Recent updates and developments to plant genome size databases

Two plant genome size databases have been recently updated and/or extended: the Plant DNA C-values database (http://data.kew.org/cvalues), and GSAD, the Genome Size in Asteraceae database (http://www.asteraceaegenomesize.com). While the first provides information on nuclear DNA contents across land plants and some algal groups, the second is focused on one of the largest and most economically important angiosperm families, Asteraceae. Genome size data have numerous applications: they can be used in comparative studies on genome evolution, or as a tool to appraise the cost of whole-genome sequencing programs. The growing interest in genome size and increasing rate of data accumulation has necessitated the continued update of these databases. Currently, the Plant DNA C-values database (Release 6.0, Dec. 2012) contains data for 8510 species, while GSAD has 1219 species (Release 2.0, June 2013), representing increases of 17 and 51%, respectively, in the number of species with genome size data, compared with previous releases. Here we provide overviews of the most recent releases of each database, and outline new features of GSAD. The latter include (i) a tool to visually compare genome size data between species, (ii) the option to export data and (iii) a webpage containing information about flow cytometry protocols.

[1]  C. R. Linder,et al.  High-resolution phylogeny for Helianthus (Asteraceae) using the 18S-26S ribosomal DNA external transcribed spacer. , 2007, American journal of botany.

[2]  M. Fay,et al.  The effects of nuclear DNA content (C-value) on the quality and utility of AFLP fingerprints. , 2005, Annals of botany.

[3]  E. Mcarthur,et al.  Evolutionary and ecological implications of genome size in the North Americanendemic sagebrushes (subgenus Tridentatae, Artemisia, Asteraceae) , 2008 .

[4]  Ulrich Rendtel,et al.  Editorial , 2014, Journal of basic microbiology.

[5]  Aljos Farjon,et al.  A new classification and linear sequence of extant gymnosperms , 2011 .

[6]  G. Hong,et al.  Nucleic Acids Research , 2015, Nucleic Acids Research.

[7]  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 .

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

[9]  Genome size increases in recently diverged hornwort clades. , 2013, Genome.

[10]  T. Gregory.  Genome Size Evolution in Animals , 2005 .

[11]  A. Leitch,et al.  Ecological and genetic factors linked to contrasting genome dynamics in seed plants. , 2012, The New phytologist.

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

[13]  D. Kapraun,et al.  Nuclear Content Estimates Suggest a Synapomorphy between Dictyota and Six Other Genera of the Dictyotales (Phaeophyceae) , 2011 .

[14]  D. Kapraun,et al.  Estimates of nuclear DNA content in red algal lineages , 2012, AoB PLANTS.

[15]  Jaroslav Dolezel,et al.  The origin, evolution and proposed stabilization of the terms 'genome size' and 'C-value' to describe nuclear DNA contents. , 2005, Annals of botany.

[16]  J. Doležel,et al.  Nuclear genome size: Are we getting closer? , 2010, Cytometry. Part A : the journal of the International Society for Analytical Cytology.

[17]  J. Greilhuber,et al.  Genome Size and the Phenotype , 2013 .

[18]  B. Patterson.  Systematics, Evolution, and Biogeography of Compositae , 2009 .

[19]  M. Canela,et al.  GSAD: A genome size in the Asteraceae database , 2011, Cytometry. Part A : the journal of the International Society for Analytical Cytology.

[20]  Sumei Chen,et al.  Limited DNA methylation variation and the transcription of MET1 and DDM1 in the genus Chrysanthemum (Asteraceae): following the track of polyploidy , 2015, Front. Plant Sci..

[21]  I. Leitch,et al.  Nuclear DNA Amounts in Angiosperms , 1995 .

[22]  J. Vallès,et al.  Genome size in 21 Artemisia L. species (Asteraceae, Anthemideae): systematic, evolutionary, and ecological implications. , 2001, Genome.

