Home LiteratureArticle Details
PMID: 21551031 Published · ppublish English Journal Article Research Support, N.I.H., Extramural Research Support, Non-U.S. Gov't Research Support, U.S. Gov't, Non-P.H.S.

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

Science (New York, N.Y.) ·Vol. 332 ·No. 6032 ·2011-05-20 ·Pages 960-3

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 LG, 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 S, Murata T, 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 WW, 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

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.

MeSH Terms
Biological Evolution Bryopsida/genetics Chlamydomonas/chemistry,genetics DNA Transposable Elements Evolution, Molecular Gene Expression Regulation, Plant Genes, Plant Genome, Plant Magnoliopsida/chemistry,genetics MicroRNAs/genetics Molecular Sequence Data Phylogeny Plant Proteins/genetics,metabolism Proteome/analysis RNA Editing RNA, Plant/genetics Repetitive Sequences, Nucleic Acid Selaginellaceae/genetics,growth & development,metabolism Sequence Analysis, DNA
Chemicals
DNA Transposable Elements MicroRNAs Plant Proteins Proteome RNA, Plant
Authors & Affiliations
103 authors, click to expand affiliations / ORCID
Banks Jo Ann
Department of Botany and Plant Pathology, Purdue University, West Lafayette, IN 47907, USA. banksj@purdue.edu
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
Murata Takashi
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
References (22)
22 references, click to expand
  1. DICER-LIKE 4 functions in trans-acting small interfering RNA biogenesis and vegetative phase change in Arabidopsis thaliana.
    Proc Natl Acad Sci U S A. 2005 Sep 6;102(36):12984-9 PMID: 16129836
  2. Paleopolyploidy in the Brassicales: analyses of the Cleome transcriptome elucidate the history of genome duplications in Arabidopsis and other Brassicales.
    Genome Biol Evol. 2009 Oct 05;1:391-9 PMID: 20333207
  3. The chloroplast genome from a lycophyte (microphyllophyte), Selaginella uncinata, has a unique inversion, transpositions and many gene losses.
    J Plant Res. 2007 Mar;120(2):281-90 PMID: 17297557
  4. Physcomitrella patens DCL3 is required for 22-24 nt siRNA accumulation, suppression of retrotransposon-derived transcripts, and normal development.
    PLoS Genet. 2008 Dec;4(12):e1000314 PMID: 19096705
  5. Pattern formation via small RNA mobility.
    Genes Dev. 2009 Mar 1;23(5):549-54 PMID: 19270155
  6. Small RNAs in angiosperms: sequence characteristics, distribution and generation.
    Bioinformatics. 2010 Jun 1;26(11):1391-4 PMID: 20378553
  7. Step-by-step acquisition of the gibberellin-DELLA growth-regulatory mechanism during land-plant evolution.
    Curr Biol. 2007 Jul 17;17(14):1225-30 PMID: 17627823
  8. APL regulates vascular tissue identity in Arabidopsis.
    Nature. 2003 Nov 13;426(6963):181-6 PMID: 14614507
  9. Synteny and collinearity in plant genomes.
    Science. 2008 Apr 25;320(5875):486-8 PMID: 18436778
  10. An expression atlas of rice mRNAs and small RNAs.
    Nat Biotechnol. 2007 Apr;25(4):473-7 PMID: 17351617
  11. Transcriptional regulation in wood formation.
    Trends Plant Sci. 2007 Feb;12(2):64-70 PMID: 17224301
  12. Unraveling ancient hexaploidy through multiply-aligned angiosperm gene maps.
    Genome Res. 2008 Dec;18(12):1944-54 PMID: 18832442
  13. Distinct developmental mechanisms reflect the independent origins of leaves in vascular plants.
    Curr Biol. 2006 Oct 10;16(19):1911-7 PMID: 17027487
  14. Common functions for diverse small RNAs of land plants.
    Plant Cell. 2007 Jun;19(6):1750-69 PMID: 17601824
  15. The GID1-mediated gibberellin perception mechanism is conserved in the Lycophyte Selaginella moellendorffii but not in the Bryophyte Physcomitrella patens.
    Plant Cell. 2007 Oct;19(10):3058-79 PMID: 17965273
  16. Bioactive flavones and biflavones from Selaginella moellendorffii Hieron.
    Fitoterapia. 2010 Jun;81(4):253-8 PMID: 19775597
  17. Small silencing RNAs: an expanding universe.
    Nat Rev Genet. 2009 Feb;10(2):94-108 PMID: 19148191
  18. Genome-wide profiling and analysis of Arabidopsis siRNAs.
    PLoS Biol. 2007 Mar;5(3):e57 PMID: 17298187
  19. A small-RNA perspective on gametogenesis, fertilization, and early zygotic development.
    Science. 2010 Oct 29;330(6004):617-22 PMID: 21030645
  20. Construction of a bacterial artificial chromosome library from the spikemoss Selaginella moellendorffii: a new resource for plant comparative genomics.
    BMC Plant Biol. 2005 Jun 14;5:10 PMID: 15955246
  21. Independent recruitment of a conserved developmental mechanism during leaf evolution.
    Nature. 2005 Mar 24;434(7032):509-14 PMID: 15791256
  22. SGS3 and SGS2/SDE1/RDR6 are required for juvenile development and the production of trans-acting siRNAs in Arabidopsis.
    Genes Dev. 2004 Oct 1;18(19):2368-79 PMID: 15466488
Article Info
Journal
Science (New York, N.Y.)
Abbr.
Science
ISSN
1095-9203
DOI
10.1126/science.1203810
Email
banksj@purdue.edu
Published
2011-05-20
Epub
2011-00-05
Pages
960-3
Language
English
Region
United States
NLM ID
0404511
PMCID
PMC3166216
Subset
IM
Grants
NIGMS NIH HHS · T32 GM007757 · United States
NHGRI NIH HHS · T32-HG00035 · United States
NIGMS NIH HHS · GM84051 · United States
NIGMS NIH HHS · R01 GM084051 · United States
NHGRI NIH HHS · R01 HG004164-04 · United States
NIGMS NIH HHS · R01 GM084051-01A1 · United States
NHGRI NIH HHS · HG004164 · United States
NHGRI NIH HHS · R01 HG004164-03 · United States
NIGMS NIH HHS · R01 GM043644 · United States
NHGRI NIH HHS · R01 HG004164-02 · United States
NIGMS NIH HHS · GM065383 · United States
NHGRI NIH HHS · R01 HG004164 · United States
Databases
GENBANK
HM173080
External Links
PubMed source DOI: 10.1126/science.1203810 PMC Full Text View journal details
Analysis Services
Analysis Services

Contact

No. 2 Wenbo Road, Zhangqiu District, Jinan, Shandong

Qilu Normal University · Genelibs Bioinformatics Lab

750 Shunhua Rd, Jinan

2F, Bldg F, University Science Park

Tel: 0531-88819269

WeChat Official Account

Follow our WeChat subscription account for real-time updates and the latest in medical and biological research.


Business Email

E-mail: product@genelibs.com

Copyright © 2026.Genelibs Jinan Honghui Biotechnology Co., Ltd. 鲁ICP备20007159号-2