Genome-wide identification and expression analysis of the SET domain-containing gene family in potato (Solanum tuberosum L.).

Genes containing the SET domain can catalyse histone lysine methylation, which in turn has the potential to cause changes to chromatin structure and regulation of the transcription of genes involved in diverse physiological and developmental processes. However, the functions of SET domain-containing (StSET) genes in potato still need to be studied. The objectives of our study can be summarized as in silico analysis to (i) identify StSET genes in the potato genome, (ii) systematically analyse gene structure, chromosomal distribution, gene duplication events, promoter sequences, and protein domains, (iii) perform phylogenetic analyses, (iv) compare the SET domain-containing genes of potato with other plant species with respect to protein domains and orthologous relationships, (v) analyse tissue-specific expression, and (vi) study the expression of StSET genes in response to drought and heat stresses. In this study, we identified 57 StSET genes in the potato genome, and the genes were physically mapped onto eleven chromosomes. The phylogenetic analysis grouped these StSET genes into six clades. We found that tandem duplication through sub-functionalisation has contributed only marginally to the expansion of the StSET gene family. The protein domain TDBD (PFAM ID: PF16135) was detected in StSET genes of potato while it was absent in all other previously studied species. This study described three pollen-specific StSET genes in the potato genome. Expression analysis of four StSET genes under heat and drought in three potato clones revealed that these genes might have non-overlapping roles under different abiotic stress conditions and durations. The present study provides a comprehensive analysis of StSET genes in potatoes, and it serves as a basis for further functional characterisation of StSET genes towards understanding their underpinning biological mechanisms in conferring stress tolerance.

The Craterostigma plantagineum glycine-rich protein CpGRP1 interacts with a cell wall-associated protein kinase 1 (CpWAK1) and accumulates in leaf cell walls during dehydration.

Craterostigma plantagineum tolerates extreme desiccation. Leaves of this plant shrink and extensively fold during dehydration and expand again during rehydration, preserving their structural integrity. Genes were analysed that may participate in the reversible folding mechanism. Analysis of transcripts abundantly expressed in desiccated leaves identified a gene putatively coding for an apoplastic glycine-rich protein (CpGRP1). We studied the expression, regulation and subcellular localization of CpGRP1 and its ability to interact with a cell wall-associated protein kinase (CpWAK1) to understand the role of CpGRP1 in the cell wall during dehydration. The CpGRP1 protein accumulates in the apoplast of desiccated leaves. Analysis of the promoter revealed that the gene expression is mainly regulated at the transcriptional level, is independent of abscisic acid (ABA) and involves a drought-responsive cis-element (DRE). CpGRP1 interacts with CpWAK1 which is down-regulated in response to dehydration. Our data suggest a role of the CpGRP1-CpWAK1 complex in dehydration-induced morphological changes in the cell wall during dehydration in C. plantagineum. Cell wall pectins and dehydration-induced pectin modifications are predicted to be involved in the activity of the CpGRP1-CpWAK1 complex.

Taxonomically restricted genes of Craterostigma plantagineum are modulated in their expression during dehydration and rehydration.

MAIN CONCLUSION: Taxonomically restricted genes are known to contribute to the evolution of new traits. In Craterostigma plantagineum two of such genes are modulated during dehydration and rehydration and seem to contribute to a successful recovery after desiccation. The resurrection plant Craterostigma plantagineum can tolerate extreme water loss. Protective molecules linked to desiccation tolerance were identified in C. plantagineum but underlying mechanisms are far from being completely understood. A transcriptome analysis revealed several genes which could not be annotated and are, therefore, interesting candidates for understanding desiccation tolerance. Genes which occur only in some species are defined as orphan or taxonomically restricted genes (TRGs) and may be important for the evolution of new traits. Several of these TRGs are modulated in expression during dehydration/rehydration in C. plantagineum. Here we report the characterisation of two of these TRGs encoding a cysteine-rich rehydration-responsive protein 1 (CpCRP1) and an early dehydration-responsive protein 1 (CpEDR1). The involvement of CpCRP1 and CpEDR1 in different phases of the dehydration/rehydration cycle is shown by transcript and protein expression analysis. In silico sequence analyses predicted that both genes are likely to interact with other cellular components and are localised in two different cellular compartments. GFP fusion proteins demonstrated that CpCRP1 is secreted into the apoplasm, whereas CpEDR1 is imported into chloroplasts. Putative homologs of CpCRP1 and CpEDR1 were identified in Lindernia brevidens and Lindernia subracemosa which belong to the same family as C. plantagineum thus suggesting a recent evolution of the genes in this family. According to expression profiles, CpCRP1 may play a role in normal conditions and during rehydration, whereas CpEDR1 may be required for the acquisition of desiccation tolerance and protect photosynthetic structures during dehydration and rehydration.