The Genomes of All Angiosperms: A Call for a Coordinated Global Census

Recent advances in biological instrumentation and associated experimental technologies now permit an unprecedented efficiency and scale for the acquisition of genomic data, at ever-decreasing costs. Further advances, with accompanying decreases in cost, are expected in the very near term. It now becomes appropriate to discuss the best uses of these technologies in the context of the angiosperms. This white paper proposes a complete genomic census of the approximately 500,000 species of flowering plants, outlines the goals of this census and their value, and provides a road map towards achieving these goals in a timely manner.

[1]  David William Galbraith.  Frontiers in Genomic Assay Technologies: The Grand Challenges in Enabling Data-Intensive Biological Research , 2011, Front. Gene..

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

[3]  C. Marshall,et al.  Has the Earth’s sixth mass extinction already arrived? , 2011, Nature.

[4]  I. Leitch,et al.  Nuclear DNA amounts in angiosperms: targets, trends and tomorrow. , 2011, Annals of botany.

[5]  J. Pires,et al.  Biodiversity assessment: state-of-the-art techniques in phylogenomics and species identification. , 2011, American journal of botany.

[6]  Sonja Siljak-Yakovlev,et al.  Towards a Genome Size and Chromosome Number Database of Balkan Flora: C-Values in 343 Taxa with Novel Values for 242 , 2010 .

[7]  B. Zonneveld,et al.  New record holders for maximum genome size in eudicots and monocots. , 2010 .

[8]  J. Chris Pires,et al.  Homoeologous recombination in allopolyploids: the polyploid ratchet. , 2010, The New phytologist.

[9]  B. Strasser,et al.  Collecting, Comparing, and Computing Sequences: The Making of Margaret O. Dayhoff’s Atlas of Protein Sequence and Structure, 1954–1965 , 2010, Journal of the history of biology.

[10]  S. Turner,et al.  Real-time DNA sequencing from single polymerase molecules. , 2010, Methods in enzymology.

[11]  N. Stork.  Re-assessing current extinction rates , 2010, Biodiversity and Conservation.

[12]  Joshua M. Stuart,et al.  Genome 10K: a proposal to obtain whole-genome sequence for 10,000 vertebrate species. , 2009, The Journal of heredity.

[13]  David A. Rasmussen,et al.  What can you do with 0.1× genome coverage? A case study based on a genome survey of the scuttle fly Megaselia scalaris (Phoridae) , 2009, BMC Genomics.

[14]  D. Galbraith.  Simultaneous flow cytometric quantification of plant nuclear DNA contents over the full range of described angiosperm 2C values , 2009, Cytometry. Part A : the journal of the International Society for Analytical Cytology.

[15]  Lex E. Flagel,et al.  Gene duplication and evolutionary novelty in plants. , 2009, The New phytologist.

[16]  F. Roets,et al.  Flow cytometry and its applications in plant population biology, ecology and biosystematics: New prospects for the Cape flora , 2009 .

[17]  P. Groom,et al.  Seeds, seedlings and phosphorus , 2009 .

[18]  D. Galbraith,et al.  Measuring genome size of desert plants using dry seeds. , 2009 .

[19]  David C. Tank,et al.  An update of the Angiosperm Phylogeny Group classification for the orders and families of flowering plants: , 2009 .

[20]  Neil Brummitt,et al.  Towards Target 1 of the Global Strategy for Plant Conservation : a working list of all known plant species-progress and prospects , 2008 .

[21]  Renyi Liu,et al.  Discovery and assembly of repeat family pseudomolecules from sparse genomic sequence data using the Assisted Automated Assembler of Repeat Families (AAARF) algorithm , 2008, BMC Bioinformatics.

[22]  A. Roberts.  The use of bead beating to prepare suspensions of nuclei for flow cytometry from fresh leaves, herbarium leaves, petals and pollen , 2007, Cytometry. Part A : the journal of the International Society for Analytical Cytology.

[23]  P. Green.  2x genomes--does depth matter? , 2007, Genome research.

[24]  E. Rodriguez,et al.  Two new nuclear isolation buffers for plant DNA flow cytometry: a test with 37 species. , 2007, Annals of botany.

[25]  J. Doležel,et al.  Estimation of nuclear DNA content in plants using flow cytometry , 2007, Nature Protocols.

