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Genome-wide identification of the expansin gene family in tobacco (Nicotiana tabacum)

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Abstract

Expansins are pH-dependent cell wall loosening proteins which form a large family in plants. They have been shown to be involved in various developmental processes and been implicated in enabling plants’ ability to absorb nutrients from the soil as well as conferring biotic and abiotic stress resistances. It is therefore clear that they can be potential targets in genetic engineering for crop improvement. Tobacco (Nicotiana tabacum) is a major crop species as well as a model organism. Considering that only a few tobacco expansins have been studied, a genome-wide analysis of the tobacco expansin gene family is necessary. In this study, we identified 52 expansins in tobacco, which were classified into four subfamilies: 36 NtEXPAs, 6 NtEXPBs, 3 NtEXLAs and 7 NtEXLBs. Compared to other species, the NtEXLB subfamily size was relatively larger. Phylogenetic analysis showed that the 52 tobacco expansins were divided into 13 subgroups. Gene structure analysis revealed that genes within subfamilies/subgroups exhibited similar characteristics such as gene structure and protein motif arrangement. Whole-genome duplication and tandem duplication events may have played important roles in the expanding of tobacco expansins. Cis-Acting element analysis revealed that each expansin gene was regulated or several expansin genes were co-regulated by both internal and environmental factors. 35 of these genes were identified as being expressed according to a microarray analysis. In contrast to most NtEXPAs which had higher expression levels in young organs, NtEXLAs and NtEXLBs were preferentially expressed in mature or senescent tissues, suggesting that they might play different roles in different organs or at different developmental stages. As the first step towards genome-wide analysis of the tobacco expansin gene family, our work provides solid background information related to structure, evolution and expression as well as regulatory cis-acting elements of the tobacco expansins. This information will provide a strong foundation for cloning and functional exploration of expansin genes in tobacco.

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    Authors and Affiliations

    1. Key Laboratory for Tobacco Gene Resources, Tobacco Research Institute of Chinese Academy of Agricultural Sciences, Qingdao, 266101, Shandong, People’s Republic of China

      Anming Ding, Prince Marowa & Yingzhen Kong

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    1. Anming Ding
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    2. Prince Marowa
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    3. Yingzhen Kong
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    Correspondence to Yingzhen Kong.

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    This study was funded by the National Key Technology R&D Program (No. 2015BAD15B03-05), the National Natural Science Foundation of China (Grant No. 31470291) and the Youth Elite Program (to YK).

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    All authors declare that she/he has no conflict of interest.

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

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    Communicated by S. Hohmann.

    A. Ding and P. Marowa contributed equally to this work.

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    Ding, A., Marowa, P. & Kong, Y. Genome-wide identification of the expansin gene family in tobacco (Nicotiana tabacum). Mol Genet Genomics 291, 1891–1907 (2016). https://doi.org/10.1007/s00438-016-1226-8

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    • DOI: https://doi.org/10.1007/s00438-016-1226-8

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