Analyses of transcriptome sequences reveal multiple ancient large-scale duplication events in the ancestor of Sphagnopsida (Bryophyta)
Abstract
Summary The goal of this research was to investigate whether there has been a whole‐genome duplication ( WGD ) in the ancestry of Sphagnum (peatmoss) or the class Sphagnopsida, and to determine if the timing of any such duplication(s) and patterns of paralog retention could help explain the rapid radiation and current ecological dominance of peatmosses. RNA sequencing ( RNA ‐seq) data were generated for nine taxa in Sphagnopsida (Bryophyta). Analyses of frequency plots for synonymous substitutions per synonymous site ( K s ) between paralogous gene pairs and reconciliation of 578 gene trees were conducted to assess evidence of large‐scale or genome‐wide duplication events in each transcriptome. Both K s frequency plots and gene tree‐based analyses indicate multiple duplication events in the history of the Sphagnopsida. The most recent WGD event predates divergence of Sphagnum from the two other genera of Sphagnopsida. Duplicate retention is highly variable across species, which might be best explained by local adaptation. Our analyses indicate that the last WGD could have been an important factor underlying the diversification of peatmosses and facilitated their rise to ecological dominance in peatlands. The timing of the duplication events and their significance in the evolutionary history of peatmore »
- Authors:
-
- Duke Univ., Durham, NC (United States)
- Univ. of Zurich, Zurich (Switzerland); Swiss Institute of Bioinformatics, Lausanne (Switzerland)
- Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States)
- Univ. of California, Berkeley, CA (United States)
- Chicago Botanic Garden, Glencoe, IL (United States)
- Publication Date:
- Research Org.:
- Oak Ridge National Laboratory (ORNL), Oak Ridge, TN (United States)
- Sponsoring Org.:
- USDOE Laboratory Directed Research and Development (LDRD) Program
- OSTI Identifier:
- 1326556
- Alternate Identifier(s):
- OSTI ID: 1379979
- Grant/Contract Number:
- AC05-00OR22725
- Resource Type:
- Accepted Manuscript
- Journal Name:
- New Phytologist
- Additional Journal Information:
- Journal Volume: 211; Journal Issue: 1; Journal ID: ISSN 0028-646X
- Publisher:
- Wiley
- Country of Publication:
- United States
- Language:
- English
- Subject:
- 59 BASIC BIOLOGICAL SCIENCES
Citation Formats
Devos, Nicolas, Szövényi, Péter, Weston, David J., Rothfels, Carl J., Johnson, Matthew G., and Shaw, A. Jonathan. Analyses of transcriptome sequences reveal multiple ancient large-scale duplication events in the ancestor of Sphagnopsida (Bryophyta). United States: N. p., 2016.
Web. doi:10.1111/nph.13887.
Devos, Nicolas, Szövényi, Péter, Weston, David J., Rothfels, Carl J., Johnson, Matthew G., & Shaw, A. Jonathan. Analyses of transcriptome sequences reveal multiple ancient large-scale duplication events in the ancestor of Sphagnopsida (Bryophyta). United States. https://doi.org/10.1111/nph.13887
Devos, Nicolas, Szövényi, Péter, Weston, David J., Rothfels, Carl J., Johnson, Matthew G., and Shaw, A. Jonathan. Mon .
"Analyses of transcriptome sequences reveal multiple ancient large-scale duplication events in the ancestor of Sphagnopsida (Bryophyta)". United States. https://doi.org/10.1111/nph.13887. https://www.osti.gov/servlets/purl/1326556.
