The Selaginella Genome Identifies Genetic Changes Associated with the Evolution of Vascular Plants
Jo Ann Banks
(1)
,
Tomoaki Nishiyama
(2, 3)
,
Mitsuyasu Hasebe
(3, 4, 5)
,
John Bowman
(6, 7)
,
Michael Gribskov
(8)
,
Claude de Pamphilis
(9)
,
Victor Albert
(10)
,
Naoki Aono
(4)
,
Tsuyoshi Aoyama
(4, 11)
,
Barbara Ambrose
(12)
,
Neil Ashton
(13)
,
Michael Axtell
(9)
,
Elizabeth Barker
(13)
,
Michael Barker
(14)
,
Jeffrey Bennetzen
(15)
,
Nicholas Bonawitz
(16)
,
Clint Chapple
(16)
,
Chaoyang Cheng
(3)
,
Luiz Gustavo Guedes Correa
(17)
,
Michael Dacre
(18)
,
Jeremy Debarry
(15)
,
Ingo Dreyer
(17)
,
Marek Elias
(19, 20)
,
Eric Engstrom
(21)
,
Mark Estelle
(22)
,
Liang Feng
(23)
,
Cedric Finet
(24)
,
Sandra Floyd
(6)
,
Wolf Frommer
(25)
,
Tomomichi Fujita
(26)
,
Lydia Gramzow
(27)
,
Michael Gutensohn
(28, 29)
,
Jesper Harholt
(30)
,
Mitsuru Hattori
(31, 32)
,
Alexender Heyl
(33)
,
Tadayoshi Hirai
(3, 34)
,
Yuji Hiwatashi
(4, 5)
,
Masaki Ishikawa
(3)
,
Mineko Iwata
(3)
,
Kenneth Karol
(12)
,
Barbara Koehler
(17)
,
Uener Kolukisaoglu
(35, 36)
,
Minoru Kubo
(3)
,
Tetsuya Kurata
(3, 37)
,
Sylvie Lalonde
(38)
,
Kejie Li
(8)
,
Ying Li
(8, 39)
,
Amy Litt
(12)
,
Eric Lyons
(40)
,
Gerard Manning
(18)
,
Takeshi Maruyama
(41)
,
Todd Michael
(42, 43)
,
Koji Mikami
(44)
,
Saori Miyazaki
(4, 45)
,
Shin-Ichi Morinaga
(4, 32)
,
Takashi Murata
(4, 5)
,
Bernd Mueller-Roeber
(46)
,
David Nelson
(47)
,
Mari Obara
(3)
,
Yasuko Oguri
(3)
,
Richard Olmstead
(48)
,
Naoko Onodera
(3, 49)
,
Bent Larsen Petersen
(30)
,
Birgit Pils
(50, 51)
,
Michael Prigge
(22)
,
Stefan Rensing
(52, 53)
,
Diego Mauricio Riaño-Pachón
(46, 54)
,
Alison Roberts
(55)
,
Yoshikatsu Sato
(3)
,
Henrik Vibe Scheller
(40, 56)
,
Burkhard Schultz
(28)
,
Christian Schultz
(57)
,
Eugene Shakirov
(58)
,
Nakako Shibagaki
(59)
,
Naoki Shinohara
(3)
,
Dorothy Shippen
(58)
,
Iben Sørensen
(30)
,
Ryo Sotooka
,
Nagisa Sugimoto
(3)
,
Mamoru Sugita
(31)
,
Naomi Sumikawa
(4)
,
Milos Tanurdzic
,
Günter Theissen
(27)
,
Peter Ulvskov
(30)
,
Sachiko Wakazuki
(3)
,
Jing-Ke Weng
(16)
,
William Willats
(30)
,
Daniel Wipf
(60)
,
Paul Wolf
,
Lixing Yang
(15)
,
Andreas Zimmer
(52)
,
Qihui Zhu
(15)
,
Therese Mitros
,
Uffe Hellsten
,
Dominique Loque
(56)
,
Robert Otillar
,
Asaf Salamov
,
Jeremy Schmutz
,
Harris Shapiro
,
Erika Lindquist
,
Susan Lucas
,
Daniel Rokhsar
,
Igor Grigoriev
1
Department of Botany and Plant Pathology
2 KU - Kanazawa University
3 JST - Japan Science and Technology Agency
4 NIBB - National Institute for Basic Biology
5 Department of Basic Biology, School of Life Science
6 School of Biological Sciences
7 UC Davis - University of California [Davis]
8 Department of Biological Sciences [Lafayette IN]
9 Penn State - Pennsylvania State University
10 Department of Biological Sciences
11 School of Life Science, Department of Basic Biology
12 NYBG - New York Botanical Garden
13 Department of Biology
14 Department of Ecology and Evolutionary Biology [University of Arizona]
15 Department of Genetics
16 Purdue University [West Lafayette]
17 University of Potsdam = Universität Potsdam
18 Salk Institute for Biological Studies
19 UK - Univerzita Karlova [Praha, Česká republika] = Charles University [Prague, Czech Republic]
20 Faculty of Science
21 WM - College of William and Mary [Williamsburg]
22 Section of Cell and Developmental Biology
23 Institute of Bioinformatics
24 RDP - Reproduction et développement des plantes
25 Carnegie Institution of Washington
26 Hokkaido University [Sapporo, Japan]
27 Friedrich-Schiller-Universität = Friedrich Schiller University Jena [Jena, Germany]
28 Department of Horticulture and Landscape Architecture
29 Martin-Luther-University Halle-Wittenberg
30 UCPH - University of Copenhagen = Københavns Universitet
31 Nagoya University
32 UTokyo - The University of Tokyo
33 FU - Free University of Berlin
34 Université de Tsukuba = University of Tsukuba
35 Center for Life Science Automation
36 Eberhard Karls Universität Tübingen = University of Tübingen
37 Nara Institute of Science and Technology
38 Department of Plant Biology
39 Division of Biomedical Statistics and Informatics
40 Department of Plant and Microbial Biology
41 Graduate School of Life Science
42 Rutgers University [Camden]
43 Monsanto Company
44 Faculty of Fisheries Sciences [Hakodate]
45 NIG - National Institute of Genetics [Shizuoka, Japan]
46 MPI-MP - Max Planck Institute of Molecular Plant Physiology
