Supplementary Table 1List of Caspar-like elements analyzed in the present study
Element, Accession number / Species / Transposasepresence / Ctg-2 presence / Afa** / Locus, chromosome / Reference / complete
\truncated
Group 1. Clifford
EU660892-1* d / T. aestivum / + / + / - / Acc-2, 3DL / Chalupska et al. 2008 / complete
FJ436984-1* / T. aestivum / + / + / - / Lr34, 7DS / Wicker et al. 2009 / complete
Caspar_TA3B54F7-2 (AM932680) * d / T. aestivum / + / + / deg / 3BL / Charles et al. 2008 / complete
Caspar_TA3B54F7-7 (AM932680) * / T. aestivum / + / + / deg / 3BL / Charles et al. 2008 / 5'-truncated
Caspar_502E9-1 (EU835980)* / T. aestivum / + / + / - / Ha (Gsp-1), 5AS / Ragupathy and Cloutier 2008 / complete
TREP1801, Clifford_294D11-1 (EF560592)* d / T.durum / + / + / deg / Pm3-3 pseudo, 1A / Wicker et al. 2007 / 5'-fragment
TREP1802,Clifford_294D11-2 (EF560592)* d / T.durum / + / + / - / Pm3-3 pseudo, 1A / Wicker et al. 2007 / complete
EF426564-1* d / T. turgidum / + / + / - / LMW-glutenin, 1AS / Gao et al. 2007 / complete
EF426564-2* / T. turgidum / + / + / - / LMW-glutenin, 1AS / Gao et al. 2007 / complete
Caspar_542K11-2 (CT009587)* d / T. turgidum / + / + / - / Ha, 5A / Chantret et al. 2005 / complete
Caspar-1 (AY534123)* / Ae. tauschii / + / - / - / WM1, 3DS / Whitford et al. 2007 / truncated
TREP776,Clifford_453N11-1 (AY146588)* d / T. monococcum / + / + / deg / LMW-glutenin, 1AmS / Wicker et al. 2003 / complete
TREP774,Clifford_426K20-1 (AY146588)* d / T. monococcum / + / + / deg / LMW-glutenin, 1AmS / Wicker et al. 2003 / complete
AF488415-1xd / T. monococcum / + / + / - / Wx1, 7Am / Ma et al.unpublished / complete
Group 2. Caspar_Triticinae / -
Caspar_2050O8-1 (GQ165812)* d / T. aestivum / + / + / deg / 4BL / Salina et al. 2009 / complete
TREP1704, Caspar_1020F19-1xd / T.aestivum / + / + / deg / - / Wicker et al. unpublished / complete
TREP3009, Caspar_42j2-12xd / T. aestivum / + / + / deg / - / Appels et al. unpublished / complete
TREP3012, Caspar_59e04-2xd / T. aestivum / + / - / deg / - / Appels et al. unpublished / 5’-fragment
Caspar_TA3B95C9-1 (AM932684) d / T. aestivum / + / + / - / 3BL / Charles et al. 2008 / complete
Caspar_326E2-1 (EF540321) * d / T. turgidum / + / + / - / VRN2, 5AL / Dubcovsky and Dvorak 2007 / complete
Caspar_60J11-1 (AY951945)d / T. monococcum / + / + / - / FR-Am2,5Am / Miller et al. 2006 / complete
TREP1303, Caspar_AY485644-2 * d / T. monococcum / + / + / deg / Snf2P(VRN2), 5AmL / Yan et al. 2004 / complete
TREP1304, Caspar_AY485644-3 * d / T. monococcum / + / + / - / Snf2P(VRN2), 5AmL / Yan et al. 2004 / complete
TREP775, Caspar_18B1-1 (AY146588) * d / T. monococcum / + / + / - / LMW-glutenin, 1AmS / Wicker et al. 2003 / complete
AF488415-2x d / T. monococcum / + / + / - / Wx1, 7Am / Ma et al. unpublished / 3’-truncated
EF081030-1xd / T. urartu / + / - / - / ALP-A3,2Au / Akhunov et al. 2007 / 5’-fragment
EU626553-1* / T. urartu / + / - / - / psi-Acc-2, 3AuL / Chalupska et al. 2008 / truncated
Group 3. Caspar_Hordeinae
Caspar_TREP788-1x / H. vulgare / + / + / 1.5 / - / Stein et al. unpublished / complete
Caspar_124A1-1 (AY642926)* / H. vulgare / + / + / - / Rph7, 3HS / Scherrer et al. 2005 / 3’-truncated
