title: Integrated syntenic and phylogenomic analyses reveal an ancient genome duplication in monocots.
abstract: Unraveling widespread polyploidy events throughout plant evolution is a necessity for inferring the impacts of whole-genome duplication (WGD) on speciation, functional innovations, and to guide identification of true orthologs in divergent taxa. Here, we employed an integrated syntenic and phylogenomic analyses to reveal an ancient WGD that shaped the genomes of all commelinid monocots, including grasses, bromeliads, bananas (Musa acuminata), ginger, palms, and other plants of fundamental, agricultural, and/or horticultural interest. First, comprehensive phylogenomic analyses revealed 1421 putative gene families that retained ancient duplication shared by Musa (Zingiberales) and grass (Poales) genomes, indicating an ancient WGD in monocots. Intergenomic synteny blocks of Musa and Oryza were investigated, and 30 blocks were shown to be duplicated before Musa-Oryza divergence an estimated 120 to 150 million years ago. Synteny comparisons of four monocot (rice [Oryza sativa], sorghum [Sorghum bicolor], banana, and oil palm [Elaeis guineensis]) and two eudicot (grape [Vitis vinifera] and sacred lotus [Nelumbo nucifera]) genomes also support this additional WGD in monocots, herein called Tau (τ). Integrating synteny and phylogenomic comparisons achieves better resolution of ancient polyploidy events than either approach individually, a principle that is exemplified in the disambiguation of a WGD series of rho (ρ)-sigma (σ)-tau (τ) in the grass lineages that echoes the alpha (α)-beta (β)-gamma (γ) series previously revealed in the Arabidopsis thaliana lineage.
authors.affiliation: Plant Genome Mapping Laboratory, University of Georgia, Athens, Georgia 30602.
authors.forename: Yuannian
authors.identifier: http://orcid.org/0000-0002-8987-2782
authors.initials: Y
authors.lastname: Jiao
authors.affiliation: Plant Genome Mapping Laboratory, University of Georgia, Athens, Georgia 30602 Institute of Bioinformatics, University of Georgia, Athens, Georgia 30602.
authors.forename: Jingping
authors.initials: J
authors.lastname: Li
authors.affiliation: Center for Genomics and Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, Fujian Province 350002, China J. Craig Venter Institute, Rockville, Maryland 20850.
authors.forename: Haibao
authors.identifier: http://orcid.org/0000-0002-3460-8570
authors.initials: H
authors.lastname: Tang
authors.affiliation: Plant Genome Mapping Laboratory, University of Georgia, Athens, Georgia 30602 paterson@plantbio.uga.edu.
authors.forename: Andrew H
authors.initials: AH
authors.lastname: Paterson
mesh_terms: D019143:Evolution, Molecular; D020440:Gene Duplication; D018745:Genome, Plant / Q000235:genetics*; D023281:Genomics; D019684:Magnoliopsida / Q000235:genetics*; D010802:Phylogeny; D011123:Polyploidy; D016415:Sequence Alignment; D017422:Sequence Analysis, DNA; D026801:Synteny
references.citation: Proc Natl Acad Sci U S A. 2000 Apr 11;97(8):4168-73
references.pmid: 10759555
references.citation: Science. 2000 Nov 10;290(5494):1151-5
references.pmid: 11073452
references.citation: Genetics. 1994 Oct;138(2):499-510
references.pmid: 7828831
references.citation: Nature. 2004 Apr 8;428(6983):617-24
references.pmid: 15004568
references.citation: Genome Biol. 2013 May 10;14(5):R41
references.pmid: 23663246
references.citation: BMC Evol Biol. 2007 Aug 09;7:135
references.pmid: 17688696
references.citation: Genome Res. 2003 Sep;13(9):2178-89
references.pmid: 12952885
references.citation: Nature. 2011 May 5;473(7345):97-100
references.pmid: 21478875
references.citation: Bioinformatics. 2009 Aug 1;25(15):1972-3
references.pmid: 19505945
references.citation: Curr Opin Plant Biol. 2012 Apr;15(2):140-6
references.pmid: 22480430
references.citation: Science. 2005 Nov 18;310(5751):1177-80
references.pmid: 16293759
references.citation: Science. 2013 Dec 20;342(6165):1241089
references.pmid: 24357323
references.citation: Mol Biol Evol. 2002 Sep;19(9):1464-73
references.pmid: 12200474
references.citation: Nature. 2007 Sep 27;449(7161):463-7
references.pmid: 17721507
references.citation: Annu Rev Plant Biol. 2010;61:349-72
references.pmid: 20441528
references.citation: Bioinformatics. 2004 Dec 12;20(18):3643-6
references.pmid: 15247098
references.citation: Bioinformatics. 2007 Nov 1;23(21):2947-8