@article{osti_1326556,
title = {Analyses of transcriptome sequences reveal multiple ancient large-scale duplication events in the ancestor of Sphagnopsida (Bryophyta)},
author = {Devos, Nicolas and Szövényi, Péter and Weston, David J. and Rothfels, Carl J. and Johnson, Matthew G. and Shaw, A. Jonathan},
abstractNote = {Summary The goal of this research was to investigate whether there has been a whole‐genome duplication ( WGD ) in the ancestry of Sphagnum (peatmoss) or the class Sphagnopsida, and to determine if the timing of any such duplication(s) and patterns of paralog retention could help explain the rapid radiation and current ecological dominance of peatmosses. RNA sequencing ( RNA ‐seq) data were generated for nine taxa in Sphagnopsida (Bryophyta). Analyses of frequency plots for synonymous substitutions per synonymous site ( K s ) between paralogous gene pairs and reconciliation of 578 gene trees were conducted to assess evidence of large‐scale or genome‐wide duplication events in each transcriptome. Both K s frequency plots and gene tree‐based analyses indicate multiple duplication events in the history of the Sphagnopsida. The most recent WGD event predates divergence of Sphagnum from the two other genera of Sphagnopsida. Duplicate retention is highly variable across species, which might be best explained by local adaptation. Our analyses indicate that the last WGD could have been an important factor underlying the diversification of peatmosses and facilitated their rise to ecological dominance in peatlands. The timing of the duplication events and their significance in the evolutionary history of peat mosses are discussed.},
doi = {10.1111/nph.13887},
journal = {New Phytologist},
number = 1,
volume = 211,
place = {United States},
year = {Mon Feb 22 00:00:00 EST 2016},
month = {Mon Feb 22 00:00:00 EST 2016}
}
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Works referenced in this record:
A genome triplication associated with early diversification of the core eudicots
journal, January 2012
- Jiao, Yuannian; Leebens-Mack, Jim; Ayyampalayam, Saravanaraj
- Genome Biology, Vol. 13, Issue 1
De novo assembly and comparative analysis of the Ceratodon purpureus transcriptome
journal, June 2014
- Szövényi, Péter; Perroud, Pierre-François; Symeonidi, Aikaterini
- Molecular Ecology Resources, Vol. 15, Issue 1
Phylotranscriptomic analysis of the origin and early diversification of land plants
journal, October 2014
- Wickett, Norman J.; Mirarab, Siavash; Nguyen, Nam
- Proceedings of the National Academy of Sciences, Vol. 111, Issue 45
Data access for the 1,000 Plants (1KP) project
journal, October 2014
- Matasci, Naim; Hung, Ling-Hong; Yan, Zhixiang
- GigaScience, Vol. 3, Issue 1
The EMMIX Algorithm for the Fitting of Normal and -Components
journal, January 1999
- McLachlan, Geoff J.; Peel, David
- Journal of Statistical Software, Vol. 4, Issue 2
Two-Phase Resolution of Polyploidy in the Arabidopsis Metabolic Network Gives Rise to Relative and Absolute Dosage Constraints
journal, May 2011
- Bekaert, Michaël; Edger, Patrick P.; Pires, J. Chris
- The Plant Cell, Vol. 23, Issue 5
Multiple Polyploidy Events in the Early Radiation of Nodulating and Nonnodulating Legumes
journal, October 2014
- Cannon, Steven B.; McKain, Michael R.; Harkess, Alex
- Molecular Biology and Evolution, Vol. 32, Issue 1
Gapped BLAST and PSI-BLAST: a new generation of protein database search programs
journal, September 1997
- Altschul, Stephen F.; Madden, Thomas L.; Schäffer, Alejandro A.
- Nucleic Acids Research, Vol. 25, Issue 17, p. 3389-3402
Ancestral polyploidy in seed plants and angiosperms
journal, April 2011
- Jiao, Yuannian; Wickett, Norman J.; Ayyampalayam, Saravanaraj
- Nature, Vol. 473, Issue 7345
Bias in Plant Gene Content Following Different Sorts of Duplication: Tandem, Whole-Genome, Segmental, or by Transposition
journal, June 2009
- Freeling, Michael
- Annual Review of Plant Biology, Vol. 60, Issue 1
CD-HIT: accelerated for clustering the next-generation sequencing data
journal, October 2012
- Fu, Limin; Niu, Beifang; Zhu, Zhengwei
- Bioinformatics, Vol. 28, Issue 23
Newly resolved relationships in an early land plant lineage: Bryophyta class Sphagnopsida (peat mosses)
journal, September 2010
- Shaw, A. Jonathan; Cox, Cymon J.; Buck, William R.
