Expansion of the gamma-gliadin gene family in Aegilops and Triticum
1 Wageningen UR Plant Breeding, Wageningen UR, P.O. Box 16, Wageningen, NL-6700 AA, The Netherlands
2 Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, 119991, Russia
3 Plant Research International, Wageningen UR, P.O. Box 16, Wageningen, NL-6700 AA, The Netherlands
4 All-Russian Institute of Plant Industry, St. Petersburg, 190000, Russia
5 Bioengineering Center, Moscow, 117312, Russia
6 Allergy Consortium, Wageningen, The Netherlands
BMC Evolutionary Biology 2012, 12:215 doi:10.1186/1471-2148-12-215Published: 8 November 2012
Additional file 1:
List of all contigs, number of sequences, and Genbank accessions numbers.
Format: XLSX Size: 16KB Download file
Additional file 2:
Alignment of gamma-gliadin nucleotide sequences (Nexus format).
Format: TXT Size: 278KB Download file
Additional file 3:
Alignment of gamma-gliadin amino acid sequences (Nexus format).
Format: TXT Size: 93KB Download file
Additional file 4:
Maximum-likelihood tree of the gamma-gliadins (based on nucleotide sequences) from diploid species of tribe Triticeae. A maximum-likelihood (ML) analysis was performed with PhyML 3.0 using the GTR-substitution model. SH-like approximate likelihood-ratio test was used for estimation of branch support. Sequences that had length in the alignment less than 600 bp were excluded from the analysis. The gamma-gliadins fall into six groups (1–6 on the right) in two branches (1–2 and 3-4-5-6). Key for the sequence codes in Additional file 1.
Format: TIFF Size: 1015KB Download file
Additional file 5:
Ks/Ka ratio of intact and pseudogene gamma-gliadins. Scatter plot of the numbers of synonymous substitutions (Ks) and non-synonymous substitutions (Ka) per site for pairwise comparisons among full open reading frame gamma-gliadins and pseudogene sequences. Linear trendlines with the intercept set to zero are shown both for full-open reading frame (ORF) sequences and pseudogene sequences.
Format: DOCX Size: 51KB Download file