- Genome-wide analysis of the potato Hsp20 gene family: identification, genomic. - 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. - 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. - 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. - The relative expression levels of 14 StHsp20 genes ( StHsp 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.. - F University, Yangling, Shaanxi 712100, China Full list of author information is available at the end of the article. - 2018 Open Access This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0. - With the avail- ability of the whole-genome sequence of potato, it is now possible to more fully study the potato Hsp20 gene family.. - The re- sults provide useful information for further functional investigations of the StHsp20 gene family.. - Identification of the Hsp20 family members in potato genome. - After removing all of the redundant sequences, the output putative Hsp20 protein sequences were submitted to CDD (https://. - The predicted protein sequences lacking the Hsp20 domain or with a molecular weight outside of the 15–42-kDa range were excluded. - All of the non-redundant and high-confidence genes were assigned as potato Hsp20 s ( StHsp20s. - These StHsp20 genes were named on the basis of their posi- tions on pseudomolecules [24].. - All of the high-confidence Hsp20 sequences were sub- mitted to ExPASy (http://web.expasy.org/protparam/) to calculate the number of amino acids, molecular weights and theoretical isoelectric points (pI). - The exon–intron structures of the StHsp20 genes were identified on the Gene Structure Display Server (GSDS, http://gsds.cbi.- pku.edu.cn/) [30].. - The chromosomal positions of the StHsp20 genes were acquired from the potato genome browser at the PGSC.. - StHsp20 genes’ chromosomal positions and relative dis- tances. - The StHsp20 gene duplication was confirmed based on two criteria: (a) the length of the shorter aligned sequence covered >. - 70% of the longer sequence;. - and (b) the similarity of the two aligned sequences were. - All of the acquired sequences were first aligned by ClustalX (version 1.83) software [37] with the default parameters. - Analysis of Cis -acting element in StHsp20 genes ’ promoters. - The upstream sequences (1.5 kb) of the StHsp20 -coding sequences were retrieved from the PGSC and then sub- mitted to PlantCARE (http://bioinformatics.psb.ugent.be/. - All of the lines were cultured in Murashige and Skoog (MS) medium [40] containing 3% sucrose and 0.8% agar at pH 5.9. - All of the col- lected samples were froze in liquid nitrogen rapidly and stored at − 80 °C refrigerator before RNA extraction.. - To render the data suitable for cluster displays, absolute FPKM values were divided by the mean of all of the values, and the ratios were transformed by log2.. - Primer Premier 5 was used to design primers specific to the StHsp20 genes (Additional file 3: Table S3). - All of the operational procedures followed the manufacturer’ s protocols. - The relative expression levels of the StHsp20 genes were calculated using the standard curve and normalized by the control’s expression. - Identification and analysis of StHsp20 genes. - Sequences without a typical ACD domain and with a molecular weight outside of the 15–42-kDa range were excluded. - The lengths of the StHsp20 proteins ranged from 133 (StHsp20-36) to 303 amino acids (StHsp20-15). - StHsp20 genes were distributed on 12 potato chro- mosomes. - Interestingly, all of the tan- dem duplicated genes were intronless and the pair of segmentally duplicated genes, StHsp15 and StHsp48 , had multiple introns. - Details of the 10 putative motifs are outlined in Table 2. - Based on analyses of Pfam, CDD and SMART, Motif 1 completely corresponded to the region of the conserved ACD. - The majority of the StHsp20 proteins (58.3%) contained Motif 1 or the combination of Motifs 2, 3 and 7. - The different compo- sitions of the ACD domain may indicate functional di- versity. - Phylogenetic analysis of StHsp20 genes. - Most of the Hsp20s, including 29 StHsp20s, were classified into CI–CVII, which indicated that cytosol might be the main functional area for plant Hsp20s. - Most StHsp20 members of the CI subfamily lacked introns, and the CII and ER subfam- ilies had no introns. - However, all of the members of the CV, CVI, CVII, Po, MI and MII subfamilies had one in- tron, which indicated a close phylogenetic relationship (Fig. - Table 1 Features of StHsp20 genes identified in potato. - Chromosomal location and gene duplication of StHsp20s The 48 StHsp20 genes were distributed on 12 potato chromosomes randomly (Fig. - The majority of StHsp20 genes were located on the proximate or the dis- tal ends of the chromosomes. - Thus, we analyzed the duplication events of StHsp20 genes. - Based on the Table 1 Features of StHsp20 genes identified in potato (Continued). - 1 Phylogenetic relationship, gene structure and conserved motif analysis of StHsp20 genes. - b Exon/intron organization of StHsp20 genes. - The upstream/downstream region of StHsp20 genes are indicated in blue boxes. - c Distributions of conserved motifs in StHsp20 genes. - of the StHsp20 genes. - To further study the potential regulatory mechanisms of