- American Journal of Botany, Vol. 97, Issue 9
Full-length transcriptome assembly from RNA-Seq data without a reference genome
journal, May 2011
- Grabherr, Manfred G.; Haas, Brian J.; Yassour, Moran
- Nature Biotechnology, Vol. 29, Issue 7
An ancient genome duplication contributed to the abundance of metabolic genes in the moss Physcomitrella patens
journal, January 2007
- Rensing, Stefan A.; Ick, Julia; Fawcett, Jeffrey A.
- BMC Evolutionary Biology, Vol. 7, Issue 1
Contrasting patterns of evolution following whole genome versus tandem duplication events in Populus
journal, October 2011
- Rodgers-Melnick, E.; Mane, S. P.; Dharmawardhana, P.
- Genome Research, Vol. 22, Issue 1
Widespread Paleopolyploidy in Model Plant Species Inferred from Age Distributions of Duplicate Genes
journal, June 2004
- Blanc, Guillaume; Wolfe, Kenneth H.
- The Plant Cell, Vol. 16, Issue 7
Evolutionary Dynamics and Functional Specialization of Plant Paralogs Formed by Whole and Small-Scale Genome Duplications
journal, July 2012
- Carretero-Paulet, Lorenzo; Fares, Mario A.
- Molecular Biology and Evolution, Vol. 29, Issue 11
Methods for studying polyploid diversification and the dead end hypothesis: a reply to Soltis et al . (2014)
journal, December 2014
- Mayrose, Itay; Zhan, Shing H.; Rothfels, Carl J.
- New Phytologist, Vol. 206, Issue 1
Developmental basis of evolutionary digit loss in the Australian lizardHemiergis
journal, May 2003
- Shapiro, Michael D.; Hanken, James; Rosenthal, Nadia
- Journal of Experimental Zoology, Vol. 297B, Issue 1
Bioaccumulation and glutathione-mediated detoxification of copper and cadmium in Sphagnum squarrosum Crome Samml.
journal, August 2011
- Saxena, Anuj; Saxena, Anjali
- Environmental Monitoring and Assessment, Vol. 184, Issue 7
Peatmoss (Sphagnum) diversification associated with Miocene Northern Hemisphere climatic cooling?
journal, June 2010
- Shaw, A. Jonathan; Devos, Nicolas; Cox, Cymon J.
- Molecular Phylogenetics and Evolution, Vol. 55, Issue 3
The draft genome of the transgenic tropical fruit tree papaya (Carica papaya Linnaeus)
journal, April 2008
- Ming, Ray; Hou, Shaobin; Feng, Yun
- Nature, Vol. 452, Issue 7190
The polyploidy revolution then...and now: Stebbins revisited
journal, July 2014
- Soltis, D. E.; Visger, C. J.; Soltis, P. S.
- American Journal of Botany, Vol. 101, Issue 7
RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies
journal, January 2014
- Stamatakis, Alexandros
- Bioinformatics, Vol. 30, Issue 9
Duplications and Turnover in Plant Genomes
book, January 2012
- Barker, Michael S.; Baute, Gregory J.; Liu, Shao-Lun
- Plant Genome Diversity Volume 1
Many or most genes in Arabidopsis transposed after the origin of the order Brassicales
journal, October 2008
- Freeling, M.; Lyons, E.; Pedersen, B.