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

[24]  T. Garner.  Genome size and microsatellites: the effect of nuclear size on amplification potential. , 2002, Genome.

[25]  L. Forrest,et al.  Nuclear DNA content variation and evolution in liverworts. , 2013, Molecular phylogenetics and evolution.

[26]  David J. Mabberley,et al.  Mabberley's Plant-book: A Portable Dictionary of Plants, their Classification and Uses , 2017 .

[27]  J. Doležel,et al.  Nuclear DNA content and genome size of trout and human. , 2003, Cytometry. Part A : the journal of the International Society for Analytical Cytology.

[28]  I. Leitch,et al.  Nuclear DNA Amounts in Pteridophytes , 2001 .

[29]  B. Zonneveld.  Genome sizes for all genera of Cycadales. , 2011, Plant biology.

[30]  L. Rieseberg,et al.  Sunflower genetic, genomic and ecological resources , 2013, Molecular ecology resources.

[31]  I. Leitch,et al.  Nuclear DNA amounts in angiosperms: progress, problems and prospects. , 2005, Annals of botany.

[32]  D. Soltis,et al.  Rapid diversification of Tragopogon and ecological associates in Eurasia , 2012, Journal of evolutionary biology.

[33]  R. Vendrely,et al.  La teneur du noyau cellulaire en acide désoxyribonucléique à travers les organes, les individus et les espèces animales , 1948, Experientia.

[34]  J. Suda,et al.  The quest for suitable reference standards in genome size research , 2010, Cytometry. Part A : the journal of the International Society for Analytical Cytology.

[35]  L. Farinelli,et al.  The complete sequence of the smallest known nuclear genome from the microsporidian Encephalitozoon intestinalis , 2010, Nature communications.

[36]  E. Serrão,et al.  Mediterranean Species of Caulerpa Are Polyploid with Smaller Genomes in the Invasive Ones , 2012, PloS one.

[37]  Ilia J. Leitch,et al.  The largest eukaryotic genome of them all , 2010 .

[38]  Raymond J. Lewis,et al.  Estimates of nuclear DNA content in 98 species of brown algae (Phaeophyta) , 2011, AoB PLANTS.

[39]  V. Funk.  Systematics, evolution, and biogeography of Compositae , 2009 .

[40]  L. Rieseberg,et al.  Progress towards a reference genome for sunflower , 2011 .

[41]  H. Swift.  The constancy of desoxyribose nucleic acid in plant nuclei. , 1950, Proceedings of the National Academy of Sciences of the United States of America.

[42]  M. Kimmel,et al.  Conflict of interest statement. None declared. , 2010 .

[43]  I. Leitch,et al.  Nuclear DNA Amounts in Angiosperms—583 New Estimates , 1997 .

[44]  T. Ryan Gregory,et al.  Eukaryotic genome size databases , 2006, Nucleic Acids Res..

[45]  M. Canela,et al.  Genome size dynamics in Artemisia L. (Asteraceae): following the track of polyploidy. , 2010, Plant biology.

[46]  B. Zonneveld,et al.  Conifer genome sizes of 172 species, covering 64 of 67 genera, range from 8 to 72 picogram , 2012 .

[47]  R. Gregory.  The evolution of the genome , 2005 .

[48]  J. Martin,et al.  Polyploidy and other changes at chromosomal level and in genome size: Its role in systematics and evolution exemplified by some genera of Anthemideae and Cardueae (Asteraceae) , 2012 .

[49]  M. Fay,et al.  Why size really matters when sequencing plant genomes , 2012 .

[50]  T. Teeri,et al.  Evolution and diversification of the CYC/TB1 gene family in Asteraceae--a comparative study in Gerbera (Mutisieae) and sunflower (Heliantheae). , 2012, Molecular biology and evolution.

[51]  S. Garcia,et al.  Genome size variation in the genus Carthamus (Asteraceae, Cardueae): systematic implications and additive changes during allopolyploidization. , 2006, Annals of botany.