One thousand plant transcriptomes and the phylogenomics of green plants

Xun Xu | Fan Yang | Ivo Grosse | Xia Li | Dennis W. Stevenson | Andrew J. Lowe | Claude W. dePamphilis | Tandy Warnow | Xuemei Tan | Anders Larsson | Siavash Mirarab | Ramona L. Walls | Steven B. Cannon | Elizabeth A. Kellogg | Stefan A. Rensing | C. N. Stewart | Saravanaraj N. Ayyampalayam | C. Neal Stewart | Xiaofeng Wei | Yanhui Peng | Mark W. Chase | Verónica S. Di Stilio | Erfan Sayyari | David J. Beerling | Jun Wang | Nils Arrigo | Gane Ka-Shu Wong | Lydia Gramzow | Günter Theißen | Jason N. Burris | Feiyu Zhou | Blake L. Joyce | Douglas E. Soltis | Marcus A. Koch | Pamela S. Soltis | Fay-Wei Li | Stephan Greiner | Eric J. Carpenter | Nicolás García | N. D. Clarke | Neil D. Clarke | Michael S. Barker | Tao Liu | Toni M. Kutchan | Caspar Chater | Naim Matasci | Zhixiang Yan | Saravanaraj Ayyampalayam | Michael Melkonian | Lisa Pokorny | Lisa DeGironimo | Juan Carlos Villarreal | Tao Chen | Daniel Real | J. Chris Pires | Nam-phuong Nguyen | Blake Joyce | Stephen G. Weller | Zhijian Tian | Michael K. Deyholos | Martin Porsch | John R. Stinchcombe | Hong An | Bruno Fogliani | John M. Cheeseman | Jingbo Tang | Shona Ellis | Patrick P. Edger | Julian M. Hibberd | James H. Leebens-Mack | Matthew A. Gitzendanner | Peter M. Hollingsworth | T. Warnow | G. Wong | D. Soltis | I. Grosse | Yong Zhang | Xia Li | J. Leebens-Mack | P. Soltis | C. dePamphilis | M. Chase | Jun Wang | S. Cannon | M. Melkonian | Shifeng Cheng | Xun Xu | D. Stevenson | P. Hollingsworth | B. Crandall-Stotler | Li Chen | Fay‐Wei Li | C. Rothfels | A. Larsson | S. Graham | S. Mirarab | Xiaofeng Wei | Fan Yang | E. Kellogg | J. Pires | R. Walls | S. Rensing | D. Beerling | J. Stinchcombe | D. Nelson | G. Theißen | R. Baucom | M. Quint | H. Sederoff | J. Westwood | S. Floyd | Martin Porsch | E. Biffin | P. Edger | H. An | Xinshuai Qi | J. Burris | K. Ullrich | R. Jost | P. Finnegan | A. Lowe | Elena Kazamia | R. Sage | D. Whigham | S. Weller | M. Deyholos | Ingrid E Jordon-Thaden | M. Koch | A. Leitch | K. Helliwell | Alison G. Smith | M. Barrett | E. Schilling | Haorong Lu | J. Cheeseman | J. Hibberd | M. McCormick | S. Zhan | K. Burris | Shuangxiu Wu | P. Szövényi | Marc T. J. Johnson | J. Der | Juanjuan Li | Jun Yu | M. Nelson | M. McKain | Hannah E. Marx | Nam-phuong Nguyen | A. J. Shaw | Richard E. Miller | Emily B. Sessa | Erin M. Sigel | Stina Weststrand | M. Ludwig | Grant T. Godden | E. Wafula | Jingbo Tang | N. Wickett | E. Carpenter | Naim Matasci | M. Gitzendanner | N. Miles | L. Pokorny | Lisa DeGironimo | J. C. Villarreal | Tao Chen | T. Kutchan | M. Augustin | Z. Tian | Zhixiang Yan | Xiao Sun | Cui Chen | J. Tate | A. Harkess | F. Goh | Lydia Gramzow | G. Gâteblé | A. Caicedo | T. Barkman | Xuemei Tan | T. Mclellan | A. Smithson | M. von Konrat | Shana R. Welles | Roswitha Lentz | Ying Zhu | Michaela Wenzel | N. Arrigo | Chun-Neng Wang | Yan Ou | Zheng Li | Nicolás García | P. Manos | M. Kapralov | James H. Michael S. Eric J. Michael K. Matthew A. Sean W Leebens-Mack Barker Carpenter Deyholos Gitz | Steve Joya | Tao Liu | B. Melkonian | Charlotte T C Quigley | P. Thomas | Ruben M Benstein | S. Brockington | D. Burge | V. Burtet-Sarramegna | Zehra Çebi | Ying Chang | C. Chater | Harmony Clayton | Sarah Covshoff | Hugh B. Cross | R. Determann | Rowan C. Dickson | V. S. Di Stilio | S. Ellis | E. Fast | N. Feja | Katie J. Field | D. Filatov | B. Fogliani | S. Greiner | James Mike Heaney | Karolina Heyduk | R. G. Hodel | B. Joyce | K. Könyves | V. Lam | E. Mavrodiev | J. McNeal | Yanhui Peng | Paula E. Ralph | D. Real | C. Riggins | M. Ruhsam | A. Sakai | Moira Scascitella | Eva-Marie Schlösser | Stein V. Servick | S. W. Shaw | C. Skema | H. Tiebel | D. Trapnell | Matthieu Villegente | Adrien S. Wulff | Yu Yang | Dan Zhu | Cuili Zhuang | Jennifer Zuidof | Ran Li | Feng Wang | Xiao-ling Zhong | Feiyu Zhou | Erfan Sayyari | Anthony E Baniaga | Sally R. Galuska | Stacy A. Jorgensen | Thomas I. Kidder | Hanghui Kong | Patricia Lu-Irving | Chris R. Reardon | B. Sutherland | G. Tiley | Rongpei Yu | Yong Zhang | Zheng Li | Shifeng Cheng | Haorong Lu | Paul S. Manos | David R. Nelson | Elena Kazamia | Sean W. Graham | Marcel Quint | Kristian K. Ullrich | Norman J. Wickett | Ingrid E. Jordon-Thaden | Steve Joya | Barbara Melkonian | Nicholas W. Miles | Charlotte Quigley | Philip Thomas | Megan M. Augustin | Matthew D. Barrett | Regina S. Baucom | Ruben Maximilian Benstein | Ed Biffin | Samuel F. Brockington | Dylan O. Burge | Kellie P. Burris | Valérie Burtet-Sarramegna | Ana L. Caicedo | Zehra Çebi | Ying Chang | Harmony Clayton | Sarah Covshoff | Barbara J. Crandall-Stotler | Hugh Cross | Joshua P. Der | Ron Determann | Eva Fast | Nicole Feja | Dmitry A. Filatov | Patrick M. Finnegan | Sandra K. Floyd | Gildas Gâteblé | Falicia (Qi Yun) Goh | Alex Harkess | Katherine E. Helliwell | Karolina Heyduk | Richard G. J. Hodel | Ricarda Jost | Maxim V. Kapralov | Matt Von Konrat | Kálmán Könyves | Vivienne Lam | Andrew R. Leitch | Roswitha Lentz | Martha Ludwig | Evgeny Mavrodiev | Melissa K. McCormick | Michael McKain | Tracy McLellan | Joel R. McNeal | Matthew N. Nelson | Paula Ralph | Chance W. Riggins | Markus Ruhsam | Rowan F. Sage | Ann K. Sakai | Moira Scascitella | Edward E. Schilling | Eva-Marie Schlösser | Heike Sederoff | Stein Servick | A. Jonathan Shaw | Shane W. Shaw | Cynthia Skema | Ann Smithson | Peter Szövényi | Jennifer A. Tate | Helga Tiebel | Dorset Trapnell | Matthieu Villegente | Chun-Neng Wang | Michael Wenzel | Stina Weststrand | James H. Westwood | Dennis F. Whigham | Shuangxiu Wu | Yu Yang | Dan Zhu | Cuili Zhuang | Jennifer Zuidof | Carl J. Rothfels | Jun Yu | Cui Chen | Li Chen | Juanjuan Li | Ran Li | Yanxiang Ou | Xiao Sun | Feng Wang | Xiaoni Zhong | Ying Zhu | Todd J. Barkman | Eric K. Wafula | Anthony E. Baniaga | Sally Galuska | Hanghui Kong | Patricia Lu-Irving | Xinshuai Qi | Brittany L. Sutherland | George P. Tiley | Rongpei Yu | Shing Zhan | Fay-Wei Li | Chun‐Neng Wang | E. Sigel | Zhijian Tian | N. Clarke | Ruben M. Benstein | Ed Biffin | Tao Chen | Dorset W. Trapnell | Stephan Greiner | C. Stewart | J. Mcneal | Ricarda Jost | K. Field | V. D. Di Stilio

[1]  Erin K. Molloy,et al.  The performance of coalescent-based species tree estimation methods under models of missing data , 2018, BMC Genomics.