- Genome Research, Vol. 18, Issue 12
Genetic diversity, sexual condition, and microhabitat preference determine mating patterns in S phagnum (Sphagnaceae) peat-mosses : Mating Patterns in
journal, March 2015
- Johnson, Matthew G.; Shaw, A. Jonathan
- Biological Journal of the Linnean Society, Vol. 115, Issue 1
Ancient whole genome duplications, novelty and diversification: the WGD Radiation Lag-Time Model
journal, April 2012
- Eric Schranz, M.; Mohammadin, Setareh; Edger, Patrick P.
- Current Opinion in Plant Biology, Vol. 15, Issue 2
Gene-balanced duplications, like tetraploidy, provide predictable drive to increase morphological complexity
journal, July 2006
- Freeling, M.
- Genome Research, Vol. 16, Issue 7
Natural Pathways to Polyploidy in Plants and Consequences for Genome Reorganization
journal, January 2013
- Tayalé, A.; Parisod, C.
- Cytogenetic and Genome Research, Vol. 140, Issue 2-4
Organ and Cell Type–Specific Complementary Expression Patterns and Regulatory Neofunctionalization between Duplicated Genes in Arabidopsis thaliana
journal, January 2011
- Liu, Shao-Lun; Baute, Gregory J.; Adams, Keith L.
- Genome Biology and Evolution, Vol. 3
Inference of Genome Duplications from Age Distributions Revisited
journal, August 2012
- Vanneste, Kevin; Van de Peer, Yves; Maere, Steven
- Molecular Biology and Evolution, Vol. 30, Issue 1
Ancient polyploidization predating divergence of the cereals, and its consequences for comparative genomics
journal, May 2004
- Paterson, A. H.; Bowers, J. E.; Chapman, B. A.
- Proceedings of the National Academy of Sciences, Vol. 101, Issue 26
Rarely successful polyploids and their legacy in plant genomes
journal, April 2012
- Arrigo, Nils; Barker, Michael S.
- Current Opinion in Plant Biology, Vol. 15, Issue 2
Microsatellite analysis of Sphagnum centrale, S. henryense, and S. palustre (Sphagnaceae)
journal, March 2010
- Karlin, Eric F.; Giusti, Melissa M.; Lake, Rebecca A.
- The Bryologist, Vol. 113, Issue 1
Karyotypic Changes through Dysploidy Persist Longer over Evolutionary Time than Polyploid Changes
journal, January 2014
- Escudero, Marcial; Martín-Bravo, Santiago; Mayrose, Itay
- PLoS ONE, Vol. 9, Issue 1
Polyploid Formation Shapes Flowering Plant Diversity
journal, October 2014
- Scarpino, Samuel V.; Levin, Donald A.; Meyers, Lauren Ancel
- The American Naturalist, Vol. 184, Issue 4
FUNC: a package for detecting significant associations between gene sets and ontological annotations
journal, February 2007
- Prüfer, Kay; Muetzel, Bjoern; Do, Hong-Hai
- BMC Bioinformatics, Vol. 8, Issue 1
Paleopolyploidy in the Brassicales: Analyses of the Cleome Transcriptome Elucidate the History of Genome Duplications in Arabidopsis and Other Brassicales
journal, January 2009
- Barker, Michael S.; Vogel, Heiko; Schranz, M. Eric
- Genome Biology and Evolution, Vol. 1
Protein?Protein and Protein?DNA Dosage Balance and Differential Paralog Transcription Factor Retention in Polyploids
journal, January 2011
- Birchler, James A.; Veitia, Reiner A.
- Frontiers in Plant Science, Vol. 2
PAL2NAL: robust conversion of protein sequence alignments into the corresponding codon alignments
journal, July 2006
- Suyama, M.; Torrents, D.; Bork, P.
- Nucleic Acids Research, Vol. 34, Issue Web Server
Plants with double genomes might have had a better chance to survive the Cretaceous-Tertiary extinction event
journal, March 2009
- Fawcett, J. A.; Maere, S.; Van de Peer, Y.
