.
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abstract = "Vascular plants appeared ∼410 million years ago, then diverged into several lineages of which only two survive: the euphyllophytes (ferns and seed plants) and the lycophytes. We report here the genome sequence of the lycophyte Selaginella moellendorffii (Selaginella), the first nonseed vascular plant genome reported. By comparing gene content in evolutionarily diverse taxa, we found that the transition from a gametophyte- to a sporophyte-dominated life cycle required far fewer new genes than the transition from a nonseed vascular to a flowering plant, whereas secondary metabolic genes expanded extensively and in parallel in the lycophyte and angiosperm lineages. Selaginella differs in posttranscriptional gene regulation, including small RNA regulation of repetitive elements, an absence of the trans-acting small interfering RNA pathway, and extensive RNA editing of organellar genes.",
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Banks, JA, Nishiyama, T, Hasebe, M, Bowman, JL, Gribskov, M, DePamphilis, C, Albert, VA, Aono, N, Aoyama, T, Ambrose, BA, Ashton, NW, Axtell, MJ, Barker, E, Barker, MS, Bennetzen, JL, Bonawitz, ND, Chapple, C, Cheng, C, Correa, LGG, Dacre, M, DeBarry, J, Dreyer, I, Elias, M, Engstrom, EM, Estelle, M, Feng, L, Finet, C, Floyd, SK, Frommer, WB, Fujita, T, Gramzow, L, Gutensohn, M, Harholt, J, Hattori, M, Heyl, A, Hirai, T, Hiwatashi, Y, Ishikawa, M, Iwata, M, Karol, KG, Koehler, B, Kolukisaoglu, U, Kubo, M, Kurata, T, Lalonde, S, Li, K, Li, Y, Litt, A, Lyons, E, Manning, G, Maruyama, T, Michael, TP, Mikami, K, Miyazaki, S, Morinaga, SI, TakashiMurata, Mueller-Roeber, B, Nelson, DR, Obara, M, Oguri, Y, Olmstead, RG, Onodera, N, Petersen, BL, Pils, B, Prigge, M, Rensing, SA, Riaño-Pachón, DM, Roberts, AW, Sato, Y, Scheller, HV, Schulz, B, Schulz, C, Shakirov, EV, Shibagaki, N, Shinohara, N, Shippen, DE, Sørensen, I, Sotooka, R, Sugimoto, N, Sugita, M, Sumikawa, N, Tanurdzic, M, Theißen, G, Ulvskov, P, Wakazuki, S, Weng, JK, Willats, WWGT, Wipf, D, Wolf, PG, Yang, L, Zimmer, AD, Zhu, Q, Mitros, T, Hellsten, U, Loqué, D, Otillar, R, Salamov, A, Schmutz, J, Shapiro, H, Lindquist, E, Lucas, S, Rokhsar, D & Grigoriev, IV 2011, 'The selaginella genome identifies genetic changes associated with the evolution of vascular plants', Science, vol. 332, no. 6032, pp. 960-963. https://doi.org/10.1126/science.1203810