[2]  Michael J. Sanderson,et al.  The prevalence of terraced treescapes in analyses of phylogenetic data sets , 2018, BMC Evolutionary Biology.

[3]  Michael S. Barker,et al.  Multiple large-scale gene and genome duplications during the evolution of hexapods , 2018, Proceedings of the National Academy of Sciences.

[4]  Mark N. Puttick,et al.  The Interrelationships of Land Plants and the Nature of the Ancestral Embryophyte , 2018, Current Biology.

[5]  Michael S. Barker,et al.  Impact of whole-genome duplication events on diversification rates in angiosperms. , 2018, American journal of botany.

[6]  S. Graham,et al.  Phylogenomic inference in extremis: A case study with mycoheterotroph plastomes. , 2018, American journal of botany.

[7]  Pamela S Soltis,et al.  Plastid phylogenomic analysis of green plants: A billion years of evolutionary history. , 2018, American journal of botany.

[8]  Siavash Mirarab,et al.  DiscoVista: Interpretable visualizations of gene tree discordance. , 2017, Molecular phylogenetics and evolution.

[9]  Siavash Mirarab,et al.  Testing for Polytomies in Phylogenetic Species Trees Using Quartet Frequencies , 2017, Genes.

[10]  Ping Liu,et al.  A genome for gnetophytes and early evolution of seed plants , 2018, Nature Plants.

[11]  S. Rensing,et al.  Comprehensive Genome-Wide Classification Reveals That Many Plant-Specific Transcription Factors Evolved in Streptophyte Algae , 2017, Genome biology and evolution.

[12]  Siavash Mirarab,et al.  Fragmentary Gene Sequences Negatively Impact Gene Tree and Species Tree Reconstruction , 2017, Molecular biology and evolution.

[13]  F. Parcy,et al.  A link between LEAFY and B-gene homologues in Welwitschia mirabilis sheds light on ancestral mechanisms prefiguring floral development. , 2017, The New phytologist.

[14]  Christian R. Boehm,et al.  Insights into Land Plant Evolution Garnered from the Marchantia polymorpha Genome , 2017, Cell.

[15]  Sudhir Kumar,et al.  TimeTree: A Resource for Timelines, Timetrees, and Divergence Times. , 2017, Molecular biology and evolution.

[16]  Rolf Lohaus,et al.  Revisiting ancestral polyploidy in plants , 2017, Science Advances.

[17]  Tandy Warnow,et al.  To include or not to include: The impact of gene filtering on species tree estimation methods , 2017, bioRxiv.

[18]  S. Rensing,et al.  Three rings for the evolution of plastid shape: a tale of land plant FtsZ , 2017, Protoplasma.

[19]  Steven Maere,et al.  The Origin of Floral Organ Identity Quartets , 2017, Plant Cell.

[20]  Naomi S. Altman,et al.  Horizontal gene transfer is more frequent with increased heterotrophy and contributes to parasite adaptation , 2016, Proceedings of the National Academy of Sciences.

[21]  J. Bowman,et al.  Field Guide to Plant Model Systems , 2016, Cell.

[22]  M. Melkonian,et al.  Apparition of the NAC Transcription Factors Predates the Emergence of Land Plants. , 2016, Molecular plant.

[23]  R. Govaerts,et al.  Counting counts: revised estimates of numbers of accepted species of flowering plants, seed plants, vascular plants and land plants with a review of other recent estimates , 2016 .

[24]  S. Kelly,et al.  The Stepwise Increase in the Number of Transcription Factor Families in the Precambrian Predated the Diversification of Plants On Land. , 2016, Molecular biology and evolution.

