title: Deciphering the diploid ancestral genome of the Mesohexaploid Brassica rapa.
abstract: The genus Brassica includes several important agricultural and horticultural crops. Their current genome structures were shaped by whole-genome triplication followed by extensive diploidization. The availability of several crucifer genome sequences, especially that of Chinese cabbage (Brassica rapa), enables study of the evolution of the mesohexaploid Brassica genomes from their diploid progenitors. We reconstructed three ancestral subgenomes of B. rapa (n = 10) by comparing its whole-genome sequence to ancestral and extant Brassicaceae genomes. All three B. rapa paleogenomes apparently consisted of seven chromosomes, similar to the ancestral translocation Proto-Calepineae Karyotype (tPCK; n = 7), which is the evolutionarily younger variant of the Proto-Calepineae Karyotype (n = 7). Based on comparative analysis of genome sequences or linkage maps of Brassica oleracea, Brassica nigra, radish (Raphanus sativus), and other closely related species, we propose a two-step merging of three tPCK-like genomes to form the hexaploid ancestor of the tribe Brassiceae with 42 chromosomes. Subsequent diversification of the Brassiceae was marked by extensive genome reshuffling and chromosome number reduction mediated by translocation events and followed by loss and/or inactivation of centromeres. Furthermore, via interspecies genome comparison, we refined intervals for seven of the genomic blocks of the Ancestral Crucifer Karyotype (n = 8), thus revising the key reference genome for evolutionary genomics of crucifers.
authors: Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China.
authors: Feng
authors: F
authors: Cheng
authors: Terezie
authors: T
authors: Mandáková
authors: Jian
authors: J
authors: Wu
authors: Qi
authors: Q
authors: Xie
authors: Martin A
authors: MA
authors: Lysak
authors: Xiaowu
authors: X
authors: Wang
mesh_terms: D017360:Arabidopsis / Q000145:classification / Q000235:genetics; D029681:Arabidopsis Proteins / Q000235:genetics; D001937:Brassica / Q000145:classification / Q000235:genetics; D029741:Brassica rapa / Q000145:classification / Q000235:genetics*; D002503:Centromere / Q000235:genetics; D002874:Chromosome Mapping; D032461:Chromosomes, Plant / Q000235:genetics; D004171:Diploidy; D019143:Evolution, Molecular; D018745:Genome, Plant / Q000235:genetics*; D010802:Phylogeny; D010940:Plant Proteins / Q000235:genetics; D011123:Polyploidy; D026801:Synteny; D014178:Translocation, Genetic
chemical_list: D029681:Arabidopsis Proteins; D010940:Plant Proteins
references: Theor Appl Genet. 1991 Jul;82(1):81-92
references: 24212864
references: Genome Biol. 2004;5(2):R12
references: 14759262
references: BMC Evol Biol. 2010 Nov 29;10:367
references: 21114825
references: BMC Genomics. 2009 Nov 18;10:539
references: 19922648
references: Plant Physiol. 2004 Jun;135(2):735-44
references: 15208421
references: Mol Biol Evol. 2011 Oct;28(10):2731-9
references: 21546353
references: Trends Genet. 2011 Jun;27(6):207-16
references: 21592609
references: Genome. 2011 Jan;54(1):33-41
references: 21217804
references: Theor Appl Genet. 2004 Nov;109(7):1346-52
references: 15365626
references: Genome Biol. 2010;11(9):R94
references: 20875114
references: Front Plant Sci. 2012 Jul 31;3:172
references: 22866056
references: Genetics. 2004 Nov;168(3):1575-84
references: 15579708
references: Am J Bot. 2008 Oct;95(10):1307-27
references: 21632335
references: Proc Natl Acad Sci U S A. 2009 Sep 15;106(37):15780-5
references: 19717446
references: Genome Res. 2005 Apr;15(4):516-25
references: 15781573
references: Proc Natl Acad Sci U S A. 2009 Sep 1;106(35):14908-13
references: 19706486
references: Front Plant Sci. 2012 Aug 30;3:198
references: 22969786
references: Mol Genet Genomics. 2003 Feb;268(5):656-65
references: 12589440
references: DNA Res. 2011 Aug;18(4):221-32
references: 21669962
references: Trends Plant Sci. 2011 Feb;16(2):108-16
references: 21177137
references: Genome Res. 2010 Nov;20(11):1545-57
references: 20876790
references: Trends Plant Sci. 2006 Nov;11(11):535-42
references: 17029932
references: Nat Genet. 2011 May;43(5):476-81
references: 21478890
references: Genetics. 2012 Apr;190(4):1563-74
references: 22308264
references: Plant J. 2006 Jul;47(1):63-74
references: 16824180
references: Genomics Proteomics Bioinformatics. 2006 Nov;4(4):259-63
references: 17531802
references: Nat Genet. 2011 Aug 28;43(10):1035-9
references: 21873998
references: Genetics. 1998 Nov;150(3):1217-28
references: 9799273
references: Proc Natl Acad Sci U S A. 2012 Jul 24;109(30):12219-24
references: 22778405
references: BMC Genomics. 2009 Sep 15;10:432
references: 19751531
references: DNA Res. 2011 Oct;18(5):401-11
references: 21816873
references: Genetics. 1996 Dec;144(4):1903-10
references: 8978073
references: Plant Physiol. 2007 Oct;145(2):402-10
references: 17720758
references: Chromosoma. 1960;11:205-28
references: 14438262
references: PLoS One. 2012;7(5):e36442
references: 22567157
references: Genetics. 2005 Oct;171(2):765-81
references: 16020789
references: BMC Genomics. 2008 Mar 03;9:113
references: 18315867
references: Plant Cell. 2008 Oct;20(10):2559-70
references: 18836039
references: Plant J. 2007 Jan;49(2):173-83
references: 17156411
references: Genomics. 2011 Mar;97(3):173-85
references: 21159321
references: Theor Appl Genet. 1996 Dec;93(8):1225-33
references: 24162534
references: Mol Cells. 2005 Jun 30;19(3):436-44
references: 15995362
references: Nat Genet. 2011 Aug 07;43(9):913-8
references: 21822265
references: Am J Bot. 2006 Apr;93(4):607-19
references: 21646222
references: Mol Biol Evol. 2000 Oct;17(10):1483-98
references: 11018155
references: Mol Ecol. 2011 Feb;20(4):784-98
references: 21284744
references: BMC Plant Biol. 2011 Oct 13;11:136
references: 21995777
references: Nucleic Acids Res. 2004 Mar 19;32(5):1792-7
references: 15034147
references: Proc Natl Acad Sci U S A. 2006 Mar 28;103(13):5224-9
references: 16549785