- Proceedings of the National Academy of Sciences, Vol. 106, Issue 14
Ancient genome duplications during the evolution of kiwifruit (Actinidia) and related Ericales
journal, June 2010
- Shi, Tao; Huang, Hongwen; Barker, Michael S.
- Annals of Botany, Vol. 106, Issue 3
Dosage, duplication, and diploidization: clarifying the interplay of multiple models for duplicate gene evolution over time
journal, June 2014
- Conant, Gavin C.; Birchler, James A.; Pires, J. Chris
- Current Opinion in Plant Biology, Vol. 19
Gene and genome duplications: the impact of dosage-sensitivity on the fate of nuclear genes
journal, July 2009
- Edger, Patrick P.; Pires, J. Chris
- Chromosome Research, Vol. 17, Issue 5
Phylogenomic analysis of transcriptome data elucidates co-occurrence of a paleopolyploid event and the origin of bimodal karyotypes in Agavoideae (Asparagaceae)
journal, February 2012
- McKain, Michael R.; Wickett, Norman; Zhang, Yeting
- American Journal of Botany, Vol. 99, Issue 2
De novo transcript sequence reconstruction from RNA-seq using the Trinity platform for reference generation and analysis
journal, July 2013
- Haas, Brian J.; Papanicolaou, Alexie; Yassour, Moran
- Nature Protocols, Vol. 8, Issue 8
Multiple Paleopolyploidizations during the Evolution of the Compositae Reveal Parallel Patterns of Duplicate Gene Retention after Millions of Years
journal, August 2008
- Barker, M. S.; Kane, N. C.; Matvienko, M.
- Molecular Biology and Evolution, Vol. 25, Issue 11
Twilight zone of protein sequence alignments
journal, February 1999
- Rost, Burkhard
- Protein Engineering, Design and Selection, Vol. 12, Issue 2
Ohnologs in the human genome are dosage balanced and frequently associated with disease
journal, May 2010
- Makino, T.; McLysaght, A.
- Proceedings of the National Academy of Sciences, Vol. 107, Issue 20
Large-Scale Gene and Ancient Genome Duplications
book, January 2005
- Van De Peer, Yves; Meyer, Axel
- The Evolution of the Genome
Comparative Genomics as a Time Machine: How Relative Gene Dosage and Metabolic Requirements Shaped the Time-dependent Resolution of Yeast Polyploidy
journal, August 2014
- Conant, Gavin C.
- Molecular Biology and Evolution, Vol. 31, Issue 12
Dosage sensitivity and the evolution of gene families in yeast
journal, July 2003
- Papp, Balázs; Pál, Csaba; Hurst, Laurence D.
- Nature, Vol. 424, Issue 6945
Gene duplication as a driver of plant morphogenetic evolution
journal, February 2014
- Rensing, Stefan A.
- Current Opinion in Plant Biology, Vol. 17
Ethylene-induced stomatal closure in Arabidopsis occurs via AtrbohF-mediated hydrogen peroxide synthesis
journal, September 2006
- Desikan, Radhika; Last, Kathryn; Harrett-Williams, Rhian
- The Plant Journal, Vol. 47, Issue 6
Gene Ontology: tool for the unification of biology
journal, May 2000
- Ashburner, Michael; Ball, Catherine A.; Blake, Judith A.
- Nature Genetics, Vol. 25, Issue 1
Blast2GO: a universal tool for annotation, visualization and analysis in functional genomics research
journal, August 2005
- Conesa, A.; Gotz, S.; Garcia-Gomez, J. M.
- Bioinformatics, Vol. 21, Issue 18
Legume genome evolution viewed through the Medicago truncatula and Lotus japonicus genomes
journal, September 2006
- Cannon, S. B.; Sterck, L.; Rombauts, S.
- Proceedings of the National Academy of Sciences, Vol. 103, Issue 40
The Origins of Genomic Duplications in Arabidopsis
journal, December 2000
- Vision, T. J.; Brown, D. G.; Tanksley, S. D.
