title: Evolution of gene structure in the conifer Picea glauca: a comparative analysis of the impact of intron size.
abstract: BACKGROUND
  A positive relationship between genome size and intron length is observed across eukaryotes including Angiosperms plants, indicating a co-evolution of genome size and gene structure. Conifers have very large genomes and longer introns on average than most plants, but impacts of their large genome and longer introns on gene structure has not be described.
  
  
  RESULTS
  Gene structure was analyzed for 35 genes of Picea glauca obtained from BAC sequencing and genome assembly, including comparisons with A. thaliana, P. trichocarpa and Z. mays. We aimed to develop an understanding of impact of long introns on the structure of individual genes. The number and length of exons was well conserved among the species compared but on average, P. glauca introns were longer and genes had four times more intronic sequence than Arabidopsis, and 2 times more than poplar and maize. However, pairwise comparisons of individual genes gave variable results and not all contrasts were statistically significant. Genes generally accumulated one or a few longer introns in species with larger genomes but the position of long introns was variable between plant lineages. In P. glauca, highly expressed genes generally had more intronic sequence than tissue preferential genes. Comparisons with the Pinus taeda BACs and genome scaffolds showed a high conservation for position of long introns and for sequence of short introns. A survey of 1836 P. glauca genes obtained by sequence capture mostly containing introns <1 Kbp showed that repeated sequences were 10× more abundant in introns than in exons.
  
  
  CONCLUSIONS
  Conifers have large amounts of intronic sequence per gene for seed plants due to the presence of few long introns and repetitive element sequences are ubiquitous in their introns. Results indicate a complex landscape of intron sizes and distribution across taxa and between genes with different expression profiles.
authors.affiliation: Center for Forest Research and Institute for Systems and Integrative Biology, 1030 rue de la Médecine, Université Laval, Québec, QC G1V 0A6, Canada. juliana.sena.1@ulaval.ca.
authors.forename: Juliana
authors.initials: J
authors.lastname: Stival Sena
authors.forename: Isabelle
authors.initials: I
authors.lastname: Giguère
authors.forename: Brian
authors.initials: B
authors.lastname: Boyle
authors.forename: Philippe
authors.initials: P
authors.lastname: Rigault
authors.forename: Inanc
authors.initials: I
authors.lastname: Birol
authors.forename: Andrea
authors.initials: A
authors.lastname: Zuccolo
authors.forename: Kermit
authors.initials: K
authors.lastname: Ritland
authors.forename: Carol
authors.initials: C
authors.lastname: Ritland
authors.forename: Joerg
authors.initials: J
authors.lastname: Bohlmann
authors.forename: Steven
authors.initials: S
authors.lastname: Jones
authors.forename: Jean
authors.initials: J
authors.lastname: Bousquet
authors.forename: John
authors.initials: J
authors.lastname: Mackay
mesh_terms: D001483:Base Sequence; D030541:Databases, Genetic; D019143:Evolution, Molecular; D005091:Exons / Q000235:genetics; D020869:Gene Expression Profiling; D018506:Gene Expression Regulation, Plant; D017343:Genes, Plant; D059646:Genome Size; D007438:Introns / Q000235:genetics*; D028222:Picea / Q000235:genetics*; D028223:Pinus / Q000235:genetics; D012333:RNA, Messenger / Q000235:genetics / Q000378:metabolism; D012091:Repetitive Sequences, Nucleic Acid / Q000235:genetics; D012689:Sequence Homology, Nucleic Acid
chemical_list: D012333:RNA, Messenger
references.citation: Nature. 2013 May 30;497(7451):579-84
references.pmid: 23698360
references.citation: Nat Genet. 2002 Aug;31(4):415-8
references.pmid: 12134150
references.citation: Nat Genet. 2011 May;43(5):476-81
references.pmid: 21478890
references.citation: Planta. 2006 Jun;224(1):83-95
references.pmid: 16425030
references.citation: PLoS One. 2011 Jan 21;6(1):e16214
references.pmid: 21283709
references.citation: BMC Genomics. 2012 Aug 29;13:434