The selaginella genome identifies genetic changes associated with the evolution of vascular plants. / Banks, Jo Ann; Nishiyama, Tomoaki; Hasebe, Mitsuyasu; Bowman, John L.; Gribskov, Michael; DePamphilis, Claude; Albert, Victor A.; Aono, Naoki; Aoyama, Tsuyoshi; Ambrose, Barbara A.; Ashton, Neil W.; Axtell, Michael J.; Barker, Elizabeth; Barker, Michael S.; Bennetzen, Jeffrey L.; Bonawitz, Nicholas D.; Chapple, Clint; Cheng, Chaoyang; Correa, Luiz Gustavo Guedes; Dacre, Michael; DeBarry, Jeremy; Dreyer, Ingo; Elias, Marek; Engstrom, Eric M.; Estelle, Mark; Feng, Liang; Finet, Cédric; Floyd, Sandra K.; Frommer, Wolf B.; Fujita, Tomomichi; Gramzow, Lydia; Gutensohn, Michael; Harholt, Jesper; Hattori, Mitsuru; Heyl, Alexander; Hirai, Tadayoshi; Hiwatashi, Yuji; Ishikawa, Masaki; Iwata, Mineko; Karol, Kenneth G.; Koehler, Barbara; Kolukisaoglu, Uener; Kubo, Minoru; Kurata, Tetsuya; Lalonde, Sylvie; Li, Kejie; Li, Ying; Litt, Amy; Lyons, Eric; Manning, Gerard; Maruyama, Takeshi; Michael, Todd P.; Mikami, Koji; Miyazaki, Saori; Morinaga, Shin Ichi; TakashiMurata; Mueller-Roeber, Bernd; Nelson, David R.; Obara, Mari; Oguri, Yasuko; Olmstead, Richard G.; Onodera, Naoko; Petersen, Bent Larsen; Pils, Birgit; Prigge, Michael; Rensing, Stefan A.; Riaño-Pachón, Diego Mauricio; Roberts, Alison W.; Sato, Yoshikatsu; Scheller, Henrik Vibe; Schulz, Burkhard; Schulz, Christian; Shakirov, Eugene V.; Shibagaki, Nakako; Shinohara, Naoki; Shippen, Dorothy E.; Sørensen, Iben; Sotooka, Ryo; Sugimoto, Nagisa; Sugita, Mamoru; Sumikawa, Naomi; Tanurdzic, Milos; Theißen, Günter; Ulvskov, Peter; Wakazuki, Sachiko; Weng, Jing Ke; Willats, William W.G.T.; Wipf, Daniel; Wolf, Paul G.; Yang, Lixing; Zimmer, Andreas D.; Zhu, Qihui; Mitros, Therese; Hellsten, Uffe; Loqué, Dominique; Otillar, Robert; Salamov, Asaf; Schmutz, Jeremy; Shapiro, Harris; Lindquist, Erika; Lucas, Susan; Rokhsar, Daniel; Grigoriev, Igor V.

In: Science, Vol. 332, No. 6032, 20.05.2011, p. 960-963.

Research output: Contribution to journalArticle

TY - JOUR

T1 - The selaginella genome identifies genetic changes associated with the evolution of vascular plants

AU - Banks, Jo Ann

AU - Nishiyama, Tomoaki

AU - Hasebe, Mitsuyasu

AU - Bowman, John L.

AU - Gribskov, Michael

AU - DePamphilis, Claude

AU - Albert, Victor A.

AU - Aono, Naoki

AU - Aoyama, Tsuyoshi

AU - Ambrose, Barbara A.

AU - Ashton, Neil W.

AU - Axtell, Michael J.

AU - Barker, Elizabeth

AU - Barker, Michael S.

AU - Bennetzen, Jeffrey L.

AU - Bonawitz, Nicholas D.

AU - Chapple, Clint

AU - Cheng, Chaoyang

AU - Correa, Luiz Gustavo Guedes

AU - Dacre, Michael

AU - DeBarry, Jeremy

AU - Dreyer, Ingo

AU - Elias, Marek

AU - Engstrom, Eric M.

AU - Estelle, Mark

AU - Feng, Liang

AU - Finet, Cédric

AU - Floyd, Sandra K.

AU - Frommer, Wolf B.

AU - Fujita, Tomomichi

AU - Gramzow, Lydia

AU - Gutensohn, Michael

AU - Harholt, Jesper

AU - Hattori, Mitsuru

AU - Heyl, Alexander

AU - Hirai, Tadayoshi

AU - Hiwatashi, Yuji

AU - Ishikawa, Masaki

AU - Iwata, Mineko

AU - Karol, Kenneth G.