[25]  Claudia R. Solís-Lemus,et al.  Inconsistency of Species Tree Methods under Gene Flow. , 2016, Systematic biology.

[26]  Tandy Warnow,et al.  Evaluating Summary Methods for Multilocus Species Tree Estimation in the Presence of Incomplete Lineage Sorting. , 2016, Systematic biology.

[27]  Stephen J. Callister,et al.  Evidence-based green algal genomics reveals marine diversity and ancestral characteristics of land plants , 2016, BMC Genomics.

[28]  J. Gordon Burleigh,et al.  Evaluating and Characterizing Ancient Whole-Genome Duplications in Plants with Gene Count Data , 2016, Genome biology and evolution.

[29]  R. Corlett Plant diversity in a changing world: Status, trends, and conservation needs , 2016, Plant diversity.

[30]  Siavash Mirarab,et al.  Fast Coalescent-Based Computation of Local Branch Support from Quartet Frequencies , 2016, Molecular biology and evolution.

[31]  Michael S. Barker,et al.  Early genome duplications in conifers and other seed plants , 2015, Science Advances.

[32]  Dennis W. Stevenson,et al.  Algal ancestor of land plants was preadapted for symbiosis , 2015, Proceedings of the National Academy of Sciences.

[33]  C. Delwiche,et al.  The Evolutionary Origin of a Terrestrial Flora , 2015, Current Biology.

[34]  Evgeny M. Zdobnov,et al.  BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs , 2015, Bioinform..

[35]  S. Kelly,et al.  OrthoFinder: solving fundamental biases in whole genome comparisons dramatically improves orthogroup inference accuracy , 2015, Genome Biology.

[36]  Stephen A. Smith,et al.  Analysis of phylogenomic datasets reveals conflict, concordance, and gene duplications with examples from animals and plants , 2015, BMC Evolutionary Biology.

[37]  E. Yang,et al.  Evidence of ancient genome reduction in red algae (Rhodophyta) , 2015, Journal of phycology.

[38]  David C. Tank,et al.  Nested radiations and the pulse of angiosperm diversification: increased diversification rates often follow whole genome duplications. , 2015, The New phytologist.

[39]  C. N. Stewart,et al.  The evolutionary history of ferns inferred from 25 low-copy nuclear genes. , 2015, American journal of botany.

[40]  Tandy J. Warnow,et al.  ASTRAL-II: coalescent-based species tree estimation with many hundreds of taxa and thousands of genes , 2015, Bioinform..

[41]  Matthew A. Gitzendanner,et al.  Modified CTAB and TRIzol protocols improve RNA extraction from chemically complex Embryophyta , 2015, Applications in plant sciences.

[42]  Tandy J. Warnow,et al.  Ultra-large alignments using phylogeny-aware profiles , 2015, Genome Biology.

[43]  Alexey M. Kozlov,et al.  ExaML version 3: a tool for phylogenomic analyses on supercomputers , 2015, Bioinform..

[44]  Md. Shamsuzzoha Bayzid,et al.  Weighted Statistical Binning: Enabling Statistically Consistent Genome-Scale Phylogenetic Analyses , 2014, PloS one.

[45]  C. N. Stewart,et al.  Multiple polyploidy events in the early radiation of nodulating and nonnodulating legumes. , 2015, Molecular biology and evolution.

[46]  Md. Shamsuzzoha Bayzid,et al.  Statistical binning enables an accurate coalescent-based estimation of the avian tree , 2014, Science.

[47]  Saravanaraj N. Ayyampalayam,et al.  Phylotranscriptomic analysis of the origin and early diversification of land plants , 2014, Proceedings of the National Academy of Sciences.

[48]  Steven Maere,et al.  Tangled up in two: a burst of genome duplications at the end of the Cretaceous and the consequences for plant evolution , 2014, Philosophical Transactions of the Royal Society B: Biological Sciences.

[49]  Guy Baele,et al.  Analysis of 41 plant genomes supports a wave of successful genome duplications in association with the Cretaceous–Paleogene boundary , 2014, Genome research.

[50]  Tandy J. Warnow,et al.  PASTA: Ultra-Large Multiple Sequence Alignment , 2014, RECOMB.

