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Genome-wide analysis of the LEA (late embryogenesis abundant) protein gene family in Populus trichocarpa

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Abstract

Late embryogenesis abundant (LEA) proteins are a large and highly diverse group of polypeptides that are believed to function in desiccation and freezing tolerance in plants. This report presents a genome-wide analysis of LEA proteins and their encoding genes in Populus trichocarpa. Fifty-three LEA genes were identified from the Populus genome and divided into eight groups. The LEA4 and LEA5 groups were found in green algae and all land plants, whereas the other six groups existed only in land plants, indicating that the LEA family underwent rapid expansion during the early evolution of land plants. A majority of Populus LEA proteins contained repeated motifs that were often specific to a LEA group. Except for PtLEA2-1 and PtLEA2-3, all Populus LEA proteins were highly hydrophilic. Examination of the chromosomal locations of Populus LEA genes revealed that 30 % were arranged in tandem repeats, indicating that tandem duplications significantly contributed to the expansion of this gene family in Populus. Expression patterns of all Populus LEA genes under normal growth conditions and abiotic stress (salinity and drought) were investigated by reverse transcription polymerase chain reaction. Twelve of 53 Populus LEA genes were selectively expressed in a specific tissue and/or in response to a specific treatment. LEA genes also showed extensive divergence in expression patterns, even among those from the same group or gene cluster. The expression profiles revealed that the Populus LEA gene family was not involved systematically in the same regulatory pathway.

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Acknowledgments

This study was supported by grants from the National Basic Research Program of China (2009CB119104), the Natural Science Foundation of China (NSFC 30800873) and the Knowledge Innovation Program of the Chinese Academy of Sciences (KSCX2-EW-J-1).

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Authors and Affiliations

  1. State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China

    Ting Lan, Jie Gao & Qing-Yin Zeng

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  1. Ting Lan
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  2. Jie Gao
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  3. Qing-Yin Zeng
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Correspondence to Qing-Yin Zeng.

Additional information

Communicated by P. Ingvarsson

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Supplemental Figure 1

WebLogo illustration of the conserved motif sequences in Populus LEA genes (JPEG 185 kb)

High Resolution Image

(TIFF 497 kb)

Supplemental Table 1

RT-PCR primers used to detect the expression of Populus LEA genes. (XLS 28 kb)

Supplemental Table 2

LEA genes from the Arabidopsis, rice, Pinus, Selaginella, moss, and green algae. (XLS 100 kb)

Supplemental Table 3

Characteristics of the Populus LEA proteins. (XLS 32 kb)

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Lan, T., Gao, J. & Zeng, QY. Genome-wide analysis of the LEA (late embryogenesis abundant) protein gene family in Populus trichocarpa . Tree Genetics & Genomes 9, 253–264 (2013). https://doi.org/10.1007/s11295-012-0551-2

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  • DOI: https://doi.org/10.1007/s11295-012-0551-2

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