AU - Koehler, Barbara

AU - Kolukisaoglu, Uener

AU - Kubo, Minoru

AU - Kurata, Tetsuya

AU - Lalonde, Sylvie

AU - Li, Kejie

AU - Li, Ying

AU - Litt, Amy

AU - Lyons, Eric

AU - Manning, Gerard

AU - Maruyama, Takeshi

AU - Michael, Todd P.

AU - Mikami, Koji

AU - Miyazaki, Saori

AU - Morinaga, Shin Ichi

AU - TakashiMurata,

AU - Mueller-Roeber, Bernd

AU - Nelson, David R.

AU - Obara, Mari

AU - Oguri, Yasuko

AU - Olmstead, Richard G.

AU - Onodera, Naoko

AU - Petersen, Bent Larsen

AU - Pils, Birgit

AU - Prigge, Michael

AU - Rensing, Stefan A.

AU - Riaño-Pachón, Diego Mauricio

AU - Roberts, Alison W.

AU - Sato, Yoshikatsu

AU - Scheller, Henrik Vibe

AU - Schulz, Burkhard

AU - Schulz, Christian

AU - Shakirov, Eugene V.

AU - Shibagaki, Nakako

AU - Shinohara, Naoki

AU - Shippen, Dorothy E.

AU - Sørensen, Iben

AU - Sotooka, Ryo

AU - Sugimoto, Nagisa

AU - Sugita, Mamoru

AU - Sumikawa, Naomi

AU - Tanurdzic, Milos

AU - Theißen, Günter

AU - Ulvskov, Peter

AU - Wakazuki, Sachiko

AU - Weng, Jing Ke

AU - Willats, William W.G.T.

AU - Wipf, Daniel

AU - Wolf, Paul G.

AU - Yang, Lixing

AU - Zimmer, Andreas D.

AU - Zhu, Qihui

AU - Mitros, Therese

AU - Hellsten, Uffe

AU - Loqué, Dominique

AU - Otillar, Robert

AU - Salamov, Asaf

AU - Schmutz, Jeremy

AU - Shapiro, Harris

AU - Lindquist, Erika

AU - Lucas, Susan

AU - Rokhsar, Daniel

AU - Grigoriev, Igor V.

PY - 2011/5/20

Y1 - 2011/5/20

N2 - Vascular plants appeared ∼410 million years ago, then diverged into several lineages of which only two survive: the euphyllophytes (ferns and seed plants) and the lycophytes. We report here the genome sequence of the lycophyte Selaginella moellendorffii (Selaginella), the first nonseed vascular plant genome reported. By comparing gene content in evolutionarily diverse taxa, we found that the transition from a gametophyte- to a sporophyte-dominated life cycle required far fewer new genes than the transition from a nonseed vascular to a flowering plant, whereas secondary metabolic genes expanded extensively and in parallel in the lycophyte and angiosperm lineages. Selaginella differs in posttranscriptional gene regulation, including small RNA regulation of repetitive elements, an absence of the trans-acting small interfering RNA pathway, and extensive RNA editing of organellar genes.

AB - Vascular plants appeared ∼410 million years ago, then diverged into several lineages of which only two survive: the euphyllophytes (ferns and seed plants) and the lycophytes. We report here the genome sequence of the lycophyte Selaginella moellendorffii (Selaginella), the first nonseed vascular plant genome reported. By comparing gene content in evolutionarily diverse taxa, we found that the transition from a gametophyte- to a sporophyte-dominated life cycle required far fewer new genes than the transition from a nonseed vascular to a flowering plant, whereas secondary metabolic genes expanded extensively and in parallel in the lycophyte and angiosperm lineages. Selaginella differs in posttranscriptional gene regulation, including small RNA regulation of repetitive elements, an absence of the trans-acting small interfering RNA pathway, and extensive RNA editing of organellar genes.

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U2 - 10.1126/science.1203810

DO - 10.1126/science.1203810

M3 - Article

C2 - 21551031

AN - SCOPUS:79956309501

VL - 332

SP - 960

EP - 963

JO - Science

JF - Science

SN - 0036-8075

IS - 6032

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