[51]  Charles-Elie Rabier,et al.  Detecting and locating whole genome duplications on a phylogeny: a probabilistic approach. , 2014, Molecular biology and evolution.

[52]  Alexandros Stamatakis,et al.  RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies , 2014, Bioinform..

[53]  R Core Team,et al.  R: A language and environment for statistical computing. , 2014 .

[54]  Amborella Genome The Amborella Genome and the Evolution of Flowering Plants , 2013, Science.

[55]  Joel Sjöstrand,et al.  GenPhyloData: realistic simulation of gene family evolution , 2013, BMC Bioinformatics.

[56]  A. Leitch,et al.  Genome Size Diversity and Evolution in Land Plants , 2013 .

[57]  Stephen A. Smith,et al.  Optimizing de novo assembly of short-read RNA-seq data for phylogenomics , 2013, BMC Genomics.

[58]  Sebastian Proost,et al.  Gamma paleohexaploidy in the stem lineage of core eudicots: significance for MADS-box gene and species diversification. , 2012, Molecular biology and evolution.

[59]  James Leebens-Mack,et al.  Evaluating Methods for Isolating Total RNA and Predicting the Success of Sequencing Phylogenetically Diverse Plant Transcriptomes , 2012, PloS one.

[60]  B. Marin Nested in the Chlorellales or independent class? Phylogeny and classification of the Pedinophyceae (Viridiplantae) revealed by molecular phylogenetic analyses of complete nuclear and plastid-encoded rRNA operons. , 2012, Protist.

[61]  Daniel W. A. Buchan,et al.  The tomato genome sequence provides insights into fleshy fruit evolution , 2012, Nature.

[62]  P. Edger,et al.  Ancient whole genome duplications, novelty and diversification: the WGD Radiation Lag-Time Model. , 2012, Current opinion in plant biology.

[63]  Manolis Kellis,et al.  Unified modeling of gene duplication, loss, and coalescence using a locus tree. , 2012, Genome research.

[64]  David M. Goodstein,et al.  Phytozome: a comparative platform for green plant genomics , 2011, Nucleic Acids Res..

[65]  Yeting Zhang,et al.  A genome triplication associated with early diversification of the core eudicots , 2012, Genome Biology.

[66]  J. Wiens,et al.  Missing data in phylogenetic analysis: reconciling results from simulations and empirical data. , 2011, Systematic biology.

[67]  Sean R. Eddy,et al.  Accelerated Profile HMM Searches , 2011, PLoS Comput. Biol..

[68]  Claude W. dePamphilis,et al.  Ancestral polyploidy in seed plants and angiosperms , 2011, Nature.

[69]  D. Nelson,et al.  A P450-centric view of plant evolution. , 2011, The Plant journal : for cell and molecular biology.

[70]  P. Szövényi,et al.  Bryophyte diversity and evolution: windows into the early evolution of land plants. , 2011, American journal of botany.

[71]  Yang Zhong,et al.  The position of gnetales among seed plants: overcoming pitfalls of chloroplast phylogenomics. , 2010, Molecular biology and evolution.

[72]  F. Leliaert,et al.  Evolution and cytological diversification of the green seaweeds (Ulvophyceae). , 2010, Molecular biology and evolution.

[73]  B. Mueller‐Roeber,et al.  Genome-Wide Phylogenetic Comparative Analysis of Plant Transcriptional Regulation: A Timeline of Loss, Gain, Expansion, and Correlation with Complexity , 2010, Genome biology and evolution.

[74]  Paramvir S. Dehal,et al.  FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments , 2010, PloS one.

[75]  Michael S. Barker,et al.  Unfurling Fern Biology in the Genomics Age , 2010 .

[76]  Michael S. Barker,et al.  EvoPipes.net: Bioinformatic Tools for Ecological and Evolutionary Genomics , 2010, Evolutionary bioinformatics online.

[77]  David R. Hunter,et al.  mixtools: An R Package for Analyzing Mixture Models , 2009 .

[78]  Noah A Rosenberg,et al.  Gene tree discordance, phylogenetic inference and the multispecies coalescent. , 2009, Trends in ecology & evolution.

[79]  B. Marin,et al.  Streptophyte algae and the origin of embryophytes. , 2009, Annals of botany.

[80]  D. Sankoff,et al.  Polyploidy and angiosperm diversification. , 2009, American journal of botany.