47 University of Tennessee
48 Department of Biology
49 Dalhousie University [Halifax]
50 Wellcome Trust
51 SIAS AG
52 Faculty of Biology
53 Albert-Ludwigs-Universität Freiburg = University of Freiburg
54 UNIANDES - Departamento de Ciencias Biológicas [Univ de los Andes Colombia]
55 Department of Biological Sciences
56 Joint BioEnergy Institute
57 RUB - Ruhr University Bochum = Ruhr-Universität Bochum
58 Texas A&M University System
59 Osaka University [Osaka]
60 PMEBBCE - Plante - microbe - environnement : biochimie, biologie cellulaire et écologie
2 KU - Kanazawa University
3 JST - Japan Science and Technology Agency
4 NIBB - National Institute for Basic Biology
5 Department of Basic Biology, School of Life Science
6 School of Biological Sciences
7 UC Davis - University of California [Davis]
8 Department of Biological Sciences [Lafayette IN]
9 Penn State - Pennsylvania State University
10 Department of Biological Sciences
11 School of Life Science, Department of Basic Biology
12 NYBG - New York Botanical Garden
13 Department of Biology
14 Department of Ecology and Evolutionary Biology [University of Arizona]
15 Department of Genetics
16 Purdue University [West Lafayette]
17 University of Potsdam = Universität Potsdam
18 Salk Institute for Biological Studies
19 UK - Univerzita Karlova [Praha, Česká republika] = Charles University [Prague, Czech Republic]
20 Faculty of Science
21 WM - College of William and Mary [Williamsburg]
22 Section of Cell and Developmental Biology
23 Institute of Bioinformatics
24 RDP - Reproduction et développement des plantes
25 Carnegie Institution of Washington
26 Hokkaido University [Sapporo, Japan]
27 Friedrich-Schiller-Universität = Friedrich Schiller University Jena [Jena, Germany]
28 Department of Horticulture and Landscape Architecture
29 Martin-Luther-University Halle-Wittenberg
30 UCPH - University of Copenhagen = Københavns Universitet
31 Nagoya University
32 UTokyo - The University of Tokyo
33 FU - Free University of Berlin
34 Université de Tsukuba = University of Tsukuba
35 Center for Life Science Automation
36 Eberhard Karls Universität Tübingen = University of Tübingen
37 Nara Institute of Science and Technology
38 Department of Plant Biology
39 Division of Biomedical Statistics and Informatics
40 Department of Plant and Microbial Biology
41 Graduate School of Life Science
42 Rutgers University [Camden]
43 Monsanto Company
44 Faculty of Fisheries Sciences [Hakodate]
45 NIG - National Institute of Genetics [Shizuoka, Japan]
46 MPI-MP - Max Planck Institute of Molecular Plant Physiology
47 University of Tennessee
48 Department of Biology
49 Dalhousie University [Halifax]
50 Wellcome Trust
51 SIAS AG
52 Faculty of Biology
53 Albert-Ludwigs-Universität Freiburg = University of Freiburg
54 UNIANDES - Departamento de Ciencias Biológicas [Univ de los Andes Colombia]
55 Department of Biological Sciences
56 Joint BioEnergy Institute
57 RUB - Ruhr University Bochum = Ruhr-Universität Bochum
58 Texas A&M University System
59 Osaka University [Osaka]
60 PMEBBCE - Plante - microbe - environnement : biochimie, biologie cellulaire et écologie
John Bowman
- Fonction : Auteur
- PersonId : 801116
- ORCID : 0000-0001-7347-3691
Michael Barker
- Fonction : Auteur
- PersonId : 801117
- ORCID : 0000-0001-7173-1319
Mark Estelle
- Fonction : Auteur
- PersonId : 768611
- ORCID : 0000-0002-2613-8652
Ying Li
- Fonction : Auteur
- PersonId : 800973
- ORCID : 0000-0002-3060-9058
Stefan Rensing
- Fonction : Auteur
- PersonId : 791054
- ORCID : 0000-0002-0225-873X
Ryo Sotooka
- Fonction : Auteur
Milos Tanurdzic
- Fonction : Auteur
Daniel Wipf
- Fonction : Auteur
- PersonId : 753126
- IdHAL : daniel-wipf
- ORCID : 0000-0001-7197-5612
- IdRef : 145295761
Paul Wolf
- Fonction : Auteur
Therese Mitros
- Fonction : Auteur
Uffe Hellsten
- Fonction : Auteur
Dominique Loque
- Fonction : Auteur
- PersonId : 1428620
- ORCID : 0000-0002-2060-6611
- IdRef : 270297928
Robert Otillar
- Fonction : Auteur
Asaf Salamov
- Fonction : Auteur
Jeremy Schmutz
- Fonction : Auteur
Harris Shapiro
- Fonction : Auteur
Erika Lindquist
- Fonction : Auteur
Susan Lucas
- Fonction : Auteur
Daniel Rokhsar
- Fonction : Auteur
Igor Grigoriev
- Fonction : Auteur
- PersonId : 791663
- ORCID : 0000-0002-3136-8903
- IdRef : 229928536
Résumé
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.