- Science, Vol. 290, Issue 5499
Inferring the higher-order phylogeny of mosses (Bryophyta) and relatives using a large, multigene plastid data set
journal, May 2011
- Chang, Y.; Graham, S. W.
- American Journal of Botany, Vol. 98, Issue 5
TranslatorX: multiple alignment of nucleotide sequences guided by amino acid translations
journal, April 2010
- Abascal, Federico; Zardoya, Rafael; Telford, Maximilian J.
- Nucleic Acids Research, Vol. 38, Issue suppl_2
Unravelling angiosperm genome evolution by phylogenetic analysis of chromosomal duplication events
journal, March 2003
- Bowers, John E.; Chapman, Brad A.; Rong, Junkang
- Nature, Vol. 422, Issue 6930
Prevalent Role of Gene Features in Determining Evolutionary Fates of Whole-Genome Duplication Duplicated Genes in Flowering Plants
journal, February 2013
- Jiang, Wen-kai; Liu, Yun-long; Xia, En-hua
- Plant Physiology, Vol. 161, Issue 4
Mining EST databases to resolve evolutionary events in major crop species
journal, October 2004
- Schlueter, Jessica A.; Dixon, Phillip; Granger, Cheryl
- Genome, Vol. 47, Issue 5
KaKs_Calculator: Calculating Ka and Ks Through Model Selection and Model Averaging
journal, January 2006
- Zhang, Zhang; Li, Jun; Zhao, Xiao-Qian
- Genomics, Proteomics & Bioinformatics, Vol. 4, Issue 4
Widespread genome duplications throughout the history of flowering plants
journal, June 2006
- Cui, L.
- Genome Research, Vol. 16, Issue 6
Trade-offs in resource allocation among moss species control decomposition in boreal peatlands
journal, November 2008
- Turetsky, Merritt R.; Crow, Susan E.; Evans, Robert J.
- Journal of Ecology, Vol. 96, Issue 6
SOAPdenovo-Trans: de novo transcriptome assembly with short RNA-Seq reads
journal, February 2014
- Xie, Y.; Wu, G.; Tang, J.
- Bioinformatics, Vol. 30, Issue 12
Evolution of niche preference in Sphagnum peat mosses : EVOLUTION OF NICHE PREFERENCE
journal, December 2014
- Johnson, Matthew G.; Granath, Gustaf; Tahvanainen, Teemu
- Evolution, Vol. 69, Issue 1
The Genome of Black Cottonwood, Populus trichocarpa (Torr. & Gray)
journal, September 2006
- Tuskan, G. A.; DiFazio, S.; Jansson, S.
- Science, Vol. 313, Issue 5793, p. 1596-1604
Finding and Comparing Syntenic Regions among Arabidopsis and the Outgroups Papaya, Poplar, and Grape: CoGe with Rosids
journal, October 2008
- Lyons, Eric; Pedersen, Brent; Kane, Josh
- Plant Physiology, Vol. 148, Issue 4
Polyploidy and angiosperm diversification
journal, January 2009
- Soltis, Douglas E.; Albert, Victor A.; Leebens-Mack, Jim
- American Journal of Botany, Vol. 96, Issue 1
Estimating Synonymous and Nonsynonymous Substitution Rates Under Realistic Evolutionary Models
journal, January 2000
- Yang, Ziheng; Nielsen, Rasmus
- Molecular Biology and Evolution, Vol. 17, Issue 1
trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses
journal, June 2009
- Capella-Gutierrez, S.; Silla-Martinez, J. M.; Gabaldon, T.
- Bioinformatics, Vol. 25, Issue 15
Environmental mutagenesis during the end-Permian ecological crisis
journal, July 2004
- Visscher, H.; Looy, C. V.; Collinson, M. E.
