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Genomic location and expression analysis of expansin gene family reveals the evolutionary and functional significance in Triticum aestivum

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Abstract

The plant-specific expansin proteins constitute an ancient and major gene family known to have roles in regulating diverse biological processes in plants. Although the functions of many expansin genes have been identified in wheat and other species, little is known about the evolution and genomic locations of the expansin genes in wheat (Triticum aestivum). In this study, a total of 87 expansin genes were identified in the wheat genome, including 52 EXPAs, 42 EXPBs and 4 EXLAs. The EXLB gene was not found in the wheat genome. Phylogenetic tree and comparative analysis revealed amplification of the EXPBs in rice, maize and wheat. The predicted wheat expansins were distributed across 14 of 21 chromosomes with different densities, 3 tightly co-located clusters and 15 paralogous pairs, indicating that tandem duplication and segmental duplication events also played roles in the evolution of expansins in wheat. In addition, the gene structures and conserved protein domains of wheat expansins suggest high levels of conservation within the phylogenetic subgroups. Analysis of a published microarray database showed that most wheat expansin genes exhibit different expression levels in different tissues and developmental stages. To our knowledge, this is the first report of a genome-wide analysis of the wheat expansin gene family, which should provide valuable information for further elucidating the classification and putative functions of the entire gene family.

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Abbreviations

BLAST:

The Basic Local Alignment Search Tool

HMM:

Hidden Markov Model

MEGA:

Molecular Evolutionary Genetics Analysis

MUSCEL:

Multiple Sequence Comparison by Log-Expectation

NJ:

The neighbor-joining

SMART:

Simple Modular Architecture Research Tool

GSDS:

Gene Structure Display Server

NCBI:

National Center for Biotechnology Information

ORF:

Open Reading Frame

UTR:

Untranslated Regions

Aa:

Amino acid

DPBB:

Double-psi beta-barrel

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Acknowledgments

This work was supported by Youth Scientific Research Foundation of Shandong Academy of Agricultural Sciences (Grant No. 2014QNM09 to Nana Li), Natural Science Foundation of Shandong Province (Grant No. ZR2014YL017 to Nana Li) and Shandong Province Science and Technology Development Program (Grant No. 2012G0021031 to Nana Li).

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Authors and Affiliations

  1. Shandong Center of Crop Germplasm Resources/Shandong Academy of Agricultural Sciences, Jinan, 250100, People’s Republic of China

    Nana Li, Yanyan Pu, Yongchao Gong & Hanfeng Ding

  2. Maize Institute, Shandong Academy of Agricultural Sciences, Jinan, 250100, People’s Republic of China

    Yanli Yu

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  1. Nana Li
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  2. Yanyan Pu
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  3. Yongchao Gong
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  4. Yanli Yu
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Correspondence to Nana Li or Hanfeng Ding.

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Nana Li, Yanyan Pu, Yongchao Gong, Yanli Yu and Hanfeng Ding declares no conflict of interest.

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The article does not contain any studies with human participants or animals performed by any of the authors.

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Figure S1

Phylogenetic tree of AtEXPs, OsEXPs, ZmEXPs and TaEXPs was constructed by maximum likelihood method (JPEG 4947 kb)

Table S1

The information of the Expansin genes in wheat (DOC 182 kb)

Table S2

Ka/Ks analysis and estimated divergence times for duplicated TaEXP paralogs (DOC 46 kb)

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Li, N., Pu, Y., Gong, Y. et al. Genomic location and expression analysis of expansin gene family reveals the evolutionary and functional significance in Triticum aestivum . Genes Genom 38, 1021–1030 (2016). https://doi.org/10.1007/s13258-016-0446-y

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