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Identification and expression analysis of LEA gene family members in cucumber genome

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Abstract

LEA (late embryogenesis abundant) proteins are firstly discovered in seeds and then identified in vegetative tissues of different plant species. They are mainly regulated under abiotic stress conditions. Although genome wide studies of different gene family members have been performed in cucumber, there is no such a study for LEA genes. We have identified 79 LEA genes in the cucumber genome. Based on phylogenetic analysis, CsLEA genes could be classified into seven groups in which structural motifs are relatively conserved. Tandem duplications play an important role in cucumber genome for LEA gene expansion. Orthologous and chromosomal relationships of CsLEA genes were observed based on comparative mapping analysis with other species. The in silico micro-RNA (miRNA) target analyses indicated that 37 CsLEA genes were targeted by different miRNAs, especially mir854 and mir414 are the most abundant identified ones. Public available RNA-seq data were analyzed for expression analysis of CsLEA genes in different tissues of cucumber. According to genome-wide expression analysis, nine CsLEA genes showed higher expression profiles in all tissues. The expression profiles of ten CsLEA genes in the root and leaf tissues of drought-stressed cucumber were examined using qRT-PCR. Among them, CsLEA-54 induced after stress application in leaf and root tissues and might provide adaptation to drought stress for cucumber. CsLEA-09, CsLEA-32 and CsLEA-57 genes responded to drought after 3 h later and might be considered as early response genes to water limitation. This research could help us to improve understanding of contribution of CsLEAs to drought tolerance in cucumber.

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Acknowledgments

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

    Yasemin Celik Altunoglu, Pinar Baloglu & Mehmet Cengiz Baloglu

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

    Pinar Baloglu

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

    Esra Nurten Yer

  4. Faculty of Education, Kastamonu University, Kastamonu, Turkey

    Sefa Pekol

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  1. Yasemin Celik Altunoglu
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Correspondence to Yasemin Celik Altunoglu.

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Fig. S1

Exon-intron organization of cucumber CsLEA genes. LEA gene family members in cucumber are classified according to Fig. 2 Clusters. Exons are showed as yellow boxes and introns are grey lines (JPEG 215 kb)

Fig. S2

Presentation of motif clades for the CsLEA proteins. Fifteen different MEME motifs are distributed as different colors (JPEG 54 kb)

Fig. S3

Comparative physical mapping indicated high degree of orthologous relationships of LEA genes located on cucumber chromosomes with poplar, Arabidopsis and maize. Orthologous genes between cucumber and poplar, Arabidopsis and maize are presented by red lines (JPEG 322 kb)

Fig. S4

Heatmap distribution of CsLEA genes, which showing expression patterns of these gene family members in the 10 different tissues and organ systems of cucumber using transcriptome data. Expression values indicated as color gradient from no expression (green) to high expression (red) levels (TIFF 3108 kb)

Supplementary material 5 (XLSX 23 kb)

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Supplementary material 7 (XLSX 18 kb)

Table S4

miRNA targets identified by psRNATarget (XLSX 14 kb)

Supplementary material 9 (DOCX 38 kb)

Supplementary material 10 (DOC 33 kb)

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Celik Altunoglu, Y., Baloglu, P., Yer, E.N. et al. Identification and expression analysis of LEA gene family members in cucumber genome. Plant Growth Regul 80, 225–241 (2016). https://doi.org/10.1007/s10725-016-0160-4

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