- Proceedings of the National Academy of Sciences, Vol. 101, Issue 35
The evolutionary significance of ancient genome duplications
journal, August 2009
- Van de Peer, Yves; Maere, Steven; Meyer, Axel
- Nature Reviews Genetics, Vol. 10, Issue 10
Recently Formed Polyploid Plants Diversify at Lower Rates
journal, August 2011
- Mayrose, I.; Zhan, S. H.; Rothfels, C. J.
- Science, Vol. 333, Issue 6047
Dissecting Plant Genomes with the PLAZA Comparative Genomics Platform
journal, December 2011
- Van Bel, Michiel; Proost, Sebastian; Wischnitzki, Elisabeth
- Plant Physiology, Vol. 158, Issue 2
All duplicates are not equal: the difference between small-scale and genome duplication
journal, January 2007
- Hakes, Luke; Pinney, John W.; Lovell, Simon C.
- Genome Biology, Vol. 8, Issue 10
The grapevine genome sequence suggests ancestral hexaploidization in major angiosperm phyla
journal, August 2007
- The French-Italian Public Consortium for Grapevine Genome Characterization,
- Nature, Vol. 449, Issue 7161, p. 463-467
The Natural History of Protein Domains
journal, June 2002
- Ponting, Chris P.; Russell, Robert R.
- Annual Review of Biophysics and Biomolecular Structure, Vol. 31, Issue 1
The dynamics of functional classes of plant genes in rediploidized ancient polyploids
journal, October 2013
- Chen, Eric CH; Buen Abad Najar, Carlos Fernando; Zheng, Chunfang
- BMC Bioinformatics, Vol. 14, Issue S15
Reannotation and extended community resources for the genome of the non-seed plant Physcomitrella patens provide insights into the evolution of plant gene structures and functions
journal, January 2013
- Zimmer, Andreas D.; Lang, Daniel; Buchta, Karol
- BMC Genomics, Vol. 14, Issue 1
De novo assembly and characterization of the transcriptome in the desiccation-tolerant moss Syntrichia caninervis
journal, January 2014
- Gao, Bei; Zhang, Daoyuan; Li, Xiaoshuang
- BMC Research Notes, Vol. 7, Issue 1
Nested radiations and the pulse of angiosperm diversification: increased diversification rates often follow whole genome duplications
journal, December 2014
- Tank, David C.; Eastman, Jonathan M.; Pennell, Matthew W.
- New Phytologist, Vol. 207, Issue 2
Tangled up in two: a burst of genome duplications at the end of the Cretaceous and the consequences for plant evolution
journal, August 2014
- Vanneste, Kevin; Maere, Steven; Van de Peer, Yves
- Philosophical Transactions of the Royal Society B: Biological Sciences, Vol. 369, Issue 1648
Simulating Evolution by Gene Duplication
journal, January 1987
- Ohta, Tomoko
- Genetics, Vol. 115, Issue 1
How often do duplicated genes evolve new functions?
journal, January 1995
- Walsh, J. B.
- Genetics, Vol. 139, Issue 1
Works referencing / citing this record:
Evolution by duplication: paleopolyploidy events in plants reconstructed by deciphering the evolutionary history of VOZ transcription factors
journal, October 2018
- Gao, Bei; Chen, Moxian; Li, Xiaoshuang
- BMC Plant Biology, Vol. 18, Issue 1
Phylogenomic synteny network analyses reveal ancestral transpositions of auxin response factor genes in plants
journal, May 2020
- Gao, Bei; Wang, Liuqiang; Oliver, Melvin
- Plant Methods, Vol. 16, Issue 1
Evolution of Auxin Response Factors in plants characterized by phylogenomic synteny network analyses
posted_content, April 2019
- Gao, Bei; Wang, Liuqiang; Oliver, Melvin
- BioRxiv
Ancient duplications and grass-specific transposition influenced the evolution of LEAFY transcription factor genes
journal, June 2019
- Gao, Bei; Chen, Moxian; Li, Xiaoshuang
- Communications Biology, Vol. 2, Issue 1
Genome-wide identification of the CLAVATA3/EMBRYO SURROUNDING REGION (CLE) family in grape (Vitis vinifera L.)