FJ477092-1* / H. vulgare / + / + / - / Rym4 and MCT-1 / Wicker et al. 2009 / complete
TREP1516, Caspar_AY661558-6* d / H. vulgare / + / + / - / eIF4E, 3HL / Wicker et al. 2005 / 5' fragment
TREP1511, Caspar_AY661558-1* d / H. vulgare / + / + / 1 / eIF4E, 3HL / Wicker et al. 2005 / complete
TREP1515, Caspar_AY661558-5* d / H. vulgare / + / + / 2 / eIF4E, 3HL / Wicker et al. 2005 / complete
TREP1514, Caspar_AY661558-4* d / H. vulgare / + / + / 2 / eIF4E, 3HL / Wicker et al. 2005 / complete
Caspar_DQ900685-2* / H. vulgare / + / + / - / VRN3, 7H / Yan et al. 2006 / complete
TREP1636, Caspar_AY643844-2* d / H. vulgare / + / + / 1 / Ha,5HS / Caldwell et al. 2004 / complete
FJ477093-2* / H. vulgare / + / - / - / Rym4 and MCT-1 / Wicker et al. 2009 / 3’-truncated
TREP1517, Caspar_AY661558-7* d / H. vulgare / + / - / 3 / eIF4E, 3HL / Wicker et al. 2005 / 5'-fragment
TREP1512,Caspar_AY661558-2* d / H. vulgare / + / - / 2 / eIF4E, 3HL / Wicker et al. 2005 / 5'-fragment
FJ477092-2* / H. vulgare / + / - / - / Rym4 and MCT-1 / Wicker et al. 2009 / 3’-truncated
Caspar-1 (AY643843)* / H. vulgare / + / - / - / Ha,5HS / Caldwell et al. 2004 / 3’-truncated
Group 4. “Mixed” / -
TREP787,Caspar_211E24-1 (AF521177)*d / H. vulgare / + / + / - / Rph7, 3HS / Brunner et al. 2003 / complete
CACTA-2p (EF426565) *d / T. durum / + / + / - / LMW-glutenin, 1BS / Gao et al. 2007 / complete
XJ-1 (AY534123)* / Ae. tauschii / + / + / - / WM1, 3DS / Whitford et al. 2007 / 5’-truncated
TREP1225,Caspar_231A16-1(AY188331)d / T. monococcum / + / + / - / Ap1 (VRN1), 5AmL / Yan et al. 2003 / complete
TREP2064, Donald_AY853252-11*d / H. vulgare / + / + / - / 7H / Cossu et al.unpublished / complete
* cloneslocated in distal third of chromosomal arm or in distal chromosomal bin (
**deg- contains truncated Afarepeat (30-70% of monomer length)
x - unknown chromosomal location
d – elements used for dot-plot comparison (Fig. 4)
References
Akhunov ED, AkhunovaAR, Dvorak J (2007) Mechanisms and rates of birth and death of dispersed duplicated genes during the evolution of a multigene family in diploid and tetraploid wheats.Mol Biol Evol 24:539-550
Brunner S, Keller B, Feuillet C (2003) A large rearrangement involving genes and low-copy DNA interrupts the microcollinearity between rice and barley at the Rph7 locus. Genetics 164:673-683
Caldwell KS, Langridge P, Powell W (2004) Comparative sequence analysis of the region harboring the hardness locus in barley and its colinear region in rice. Plant Physiol 136:3177-3190
Chalupska D, Lee HY, Faris JD, Evrard A, Chalhoub B, Haselkorn R, Gornicki P (2008) Acc homoeoloci and the evolution of wheat genomes.Proc Natl Acad Sci USA 105:9691-9696
Chantret N, Salse J, Sabot F, Rahman S, Bellec A, Laubin B, Dubois I, Dossat C, Sourdille P, Joudrier P, Gautier MF, Cattolico L, Beckert M, Aubourg S, Weissenbach J, Caboche M, Bernard M, Leroy P, Chalhoub B (2005) Molecular basis of evolutionary events that shaped the hardness locus in diploid and polyploid wheat species (Triticum and Aegilops).Plant Cell 17:1033-1045
Charles M, Belcram H, Just J, Huneau C, Viollet A, Couloux A, Segurens B, Carter M, Huteau V, Coriton O, Appels R, Samain S, Chalhoub B (2008) Dynamics and differential proliferation of transposable elements during the evolution of the B and A genomes of wheat.Genetics180:1071-1086