[81]  Marta Matvienko,et al.  Multiple paleopolyploidizations during the evolution of the Compositae reveal parallel patterns of duplicate gene retention after millions of years. , 2008, Molecular biology and evolution.

[82]  Melissa D. Lehti-Shiu,et al.  Importance of Lineage-Specific Expansion of Plant Tandem Duplicates in the Adaptive Response to Environmental Stimuli1[W][OA] , 2008, Plant Physiology.

[83]  J. Poulain,et al.  The grapevine genome sequence suggests ancestral hexaploidization in major angiosperm phyla , 2007, Nature.

[84]  Ziheng Yang PAML 4: phylogenetic analysis by maximum likelihood. , 2007, Molecular biology and evolution.

[85]  Matthew W. Hahn,et al.  Bias in phylogenetic tree reconciliation methods: implications for vertebrate genome evolution , 2007, Genome Biology.

[86]  D. Kapraun Nuclear DNA content estimates in green algal lineages: chlorophyta and streptophyta. , 2006, Annals of botany.

[87]  D. Soltis,et al.  Widespread genome duplications throughout the history of flowering plants. , 2006, Genome research.

[88]  Naiara Rodríguez-Ezpeleta,et al.  Monophyly of Primary Photosynthetic Eukaryotes: Green Plants, Red Algae, and Glaucophytes , 2005, Current Biology.

[89]  J. Raes,et al.  Modeling gene and genome duplications in eukaryotes. , 2005, Proceedings of the National Academy of Sciences of the United States of America.

[90]  Hirohisa Kishino,et al.  Incorporating gene-specific variation when inferring and evaluating optimal evolutionary tree topologies from multilocus sequence data. , 2005, Proceedings of the National Academy of Sciences of the United States of America.

[91]  R. McCourt,et al.  Green algae and the origin of land plants. , 2004, American journal of botany.

[92]  R. Durbin,et al.  GeneWise and Genomewise. , 2004, Genome research.

[93]  Robert C. Edgar,et al.  MUSCLE: multiple sequence alignment with high accuracy and high throughput. , 2004, Nucleic acids research.

[94]  J. Wiens,et al.  Missing data, incomplete taxa, and phylogenetic accuracy. , 2003, Systematic biology.

[95]  K. Katoh,et al.  MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform. , 2002, Nucleic acids research.

[96]  H. Saedler,et al.  Two ancient classes of MIKC-type MADS-box genes are present in the moss Physcomitrella patens. , 2002, Molecular biology and evolution.

[97]  Adam Godzik,et al.  Tolerating some redundancy significantly speeds up clustering of large protein databases , 2002, Bioinform..

[98]  Adam Godzik,et al.  Clustering of highly homologous sequences to reduce the size of large protein databases , 2001, Bioinform..

[99]  J. Palmer,et al.  Multigene phylogeny of land plants with special reference to bryophytes and the earliest land plants. , 2000, Molecular biology and evolution.

[100]  J. Palmer,et al.  Seed plant phylogeny inferred from all three plant genomes: monophyly of extant gymnosperms and origin of Gnetales from conifers. , 2000, Proceedings of the National Academy of Sciences of the United States of America.

[101]  C. dePamphilis,et al.  Phylogeny of seed plants based on all three genomic compartments: extant gymnosperms are monophyletic and Gnetales' closest relatives are conifers. , 2000, Proceedings of the National Academy of Sciences of the United States of America.

[102]  A. Force,et al.  Preservation of duplicate genes by complementary, degenerative mutations. , 1999, Genetics.

[103]  J A Eisen,et al.  Phylogenomics: improving functional predictions for uncharacterized genes by evolutionary analysis. , 1998, Genome research.

[104]  A. Zharkikh,et al.  Molecular phylogeny of extant gymnosperms and seed plant evolution: analysis of nuclear 18S rRNA sequences. , 1997, Molecular biology and evolution.

[105]  Dr. Susumu Ohno Evolution by Gene Duplication , 1970, Springer Berlin Heidelberg.

[106]  C. Markert,et al.  Evolution of the Gene , 1948, Nature.

[107]  Karl Pearson F.R.S. LIII. On lines and planes of closest fit to systems of points in space , 1901 .