journal, July 2019
- Wang, Pengfei; Wang, Yongmei; Ren, Fengshan
- BMC Genomics, Vol. 20, Issue 1
Genome Sequencing of Pleurozium schreberi : The Assembled and Annotated Draft Genome of a Pleurocarpous Feather Moss
journal, July 2019
- Pederson, Eric R. A.; Warshan, Denis; Rasmussen, Ulla
- G3: Genes|Genomes|Genetics, Vol. 9, Issue 9
Transcriptome-Wide Identification and Expression Analysis of DIVARICATA- and RADIALIS-Like Genes of the Mediterranean Orchid Orchis italica
journal, May 2017
- Valoroso, Maria Carmen; De Paolo, Sofia; Iazzetti, Giovanni
- Genome Biology and Evolution, Vol. 9, Issue 6
Evolutionary history and structure of nuclear matrix constituent proteins, the plant analogues of lamins
journal, March 2019
- Ciska, Malgorzata; Hikida, Riku; Masuda, Kiyoshi
- Journal of Experimental Botany, Vol. 70, Issue 10
The Sphagnome Project: enabling ecological and evolutionary insights through a genus-level sequencing project
journal, October 2017
- Weston, David J.; Turetsky, Merritt R.; Johnson, Matthew G.
- New Phytologist, Vol. 217, Issue 1
The Physcomitrella patens chromosome-scale assembly reveals moss genome structure and evolution
journal, January 2018
- Lang, Daniel; Ullrich, Kristian K.; Murat, Florent
- The Plant Journal, Vol. 93, Issue 3
Constraining the timing of whole genome duplication in plant evolutionary history
journal, July 2017
- Clark, James W.; Donoghue, Philip C. J.
- Proceedings of the Royal Society B: Biological Sciences, Vol. 284, Issue 1858
The Physcomitrella patens gene atlas project: large-scale RNA-seq based expression data
journal, June 2018
- Perroud, Pierre-François; Haas, Fabian B.; Hiss, Manuel
- The Plant Journal, Vol. 95, Issue 1
The sphagnome project: enabling ecological and evolutionary insights through a genus-level sequencing project
text, January 2018
- Weston, David J.; Turetsky, Merritt R.; Johnson, Matthew G.
- Wiley-Blackwell Publishing, Inc.
The Physcomitrella patens gene atlas project: large-scale RNA-seq based expression data
text, January 2018
- Perroud, Pierre-François; Haas, Fabian B.; Hiss, Manuel
- Wiley-Blackwell Publishing, Inc.
Ancient duplications and grass-specific transposition influenced the evolution of LEAFY transcription factor genes
journal, June 2019
- Gao, Bei; Chen, Moxian; Li, Xiaoshuang
- Communications Biology, Vol. 2, Issue 1
Assessing the performance of Ks plots for detecting ancient whole genome duplications
journal, September 2018
- Tiley, George P.; Barker, Michael S.; Burleigh, J. Gordon
- Genome Biology and Evolution
Integrated phylogenomic analyses reveal recurrent ancestral large-scale duplication events in mosses
posted_content, April 2019
- Gao, Bei; Chen, Moxian; Li, Xiaoshuang
- BioRxiv
Genome-wide identification of the CLAVATA3/EMBRYO SURROUNDING REGION (CLE) family in grape (Vitis vinifera L.)
journal, July 2019
- Wang, Pengfei; Wang, Yongmei; Ren, Fengshan
- BMC Genomics, Vol. 20, Issue 1
Evolution by duplication: paleopolyploidy events in plants reconstructed by deciphering the evolutionary history of VOZ transcription factors
journal, October 2018
- Gao, Bei; Chen, Moxian; Li, Xiaoshuang
- BMC Plant Biology, Vol. 18, Issue 1