Dubcovsky J, Dvorak J (2007) Genome plasticity a key factor in the success of polyploid wheat under domestication. Science 316:1862-1866
Gao S, Gu YQ, Wu J, Coleman-Derr D, Huo N, Crossman C, Jia J, Zuo Q, Ren Z, Anderson OD, Kong X (2007) Rapid evolution and complex structural organization in genomic regions harboring multiple prolamin genes in the polyploid wheat genome. Plant MolBiol 65:189-203
Miller AK, Galiba G, Dubcovsky J (2006) A cluster of 11 CBF transcription factors is located at the frost tolerance locus Fr-Am2 in Triticum monococcum. Mol Genet Genomics 275:193-203
Ragupathy R, Cloutier S (2008) Genome organisation and retrotransposon driven molecular evolution of the endosperm Hardness (Ha) locus in Triticum aestivum cv Glenlea. Mol Genet Genomics280:467-481
Salina EA, Sergeeva EM, Adonina IG, Shcherban AB, Afonnikov DA, Belcram H, Huneau C, Chalhoub B (2009) Isolation and sequence analysis of the wheat B genome subtelomeric DNA.BMC Genomics 10:414
Scherrer B, Isidore E, Klein P, Kim JS, Bellec A,Chalhoub B, Keller B, Feuillet C (2005) Large intraspecific haplotype variability at the Rph7 locus results from rapid and recent divergence in the barley genome. Plant Cell 17:361-374
Whitford R, Baumann U, Sutton T, Gumaelius L, Wolters P, Tingey S, Able JA, Langridge P (2007) Identification of transposons, retroelements, and a gene family predominantly expressed in floral tissues in chromosome 3DS of the hexaploid wheat progenitor Aegilops tauschii. Funct Integr Genomics7:37-52
Wicker T, Yahiaoui N, Guyot R, Schlagenhauf E, Liu ZD, Dubcovsky J, Keller B (2003) Rapid genome divergence at orthologous low molecular weight glutenin loci of the A and A(m) genomes of wheat. Plant Cell 15:1186-1197
Wicker T, Zimmermann W, Perovic D, Paterson AH, Ganal M, Graner A, Stein N (2005) A detailed look at 7 million years of genome evolution in a 439 kb contiguous sequence at the barley Hv-eIF4E locus: recombination, rearrangements and repeats.Plant J 41:184-194
Wicker T, Yahiaoui N, Keller B (2007) Illegitimate recombination is a major evolutionary mechanism for initiating size variation in plant resistance genes. Plant J 51:631-641
Wicker T, Krattinger SG, Lagudah ES, Komatsuda T, Pourkheirandish M, Matsumoto T, Cloutier S, Reiser L, Kanamori H, Sato K, Perovic D, Stein N, Keller B(2009) Analysis of intraspecies diversity in wheat and barleygenomesidentifies breakpoints of ancient haplotypes and provides insight into the structure of diploid and hexaploid Triticeae gene pools. Plant Physiol 149:258-270
Yan L, Loukoianov A, Tranquilli G, Helguera M, Fahima T, Dubcovsky J(2003) Positional cloning of the wheat vernalization gene VRN1.Proc Natl Acad SciUSA 100:6263-6268
Yan L, Loukoianov A, Blechl A, Tranquilli G, Ramakrishna W, SanMiguel P, Bennetzen JL, Echenique V, Dubcovsky J (2004) The wheat VRN2 gene is a flowering repressor down-regulated by vernalization.Science 303:1640-1644
Yan L, Fu D, Li C, Blechl A, Tranquilli G, Bonafede M, Sanchez A, Valarik M, Yasuda S, Dubcovsky J(2006)The wheat and barley vernalization gene VRN3 is an orthologue of FT. ProcNatl Acad Sci USA 103:19581-19586
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