references.pmid: 22931377
references.citation: Bioinformatics. 2013 Jun 15;29(12):1492-7
references.pmid: 23698863
references.citation: BMC Evol Biol. 2010 Jan 25;10:22
references.pmid: 20100325
references.citation: PLoS One. 2008 Aug 29;3(8):e3093
references.pmid: 18769727
references.citation: BMC Genomics. 2011 Mar 10;12:145
references.pmid: 21392393
references.citation: Genome Biol. 2007;8(2):R21
references.pmid: 17309804
references.citation: Nature. 2007 Sep 27;449(7161):463-7
references.pmid: 17721507
references.citation: Nature. 2000 Dec 14;408(6814):796-815
references.pmid: 11130711
references.citation: Tree Physiol. 2008 Jul;28(7):1099-110
references.pmid: 18450574
references.citation: BMC Biotechnol. 2009 Aug 28;9:75
references.pmid: 19715565
references.citation: Proc Natl Acad Sci U S A. 1994 May 24;91(11):5163-7
references.pmid: 8197201
references.citation: BMC Genomics. 2008 Oct 14;9:484
references.pmid: 18854048
references.citation: Genetics. 2014 Mar;196(3):891-909
references.pmid: 24653211
references.citation: Mol Biol Evol. 1998 Jun;15(6):770-3
references.pmid: 9615458
references.citation: BMC Plant Biol. 2007 Mar 30;7:17
references.pmid: 17397551
references.citation: Science. 2009 Nov 20;326(5956):1112-5
references.pmid: 19965430
references.citation: Genetics. 2000 Nov;156(3):1175-90
references.pmid: 11063693
references.citation: Genome Biol. 2014 Mar 04;15(3):R59
references.pmid: 24647006
references.citation: Yeast. 2000 Apr;17(1):22-36
references.pmid: 10797599
references.citation: BMC Genomics. 2010 Jul 07;11:420
references.pmid: 20609256
references.citation: Cytogenet Genome Res. 2005;110(1-4):462-7
references.pmid: 16093699
references.citation: BMC Bioinformatics. 2005 Feb 15;6:31
references.pmid: 15713233
references.citation: Mol Biol Evol. 2000 May;17(5):773-81
references.pmid: 10779538
references.citation: Trends Genet. 2000 Jun;16(6):276-7
references.pmid: 10827456
references.citation: Bioinformatics. 2005 Jun;21 Suppl 1:i351-8
references.pmid: 15961478
references.citation: Mol Biol Evol. 2002 Dec;19(12):2346-52
references.pmid: 12446829
references.citation: Plant Physiol. 2005 Dec;139(4):1612-24
references.pmid: 16339807
references.citation: J Mol Evol. 2009 Jan;68(1):80-9
references.pmid: 19125217
references.citation: Trends Genet. 2006 Oct;22(10):528-32
references.pmid: 16934358
references.citation: Genome Res. 2008 Jan;18(1):188-96
references.pmid: 18025269
references.citation: PLoS One. 2009;4(2):e4332
references.pmid: 19194510
references.citation: Nat Rev Genet. 2002 May;3(5):329-41
references.pmid: 11988759
references.citation: Biom J. 2008 Jun;50(3):346-63
references.pmid: 18481363
references.citation: Proc Natl Acad Sci U S A. 2002 Apr 30;99(9):6118-23
references.pmid: 11983904
references.citation: Nature. 2005 Sep 15;437(7057):376-80
references.pmid: 16056220
references.citation: Mol Ecol Resour. 2011 May;11(3):541-9
references.pmid: 21481212
references.citation: BMC Plant Biol. 2009 Aug 06;9:106
references.pmid: 19656416
references.citation: Nucleic Acids Res. 1999 Aug 1;27(15):3219-28
references.pmid: 10454621
references.citation: BMC Res Notes. 2011 Mar 08;4:52
references.pmid: 21385391
references.citation: Science. 2006 Sep 15;313(5793):1596-604
references.pmid: 16973872
references.citation: Plant Physiol. 2011 Sep;157(1):14-28
references.pmid: 21730200
references.citation: Bioinformatics. 2010 Mar 1;26(5):680-2
references.pmid: 20053844
references.citation: Nucleic Acids Res. 2012 Jan;40(Database issue):D1178-86
references.pmid: 22110026
references.citation: Genome Res. 1999 Sep;9(9):868-77
references.pmid: 10508846
references.citation: Annu Rev Genet. 1999;33:479-532
references.pmid: 10690416
references.citation: J Mol Evol. 1999 Sep;49(3):376-84
references.pmid: 10473779
references.citation: Science. 2003 Nov 21;302(5649):1401-4
references.pmid: 14631042
references.citation: In Silico Biol. 2004;4(4):387-93
references.pmid: 15217358
references.citation: BMC Biol. 2012 Oct 26;10:84
references.pmid: 23102090
references.citation: J Mol Biol. 1990 Oct 5;215(3):403-10
references.pmid: 2231712