StHsp20 during abiotic stress responses, the 1.5-kb up- stream sequences from the translation start sites of StHsp20 genes (promoter regions of StHsp20-2 , StHsp20-11 , StHsp20-15 and StHsp20-32 were absent) Table 2 List of the putative motifs of StHsp20 proteins. - StHsp20-25 , StHsp20-26 , StHsp20-29 and StHsp20-30 , were highly expressed in all of the tissues. - Some StHsp20 genes showed similar expression patterns in various tis- sues. - Generally, the relative expression level of the StHsp20 genes under all stress conditions fluctuated during the 24-h treat- ments (Fig. - Most of the StHsp20 genes. - were sensitive to heat stress, and none of the genes were down-regulated, but StHsp20-29 and StHsp20-30 showed no differences after being treated for 3 h and 24 h under heat stress. - The relative expression levels of 14 StHsp20 genes ( StHsp and 46 ) were extremely up-regulated (more than 100- fold) under heat stress compared with the control.. - The expression levels of StHsp20 genes under salt and drought stresses varied among the 47 members.. - Nearly half of the StHsp20 (40.4%) genes were down-regulated after. - The differential expression patterns compared with those under heat stress indicated there were different response and regulatory mechanisms of the StHsp20 family under various abiotic stress conditions.. - 1500 bp) of 44 StHsp20 genes (promoter regions of StHsp20-2 , StHsp20-11 , StHsp20-15 and StHsp20-32 were absent) are analyzed by PlantCARE. - FPKM values of StHsp20 genes were transformed by log2 and the heatmap was constructed by HemI software. - However, two sections of the results were not completely in accordance with each other. - Under heat stress, only 10 of the StHsp20 genes showed high expression level while 20 StHsp20s showed low ex- pression level. - With the availabilities of the whole genome sequence of many plants, several Hsp20 families have been identified, such as Arabidopsis , rice, Populus , pepper and tomato . - 6 Expression profiles of StHsp20 genes under heat, salt and drought stresses. - Additionally, StHsp20 genes of the CII and ER subfamilies, as well as most StHsp20 genes of the CI subfamily, were intronless (Fig. - Members of the CV, CVI, MI, MII, P and Po subfamilies had only one intron. - This correlation between intron numbers and motif arrangement further confirmed the classifications of the StHsp20 genes. - Most of the StHsp20 genes were highly induced under heat stress (Fig. - The StHsp20 genes existed in 11 of the 12 subfamilies. - Most of the StHsp20 genes (61.7%) were grouped into a nucleocytoplasmic subfamily, which was also illus- trated in Arabidopsis , pepper and tomato . - Furthermore, the Hsp20 genes in the same subfamily from different species were more similar than those of the same species but belonging to various subfamilies. - In this re- search, 48 StHsp20 genes were located unevenly on 12 potato chromosomes, and most of the StHsp20 genes were located on the terminal regions of the chromo- somes. - Three genes, StHsp20-18, StHsp20-26 and StHsp20-30 , were highly and indiscrim- inately expressed in all of the investigated tissues under normal condition. - The two genes ( StHsp20-29 and StHsp20-30 ) with distinctive ex- pression patterns were highly expressed in all of the in- vestigated tissues, but no induction was observed under heat stress. - During a 24-h heat treatment, the StHsp20 genes showed different transcript accumulation levels. - Based on qRT-PCR, all of the StHsp20 genes responded to salt and drought stress. - 4), and these are involved in the responses of StHsp20 genes to other abiotic stresses.. - Thus, StHsp20 genes could be induced by both heat stress and other abiotic stresses. - Here, a genome-wide analysis of potato Hsp20 family was performed, and 48 StHsp20 genes were confirmed. - Most of StHsp20 genes were sensitive to heat stress and were up-regulated rapidly, indicating that StHsp20 genes play important roles in the acquired thermotolerance of potato. - FPKM values of 48 StHsp20 genes in various potato tissues. - The primer sequences of 48 StHsp20 genes used for qRT-PCR. - The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. - All of the datasets supporting the results of this article are included within the article and its Additional files.. - All of the authors read and approved the final manuscript.. - The evolution, function, structure, and expression of the plant sHsps. - Evolution, structure and function of the small heat shock proteins in plants. - Substrate binding site flexibility of the small heat shock protein molecular chaperones. - Evolution and functional diversification of the small heat shock protein/ α -crystallin family in higher plants. - Genome-wide analysis of the Hsp20 gene family in soybean: comprehensive sequence, genomic organization and expression profile analysis under abiotic and biotic stresses. - Genome-wide analysis of the CaHsp20 gene family in pepper:. - Expression profiling and integrative analysis of the cesa/csl superfamily in rice. - Comparative analysis of the small heat shock proteins in three angiosperm genomes identifies new subfamilies and reveals diverse evolutionary patterns
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