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Genome-wide identification and comparative expression analysis of LEA genes in watermelon and melon genomes

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Abstract

Late embryogenesis abundant (LEA) proteins are large and diverse group of polypeptides which were first identified during seed dehydration and then in vegetative plant tissues during different stress responses. Now, gene family members of LEA proteins have been detected in various organisms. However, there is no report for this protein family in watermelon and melon until this study. A total of 73 LEA genes from watermelon (ClLEA) and 61 LEA genes from melon (CmLEA) were identified in this comprehensive study. They were classified into four and three distinct clusters in watermelon and melon, respectively. There was a correlation between gene structure and motif composition among each LEA groups. Segmental duplication played an important role for LEA gene expansion in watermelon. Maximum gene ontology of LEA genes was observed with poplar LEA genes. For evaluation of tissue specific expression patterns of ClLEA and CmLEA genes, publicly available RNA-seq data were analyzed. The expression analysis of selected LEA genes in root and leaf tissues of drought-stressed watermelon and melon were examined using qRT-PCR. Among them, ClLEA-12-17-46 genes were quickly induced after drought application. Therefore, they might be considered as early response genes for water limitation conditions in watermelon. In addition, CmLEA-42-43 genes were found to be up-regulated in both tissues of melon under drought stress. Our results can open up new frontiers about understanding of functions of these important family members under normal developmental stages and stress conditions by bioinformatics and transcriptomic approaches.

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Acknowledgements

This work was financially supported by The Scientific and Technological Research Council of Turkey (TUBITAK) with Grant Number 114O761.

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Authors and Affiliations

  1. Department of Genetics and Bioengineering, Faculty of Engineering and Architecture, Kastamonu University, 37150, Kastamonu, Turkey

    Yasemin Celik Altunoglu, Mehmet Cengiz Baloglu, Pinar Baloglu & Sibel Kara

  2. Research and Application Center, Kastamonu University, Kastamonu, Turkey

    Pinar Baloglu

  3. Department of Forest Engineering, Faculty of Forestry, Kastamonu University, Kastamonu, Turkey

    Esra Nurten Yer

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  1. Yasemin Celik Altunoglu
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  2. Mehmet Cengiz Baloglu
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Correspondence to Yasemin Celik Altunoglu.

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Supplementary Fig. 1

Presentation of tissue specific expression of ClLEA genes by heatmap from different tissues of watermelon. Expression levels of genes were presented by colors from low (green) to high (red) expression pattern. (TIFF 7607 kb)

Supplementary Fig. 2

Tissue specific expression patterns of CmLEA genes by heatmap from different tissues of melon. Expression levels of genes were presented by colors from low (green) to high (red) expression pattern. (TIFF 4328 kb)

Supplementary Fig. 3

A total of 10 different motif clades with different colored boxes in melon (A) and watermelon (B) LEA proteins by MEME software. (TIFF 4075 kb)

Supplementary Fig. 4

Phylogenetic relationships between melon, watermelon and cucumber LEA proteins. (TIFF 2718 kb)

Supplementary Fig. 5

Comparative physical mapping of ClLEA genes with Arabidopsis, poplar, soybean, potato, grape and maize LEA genes. (TIFF 4326 kb)

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Supplementary material 10 (DOCX 39 kb)

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Supplementary material 13 (DOC 33 kb)

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Celik Altunoglu, Y., Baloglu, M.C., Baloglu, P. et al. Genome-wide identification and comparative expression analysis of LEA genes in watermelon and melon genomes. Physiol Mol Biol Plants 23, 5–21 (2017). https://doi.org/10.1007/s12298-016-0405-8

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