The Molecular Diversity of Α-Gliadingenes in Thetribe Triticeae

The molecular diversity of α-gliadingenes in thetribe Triticeae

Peng-Fei Qi1, Qing Chen1, Thérèse Ouellet2,Zhao Wang1, Cheng-Xing Le1, Yu-Ming Wei1,Xiu-Jin Lan1, You-Liang Zheng1, 3&

1 Triticeae Research Institute, SichuanAgriculturalUniversity, Wenjiang distinct of Chengdu, Sichuan 611130, China

2Eastern Cereal and Oilseed Research Centre, Agriculture and Agri-FoodCanada, 960 Carling Ave, Ottawa, ONK1A0C6, Canada

3Ministry of Education Key Laboratory for Crop Genetic Resources and Improvement in Southwest China, Sichuan Agricultural University, Wenjiang distinct of Chengdu, Sichuan 611130, China

Corresponding authors. Y.-M. Wei, E-mail: ; Y.-L Zheng, E-Mail: ; Phone: +86-835-2882007; Fax +86-835-2883153

Submitted to Genetica

Supplementary files

Supplementary Table 1 The α-gliadin genes obtained from diploid Triticeae species. Gene fragments are in bold. The numbers on the left of the table indicate how many genes are obtained from corresponding species

Supplementary Table 2 The reported α-gliadin genes of class III

Supplementary Table 3 Amino acid substitutions in the consensus repeat unit of α-gliadins

Supplementary Table 4 The distribution of CD epitopes in putatively functional α-gliadin genes. Sheet A, distribution of the 16 epitopes in different genomes; Sheet B, the number of epitopes in each α-gliadin genes; Sheet C, the number of epitopes in each genome

Supplementary Fig. 1 Neighbor-joining tree based on alignment of nucleotide sequences of the 236 putatively functional α-gliadin genes. D, U, M and so on indicate the genome of origin for clusters of α-gliadin genes. Genes in brackets indicate that those fall exceptionallyinto the cluster of genes from the genome(s) indicated on the left. 75K γ-secalin gene HQ266677 is the out-group. A larger size triangle indicates more genes in the cluster

Supplementary Fig. 2 Relative positions of CD-toxic epitopes in the deduced mature peptides ofα-gliadinHQ875813

Supplementary Table 1 The α-gliadin genes obtained from diploid Triticeae species

Gene fragments are in bold. The numbers on the left of the table indicate how many genes are obtained from corresponding species

Supplementary Table 2The reported α-gliadin genes of class III

Genbank No. / Cys No. / Gene type / Species / Genome formula / Accession / Reference
FJ478460 / 2 / F / Triticum timopheevii ssp. armeniacum / 2n=4x=28; AAGG / PI427321 / Qi et al. (2011)
FJ478461 / 2 / F / Triticum turgidum ssp. turgidum / 2n=4x=28; AABB / AS2255 / Qi et al. (2011)
FJ478462 / 2 / F / Triticum turgidum ssp. turgidum / 2n=4x=28; AABB / AS2255 / Qi et al. (2011)
FJ478463 / 2 / F / Triticum turgidum ssp. turgidum / 2n=4x=28; AABB / AS2255 / Qi et al. (2011)
FJ478464 / 2 / F / Triticum turgidum ssp. turgidum / 2n=4x=28; AABB / AS2255 / Qi et al. (2011)
FJ478465 / 2 / F / Triticum turgidum ssp. turgidum / 2n=4x=28; AABB / AS2255 / Qi et al. (2011)
FJ478469 / 2 / P / Triticum turgidum ssp. turgidum / 2n=4x=28; AABB / AS2255 / Qi et al. (2011)
FJ478466 / 2 / P / Triticum aestivum / 2n=6x=42; AABBDD / Chinese Spring / Qi et al. (2011)
FJ478467 / 2 / P / Triticum aestivum / 2n=6x=42; AABBDD / Chinese Spring / Qi et al. (2011)
HQ875786 / 2 / P / Australopyrum retrofractum / 2n=2x=14; WW / PI 531553 / This study
HQ875787 / 2 / P / Australopyrum retrofractum / 2n=2x=14; WW / PI 531553 / This study
HQ875788 / 2 / P / Australopyrum retrofractum / 2n=2x=14; WW / PI 531553 / This study
HQ875789 / 3 / P / Australopyrum retrofractum / 2n=2x=14; WW / PI 531553 / This study
HQ875790 / 3 / P / Australopyrum retrofractum / 2n=2x=14; WW / PI 531553 / This study
HQ875791 / 3 / P / Australopyrum retrofractum / 2n=2x=14; WW / PI 531553 / This study
EU026393 / 2 / P / Australopyrum retrofractum / 2n=2x=14; WW / PI 531553 / unpublished
EU026394 / 2 / P / Australopyrum retrofractum / 2n=2x=14; WW / PI 531553 / unpublished
EU026397 / 2 / P / Australopyrum retrofractum / 2n=2x=14; WW / PI 531553 / unpublished
EU026399 / 2 / P / Australopyrum retrofractum / 2n=2x=14; WW / PI 531553 / unpublished
EU026400 / 2 / P / Australopyrum retrofractum / 2n=2x=14; WW / PI 531553 / unpublished
EU026401 / 2 / P / Australopyrum retrofractum / 2n=2x=14; WW / PI 531553 / unpublished
HQ875792 / 2 / P / Australopyrum retrofractum / 2n=2x=14; WW / PI 533014 / This study
HQ875785 / 2 / P / Taeniatherum caput-medusae ssp. crinitum / 2n=2x=14; TaTa / PI 220589 / This study
HQ875783 / 3 / P / Secale cereale / 2n=2x=14; RR / PI 561798 / This study
HQ875784 / 3 / P / Secale cereale / 2n=2x=14; RR / PI 561798 / This study
EU018215 / 2 / P / Lophopyrum elongatum / 2n=2x=14; EeEe / PI 531719 / unpublished
EU849658 / 2 / P / Thinopyrum intermedium / 2n=6x=42; E1E2St / unknown / unpublished
EU849661 / 2 / P / Thinopyrum intermedium / 2n=6x=42; E1E2St / unknown / unpublished

Gene type= functional (F) or pseudogene (P)

Supplementary Table 3 Amino acid substitutions in the consensus repeat unit of α-gliadins

Repeat Motif of α-gliadins / Replaced by
PF(PQ0-3)1-3 / A/I/L/Q/S/T
PF(PQ0-3)1-3 / A/C/G/H/I/M/Q/S/V/Y
PF(PQ0-3)1-3 / A/G/H/L/M/R/S/T/V
PF(PQ0-3)1-3 / A/E/F/G/H/K/L/N/P/R/S/T/V/W

The bold and underlined indicate the residues replaced

Supplementary Fig. 1 Neighbor-joining tree based on alignment of nucleotide sequences of the236 putatively functional α-gliadin genes. D, U, M and so on indicate the genome of origin for clusters of α-gliadin genes. Genes in brackets indicate that those fall exceptionallyinto the cluster of genes from the genome(s) indicated on the left. 75K γ-secalin gene HQ266677 is the out-group. A larger size of triangle means more genes in the cluster

Supplementary Fig. 2 Relative positions of CD-toxic epitopes in the deduced mature peptides ofα-gliadinHQ875813