references.pmid: 17846036
references.citation: Genome Res. 2008 Dec;18(12):1944-54
references.pmid: 18832442
references.citation: Proc Natl Acad Sci U S A. 2005 Apr 12;102(15):5454-9
references.pmid: 15800040
references.citation: Nucleic Acids Res. 2012 Apr;40(7):e49
references.pmid: 22217600
references.citation: Proc Natl Acad Sci U S A. 2010 Jan 5;107(1):472-7
references.pmid: 19966307
references.citation: Am J Bot. 2009 Jan;96(1):336-48
references.pmid: 21628192
references.citation: Science. 2009 Nov 20;326(5956):1112-5
references.pmid: 19965430
references.citation: BMC Genomics. 2013;14 Suppl 7:S3
references.pmid: 24564362
references.citation: New Phytol. 2005 Mar;165(3):937-46
references.pmid: 15720704
references.citation: Genome Biol. 2012 Jan 26;13(1):R3
references.pmid: 22280555
references.citation: Science. 2008 Oct 3;322(5898):86-9
references.pmid: 18832643
references.citation: Nature. 2009 Jan 29;457(7229):551-6
references.pmid: 19189423
references.citation: Curr Opin Plant Biol. 2005 Apr;8(2):135-41
references.pmid: 15752992
references.citation: Nat Commun. 2013;4:2274
references.pmid: 23917264
references.citation: Nature. 2010 Feb 11;463(7282):763-8
references.pmid: 20148030
references.citation: PLoS Biol. 2005 Oct;3(10):e314
references.pmid: 16128622
references.citation: Proc Natl Acad Sci U S A. 2000 Aug 1;97(16):9121-6
references.pmid: 10908680
references.citation: Nature. 2006 Nov 9;444(7116):171-8
references.pmid: 17086204
references.citation: Genome Res. 2006 Jul;16(7):805-14
references.pmid: 16818725
references.citation: Nature. 2008 Apr 24;452(7190):991-6
references.pmid: 18432245
references.citation: Nature. 2008 Jun 19;453(7198):1064-71
references.pmid: 18563158
references.citation: Nucleic Acids Res. 2006 Jul 1;34(Web Server issue):W609-12
references.pmid: 16845082
references.citation: Science. 2011 Sep 2;333(6047):1257
references.pmid: 21852456
references.citation: Nature. 2003 Mar 27;422(6930):433-8
references.pmid: 12660784
references.citation: Nat Genet. 2011 Aug 28;43(10):1035-9
references.pmid: 21873998
references.citation: Mol Biol Evol. 1986 Sep;3(5):418-26
references.pmid: 3444411
references.citation: Plant Cell. 2004 Jul;16(7):1667-78
references.pmid: 15208399
references.citation: Nature. 2004 Oct 21;431(7011):946-57
references.pmid: 15496914
references.citation: Annu Rev Plant Biol. 2009;60:433-53
references.pmid: 19575588
references.citation: Proc Natl Acad Sci U S A. 1987 Dec;84(24):9054-8
references.pmid: 3480529
references.citation: Science. 2000 Dec 15;290(5499):2114-7
references.pmid: 11118139
references.citation: Genome Res. 2006 Jun;16(6):738-49
references.pmid: 16702410
references.citation: Genome Biol Evol. 2009 Oct 05;1:391-9
references.pmid: 20333207
references.citation: Trends Genet. 2006 Nov;22(11):597-602
references.pmid: 16979781
references.citation: Annu Rev Genet. 2000;34:401-437
references.pmid: 11092833
references.citation: Bioinformatics. 2006 Dec 1;22(23):2971-2
references.pmid: 17021158
references.citation: Genome Biol. 2011;12(5):113
references.pmid: 21635712
references.citation: Comput Appl Biosci. 1997 Oct;13(5):555-6
references.pmid: 9367129
references.citation: Nat Biotechnol. 2012 May 13;30(6):555-61
references.pmid: 22580951
references.citation: Bioinformatics. 2006 Nov 1;22(21):2688-90
references.pmid: 16928733
references.citation: Nature. 2012 Aug 9;488(7410):213-7
references.pmid: 22801500
references.citation: Science. 1967 Jan 20;155(3760):279-84
references.pmid: 5334057
references.citation: Nature. 2013 Aug 15;500(7462):335-9
references.pmid: 23883927
references.citation: Mol Biol Evol. 2004 Jun;21(6):1146-51
references.pmid: 15014147
references.citation: Proc Natl Acad Sci U S A. 2004 Jun 29;101(26):9903-8
references.pmid: 15161969
references.citation: Proc Natl Acad Sci U S A. 2009 Apr 7;106(14):5737-42
references.pmid: 19325131
references.citation: Nat Rev Genet. 2009 Oct;10(10):725-32
references.pmid: 19652647
references.citation: Genetics. 1988 Dec;120(4):1095-103
references.pmid: 17246486
references.citation: Genome Res. 2002 Nov;12(11):1792-801
references.pmid: 12421767
references.citation: Nucleic Acids Res. 2005 Jan 20;33(2):511-8
references.pmid: 15661851
references.citation: Science. 2008 Apr 25;320(5875):486-8
references.pmid: 18436778
references.citation: Nat Genet. 1996 Dec;14(4):380-2
references.pmid: 8944014