[26]  Conceição Santos,et al.  Flow cytometric and cytogenetic analyses of Iberian Peninsula Festuca spp. , 2007, Plant Systematics and Evolution.

[27]  H. Quesneville,et al.  LTR retrotransposons in rice (Oryza sativa, L.): recent burst amplifications followed by rapid DNA loss , 2007, BMC Genomics.

[28]  J. Bennetzen,et al.  Analysis of retrotransposon structural diversity uncovers properties and propensities in angiosperm genome evolution , 2006, Proceedings of the National Academy of Sciences.

[29]  W. Barthlott,et al.  Smallest angiosperm genomes found in lentibulariaceae, with chromosomes of bacterial size. , 2006, Plant biology.

[30]  J. Suda,et al.  Reliable DNA ploidy determination in dehydrated tissues of vascular plants by DAPI flow cytometry—new prospects for plant research , 2006, Cytometry. Part A : the journal of the International Society for Analytical Cytology.

[31]  J. Bennetzen,et al.  Recombination, rearrangement, reshuffling, and divergence in a centromeric region of rice. , 2006, Proceedings of the National Academy of Sciences of the United States of America.

[32]  D. Galbraith,et al.  Flow Cytometry and Cell Sorting in Plant Biotechnology , 2005 .

[33]  Pierre Sourdille,et al.  Molecular Basis of Evolutionary Events That Shaped the Hardness Locus in Diploid and Polyploid Wheat Species (Triticum and Aegilops)w⃞ , 2005, The Plant Cell Online.

[34]  B. Keller,et al.  Ancient haplotypes resulting from extensive molecular rearrangements in the wheat A genome have been maintained in species of three different ploidy levels. , 2005, Genome research.

[35]  J. Bennetzen,et al.  Mechanisms of recent genome size variation in flowering plants. , 2005, Annals of botany.

[36]  D. Soltis,et al.  Evolution of DNA amounts across land plants (embryophyta). , 2005, Annals of botany.

[37]  Jianxin Ma,et al.  Rapid recent growth and divergence of rice nuclear genomes. , 2004, Proceedings of the National Academy of Sciences of the United States of America.

[38]  Pamela S Soltis,et al.  Darwin's abominable mystery: Insights from a supertree of the angiosperms , 2004, Proceedings of the National Academy of Sciences of the United States of America.

[39]  Jonathan A. Eisen,et al.  The age of the Arabidopsis thaliana genome duplication , 2003, Plant Molecular Biology.

[40]  J. Lundberg,et al.  An update of the Angiosperm Phylogeny Group classification for the orders and families of flowering plants : APG II THE ANGIOSPERM PHYLOGENY GROUP * , 2003 .

[41]  Rodolfo Dirzo,et al.  Global State of Biodiversity and Loss , 2003 .

[42]  D. Soltis,et al.  Evolution of genome size in the angiosperms. , 2003, American journal of botany.

[43]  J. Bennetzen,et al.  A complex history of rearrangement in an orthologous region of the maize, sorghum, and rice genomes , 2003, Proceedings of the National Academy of Sciences of the United States of America.

[44]  A. Meister,et al.  Endopolyploidy in seed plants is differently correlated to systematics, organ, life strategy and genome size , 2003 .

[45]  James K. M. Brown,et al.  Genome size reduction through illegitimate recombination counteracts genome expansion in Arabidopsis. , 2002, Genome research.

[46]  R. Thorne.  How many species of seed plants are there , 2001 .

[47]  D. Galbraith,et al.  Reference standards for determination of DNA content of plant nuclei. , 1999, American journal of botany.

[48]  J. Bennetzen,et al.  Nested Retrotransposons in the Intergenic Regions of the Maize Genome , 1996, Science.

[49]  D. Galbraith,et al.  Nuclear DNA content of monocotyledons and related taxa , 1994 .

[50]  D. Galbraith,et al.  Systemic Endopolyploidy in Arabidopsis thaliana. , 1991, Plant physiology.

[51]  D. Galbraith,et al.  Polyploid polymorphism in Andropogon gerardii , 1987 .

[52]  D. Galbraith,et al.  Rapid Flow Cytometric Analysis of the Cell Cycle in Intact Plant Tissues , 1983, Science.