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The gene space in wheat: the complete γ-gliadin gene family from the wheat cultivar Chinese Spring

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Abstract

The complete set of unique γ-gliadin genes is described for the wheat cultivar Chinese Spring using a combination of expressed sequence tag (EST) and Roche 454 DNA sequences. Assemblies of Chinese Spring ESTs yielded 11 different γ-gliadin gene sequences. Two of the sequences encode identical polypeptides and are assumed to be the result of a recent gene duplication. One gene has a 3′ coding mutation that changes the reading frame in the final eight codons. A second assembly of Chinese Spring γ-gliadin sequences was generated using Roche 454 total genomic DNA sequences. The 454 assembly confirmed the same 11 active genes as the EST assembly plus two pseudogenes not represented by ESTs. These 13 γ-gliadin sequences represent the complete unique set of γ-gliadin genes for cv Chinese Spring, although not ruled out are additional genes that are exact duplications of these 13 genes. A comparison with the ESTs of two other hexaploid cultivars (Butte 86 and Recital) finds that the most active genes are present in all three cultivars, with exceptions likely due to too few ESTs for detection in Butte 86 and Recital. A comparison of the numbers of ESTs per gene indicates differential levels of expression within the γ-gliadin gene family. Genome assignments were made for 6 of the 13 Chinese Spring γ-gliadin genes, i.e., one assignment from a match to two γ-gliadin genes found within a tetraploid wheat A genome BAC and four genes that match four distinct γ-gliadin sequences assembled from Roche 454 sequences from Aegilops tauschii, the hexaploid wheat D-genome ancestor.

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Acknowledgments

The research was supported by USDA-ARS project 5325-21000-015 and National Science Foundation grant 0701916.

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Authors and Affiliations

  1. Genomics and Gene Discovery Research Unit, Western Regional Research Unit, Agricultural Research Service, US Department of Agriculture, 800 Buchanan Street, Albany, CA, 94710, USA

    Olin D. Anderson, Naxin Huo & Yong Q. Gu

  2. University of California, Davis, CA, 95616, USA

    Naxin Huo

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  1. Olin D. Anderson
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  2. Naxin Huo
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Correspondence to Olin D. Anderson.

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Supplementary Fig. S1

γ-Gliadin gene sequence source. The sequence structure of the 11 Chinese Spring active γ-gliadin genes is diagrammed. Start (ATG) and stop (TGA) codon positions are marked. Genes CS-γ6a and CS-γ6b are diagrammed together since the flanking DNA is difficult to distinguish between the two nearly identical genes. Gray, non-coding flanking DNA; dark blue, coding sequence with at least two 454 reads covering those sections; light blue, only one 454 read; yellow, no 454 reads (JPEG 16 kb)

High Resolution Image

(TIFF 26 kb)

Supplementary Fig. S2

Origin of an anomalous carboxy terminus of a γ-gliadin. The CS-γ5 polypeptide has a different carboxy terminus from other known γ-gliadins. Shown is how a complex duplication at the 3′ end of the coding sequence changed the reading frame. The 3′ end of the CS-γ5 reading frame is compared with CS-γ2. Stop codons for both polypeptides are boxed. Encoding amino acids are indicated above and below the two DNA sequences. Brackets above and below the CS-γ5 sequence indicate duplications (JPEG 52 kb)

High Resolution Image

(TIFF 681 kb)

Supplementary File S1

A fasta file of the extended γ-gliadin sequences for hexaploid wheat cultivar Chinese Spring. Sequences are a consensus of EST and 454 sequences, as described in “Materials and methods.” Sequences gamma-13 and gamma-14 are pseudogenes whose sequences are derived completely from 454 reads (FAS 28 kb)

Supplementary File S2

A fasta file of the γ-gamma consensus sequences from ESTs of hexaploid wheat cultivars Butte 86 and Recital (FAS 17 kb)

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Anderson, O.D., Huo, N. & Gu, Y.Q. The gene space in wheat: the complete γ-gliadin gene family from the wheat cultivar Chinese Spring. Funct Integr Genomics 13, 261–273 (2013). https://doi.org/10.1007/s10142-013-0321-8

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