title: The draft genome of Primula veris yields insights into the molecular basis of heterostyly.
abstract: BACKGROUND
  The flowering plant Primula veris is a common spring blooming perennial that is widely cultivated throughout Europe. This species is an established model system in the study of the genetics, evolution, and ecology of heterostylous floral polymorphisms. Despite the long history of research focused on this and related species, the continued development of this system has been restricted due the absence of genomic and transcriptomic resources.
  
  
  RESULTS
  We present here a de novo draft genome assembly of P. veris covering 301.8 Mb, or approximately 63% of the estimated 479.22 Mb genome, with an N50 contig size of 9.5 Kb, an N50 scaffold size of 164 Kb, and containing an estimated 19,507 genes. The results of a RADseq bulk segregant analysis allow for the confident identification of four genome scaffolds that are linked to the P. veris S-locus. RNAseq data from both P. veris and the closely related species P. vulgaris allow for the characterization of 113 candidate heterostyly genes that show significant floral morph-specific differential expression. One candidate gene of particular interest is a duplicated GLOBOSA homolog that may be unique to Primula (PveGLO2), and is completely silenced in L-morph flowers.
  
  
  CONCLUSIONS
  The P. veris genome represents the first genome assembled from a heterostylous species, and thus provides an immensely important resource for future studies focused on the evolution and genetic dissection of heterostyly. As the first genome assembled from the Primulaceae, the P. veris genome will also facilitate the expanded application of phylogenomic methods in this diverse family and the eudicots as a whole.
authors: Michael D
authors: MD
authors: Nowak
authors: Giancarlo
authors: G
authors: Russo
authors: Ralph
authors: R
authors: Schlapbach
authors: Cuong Nguyen
authors: CN
authors: Huu
authors: Michael
authors: M
authors: Lenhard
authors: Elena
authors: E
authors: Conti
mesh_terms: D000595:Amino Acid Sequence; D005075:Biological Evolution; D019295:Computational Biology; D035264:Flowers / Q000235:genetics*; D020869:Gene Expression Profiling; D018506:Gene Expression Regulation, Plant; D017343:Genes, Plant; D018745:Genome, Plant; D055106:Genome-Wide Association Study; D023281:Genomics; D005838:Genotype; D059014:High-Throughput Nucleotide Sequencing; D058977:Molecular Sequence Annotation; D008969:Molecular Sequence Data; D010641:Phenotype; D010802:Phylogeny; D020641:Polymorphism, Single Nucleotide; D031825:Primula / Q000145:classification / Q000235:genetics*; D040641:Quantitative Trait Loci; D016415:Sequence Alignment; D059467:Transcriptome
references: Nat Rev Genet. 2002 Apr;3(4):274-84
references: 11967552
references: Trends Genet. 2002 Dec;18(12):613-5
references: 12446140
references: Planta. 2003 Apr;216(6):903-17
references: 12687358
references: Genome Res. 2003 Sep;13(9):2178-89
references: 12952885
references: EMBO J. 1992 Dec;11(13):4693-704
references: 1361166
references: Mutat Res. 1964 May;106:2-9
references: 14195748
references: BMC Bioinformatics. 2004 May 14;5:59
references: 15144565
references: New Phytol. 2005 Jan;165(1):63-70
references: 15720621
references: Nucleic Acids Res. 2005 Jul 1;33(Web Server issue):W116-20
references: 15980438
references: Cytogenet Genome Res. 2005;110(1-4):462-7
references: 16093699
references: New Phytol. 2006;171(3):439-42
references: 16866949
references: New Phytol. 2006;171(3):539-51
references: 16866957
references: New Phytol. 2006;171(3):591-603
references: 16866961
references: New Phytol. 2006;171(3):605-16
references: 16866962
references: New Phytol. 2006;171(3):617-32
references: 16866963
references: Bioinformatics. 2007 May 1;23(9):1061-7
references: 17332020
references: Plant J. 2007 Jul;51(1):18-31
references: 17561923
references: Nature. 2007 Sep 27;449(7161):463-7
references: 17721507
references: Nucleic Acids Res. 2008 Jan;36(Database issue):D1009-14
references: 17986450
references: Evolution. 1949 Mar;3(1):82-97
references: 18115119
references: Bioinformatics. 2008 Mar 1;24(5):637-44
references: 18218656
references: Plant J. 2008 Oct;56(1):1-12
references: 18564384
references: PLoS One. 2008;3(10):e3376
references: 18852878
references: Ann Bot. 2009 Mar;103(5):777-83
references: 19106180
references: Nat Protoc. 2009;4(1):44-57
references: 19131956
references: Bioinformatics. 2009 Aug 15;25(16):2078-9
references: 19505943
references: Mol Biol Evol. 2009 Nov;26(11):2627-45
references: 19679752
references: Bioinformatics. 2010 Jan 1;26(1):139-40
references: 19910308
references: Syst Biol. 2009 Feb;58(1):55-73
references: 20525568
references: Nat Genet. 2010 Oct;42(10):833-9
references: 20802477
references: Proc Natl Acad Sci U S A. 2011 Jan 25;108(4):1513-8
references: 21187386
references: Nat Biotechnol. 2011 May 15;29(7):644-52
references: 21572440
references: Am J Bot. 2010 May;97(5):701-16
references: 21622437
references: Ann Bot. 2011 Sep;108(4):715-26
references: 21803742
references: Curr Protoc Bioinformatics. 2011 Sep;Chapter 6:Unit 6.12.1-19
references: 21901743
references: Genome Biol. 2011 Oct 20;12(10):R102
references: 22014239
references: Nucleic Acids Res. 2012 Jan;40(Database issue):D290-301
references: 22127870
references: BMC Bioinformatics. 2011 Dec 22;12:491
references: 22192575
references: Nat Methods. 2012 Mar 04;9(4):357-9
references: 22388286
references: BMC Evol Biol. 2012 Apr 24;12:56
references: 22530870
references: Mol Phylogenet Evol. 2012 Oct;65(1):23-34
references: 22643289
references: Nature. 2012 May 30;485(7400):635-41
references: 22660326
references: Trends Ecol Evol. 2012 Sep;27(9):501-10
references: 22784409
references: Ann Bot. 2012 Nov;110(6):1233-44
references: 23002269
references: Bioinformatics. 2012 Dec 1;28(23):3150-2
references: 23060610
references: Bioinformatics. 2013 Jan 1;29(1):15-21
references: 23104886
references: PLoS One. 2012;7(11):e47768
references: 23185243
references: Genome Biol. 2013 May 10;14(5):R41
references: 23663246
references: BMC Genomics. 2013 May 14;14:329
references: 23672467
references: Nat Protoc. 2013 Aug;8(8):1494-512
references: 23845962
references: PLoS Comput Biol. 2013;9(8):e1003118
references: 23950696
references: Nat Commun. 2013;4:2445
references: 24048436
references: Nat Commun. 2013;4:2640
references: 24136039
references: Evolution. 2014 Apr;68(4):1042-57
references: 24325205
references: Curr Biol. 2014 Mar 31;24(7):R288-94
references: 24698381
references: PLoS One. 2014 Apr 03;9(4):e92644
references: 24699266
references: Proc Biol Sci. 2014 Apr 23;281(1784):20140075
references: 24759859
references: Oecologia. 2002 Feb;130(4):617-625
references: 28547265
references: Nucleic Acids Res. 1980 Oct 10;8(19):4321-5
references: 7433111
references: Development. 1996 Jan;122(1):11-22
references: 8565821