Genome-wide identification and expression profile analysis of the Hsp20 gene family in Barley (Hordeum vulgare L.)

In plants, heat shock proteins (Hsps) play important roles in response to diverse stresses. Hsp20 is the major family of Hsps, but their role remains poorly understood in barley (Hordeum vulgare L.). To reveal the mechanisms of barley Hsp20s (HvHsp20s) response to stress conditions, we performed a comprehensive genome-wide analysis of the HvHsp20 gene family using bioinformatics-based methods. In total, 38 putative HvHsp20s were identified in barley and grouped into four subfamilies (C, CP, PX, and MT) based on predicted subcellular localization and their phylogenetic relationships. A sequence analysis indicated that most HvHsp20 genes have no intron or one with a relatively short length. In addition, the same group of HvHsp20 proteins in the phylogenetic tree shared similar gene structure and motifs, indicating that they were highly conserved and might have similar function. Based on RNA-seq data analysis, we showed that the transcript levels of HvHsp20 genes could be induced largely by abiotic and biotic stresses such as heat, salt, and powdery mildew. Three HvHsp20 genes, HORVU7Hr1G036540, HORVU7Hr1G036470, and HORVU3Hr1G007500, were up-regulated under biotic and abiotic stresses, suggesting their potential roles in mediating the response of barley plants to environment stresses. These results provide valuable information for further understanding the complex mechanisms of HvHsp20 gene family in barley.

Genome-wide analysis of the potato Hsp20 gene family: identification, genomic organization and expression profiles in response to heat stress

Background

Heat shock proteins (Hsps) are essential components in plant tolerance mechanism under various abiotic stresses. Hsp20 is the major family of heat shock proteins, but little of Hsp20 family is known in potato (Solanum tuberosum), which is an important vegetable crop that is thermosensitive.

Results

To reveal the mechanisms of potato Hsp20s coping with abiotic stresses, analyses of the potato Hsp20 gene family were conducted using bioinformatics-based methods. In total, 48 putative potato Hsp20 genes (StHsp20s) were identified and named according to their chromosomal locations. A sequence analysis revealed that most StHsp20 genes (89.6%) possessed no, or only one, intron. A phylogenetic analysis indicated that all of the StHsp20 genes, except 10, were grouped into 12 subfamilies. The 48 StHsp20 genes were randomly distributed on 12 chromosomes. Nineteen tandem duplicated StHsp20s and one pair of segmental duplicated genes (StHsp20-15 and StHsp20-48) were identified. A cis-element analysis inferred that StHsp20s, except for StHsp20-41, possessed at least one stress response cis-element. A heatmap of the StHsp20 gene family showed that the genes, except for StHsp20-2 and StHsp20-45, were expressed in various tissues and organs. Real-time quantitative PCR was used to detect the expression level of StHsp20 genes and demonstrated that the genes responded to multiple abiotic stresses, such as heat, salt or drought stress. The relative expression levels of 14 StHsp20 genes (StHsp20-4, 6, 7, 9, 20, 21, 33, 34, 35, 37, 41, 43, 44 and 46) were significantly up-regulated (more than 100-fold) under heat stress.

Conclusions

These results provide valuable information for clarifying the evolutionary relationship of the StHsp20 family and in aiding functional characterization of StHsp20 genes in further research.

Electronic supplementary material

The online version of this article (dio: 10.1186/s12864-018-4443-1) contains supplementary material, which is available to authorized users.

Genome-wide analysis of the potato Hsp20 gene family: identification, genomic organization and expression profiles in response to heat stress

BACKGROUND

Heat shock proteins (Hsps) are essential components in plant tolerance mechanism under various abiotic stresses. Hsp20 is the major family of heat shock proteins, but little of Hsp20 family is known in potato (Solanum tuberosum), which is an important vegetable crop that is thermosensitive.

RESULTS

To reveal the mechanisms of potato Hsp20s coping with abiotic stresses, analyses of the potato Hsp20 gene family were conducted using bioinformatics-based methods. In total, 48 putative potato Hsp20 genes (StHsp20s) were identified and named according to their chromosomal locations. A sequence analysis revealed that most StHsp20 genes (89.6%) possessed no, or only one, intron. A phylogenetic analysis indicated that all of the StHsp20 genes, except 10, were grouped into 12 subfamilies. The 48 StHsp20 genes were randomly distributed on 12 chromosomes. Nineteen tandem duplicated StHsp20s and one pair of segmental duplicated genes (StHsp20-15 and StHsp20-48) were identified. A cis-element analysis inferred that StHsp20s, except for StHsp20-41, possessed at least one stress response cis-element. A heatmap of the StHsp20 gene family showed that the genes, except for StHsp20-2 and StHsp20-45, were expressed in various tissues and organs. Real-time quantitative PCR was used to detect the expression level of StHsp20 genes and demonstrated that the genes responded to multiple abiotic stresses, such as heat, salt or drought stress. The relative expression levels of 14 StHsp20 genes (StHsp20-4, 6, 7, 9, 20, 21, 33, 34, 35, 37, 41, 43, 44 and 46) were significantly up-regulated (more than 100-fold) under heat stress.

CONCLUSIONS

These results provide valuable information for clarifying the evolutionary relationship of the StHsp20 family and in aiding functional characterization of StHsp20 genes in further research.