Dataset Information

Genome-Wide Identification and Characterization of the Potato IQD Family During Development and Stress.

ABSTRACT: Calmodulin-binding proteins belong to the IQ67 domain (IQD) gene family and play essential roles in plant development and stress responses. However, the role of IQD gene family in potato (Solanum tuberosum L.) is yet to be known. In the present study, 23 StIQDs were identified in the potato genome and named StIQD1 to StIQD23. They were unevenly distributed on 10 of the 12 chromosomes. Phylogenetic analysis divided the IQDs into four subfamilies (IQD I-IV). StIQDs found in three of the four subfamilies. Synteny analysis confirmed that potato and tomato shared a close evolutionary relationship. Besides, RNA-Seq data analysis revealed that the expression of 19 of the 23 StIQDs was detected in at least one of the 12 tissues, and some of which showed a tissue-specific pattern. Quantitative reverse transcriptase-polymerase chain reaction results further confirmed that 14 StIQDs responded differently to various abiotic stresses, including drought, extreme temperature, and CaCl₂ treatment, suggesting their significance in stress response. This study presents a comprehensive overview of the potato IQD gene family and lays a foundation for further analysis of the StIQDs functions in plant development and stress response.

SUBMITTER: Mei C

PROVIDER: S-EPMC8354571 | biostudies-literature | 2021

REPOSITORIES: biostudies-literature

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Genome-Wide Identification and Characterization of the Potato IQD Family During Development and Stress.

Mei Chao C Liu Yuwei Y Dong Xue X Song Qianna Q Wang Huijie H Shi Hongwei H Feng Ruiyun R

Frontiers in genetics 20210727

Calmodulin-binding proteins belong to the IQ67 domain (IQD) gene family and play essential roles in plant development and stress responses. However, the role of IQD gene family in potato (Solanum tuberosum L.) is yet to be known. In the present study, 23 StIQDs were identified in the potato genome and named StIQD1 to StIQD23. They were unevenly distributed on 10 of the 12 chromosomes. Phylogenetic analysis divided the IQDs into four subfamilies (IQD I-IV). S ...[more]

PMID: 34386041

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Project description:Adenylate kinase (ADK) is widely distributed in organisms and plays an important role in cellular energy homeostasis. In plants, ADK has important functions in plant growth and development regulation as well as in adaptation to the environment. However, little information is available about the ADK genes in tomato (Solanum lycopersicum), an important economic crop. To investigate the characteristics and functions of ADK genes in tomato, a total of 11 ADK genes were identified and named according to their chromosomal locations. The ADK family in Arabidopsis, tomato, potato, and rice was divided into six groups, and motif analysis revealed that each SlADK protein contained five to eight conserved motifs. A total of 4 to 19 exons were identified in tomato ADK gene family members, and interestingly, most members possessed 4 exons. Several stress response elements were identified in the promoter regions of SlADKs. The 11 SlADKs were randomly distributed on 9 of the 12 tomato chromosomes. Three duplication events were observed between tomato chromosomes, and a high degree of conservation of synteny was demonstrated between tomato and potato. The online TomExpress platform prediction revealed that SlADKs were expressed in various tissues and organs, basically consistent with the data obtained from real-time quantitative PCR (qPCR). The qPCR verification was also performed to determine the expression level of SlADKs and demonstrated that the genes responded to multiple abiotic stresses, such as drought, salt, and cold. Besides, the qPCR results showed that SlADK transcription was responsive to most of the applied hormone treatment. For correlation network analysis under 44 global conditions, the results showed that the number of 17, 3, 4, and 6 coexpressed genes matched with SlADK5, 8, 9, and 11, respectively. For specific gene function analysis, expression of SlADK10 was inhibited using virus-induced gene silencing (VIGS). Compared to wild-type plants, plants with silenced SlADK10 gene had poor drought resistance, indicating SlADK10 regulated drought tolerance of tomato positively. In summary, the information provided in the present study will be helpful to understand the evolutionary relationship and their roles of tomato ADK gene family in further research.

Project description:BackgroundMADS-box transcription factors, besides being involved in floral organ specification, have also been implicated in several aspects of plant growth and development. In recent years, there have been reports on genomic localization, protein motif structure, phylogenetic relationships, gene structure and expression of the entire MADS-box family in the model plant system, Arabidopsis. Though there have been some studies in rice as well, an analysis of the complete MADS-box family along with a comprehensive expression profiling was still awaited after the completion of rice genome sequencing. Furthermore, owing to the role of MADS-box family in flower development, an analysis involving structure, expression and functional aspects of MADS-box genes in rice and Arabidopsis was required to understand the role of this gene family in reproductive development.ResultsA genome-wide molecular characterization and microarray-based expression profiling of the genes encoding MADS-box transcription factor family in rice is presented. Using a thorough annotation exercise, 75 MADS-box genes have been identified in rice and categorized into MIKCc, MIKC*, Malpha, Mbeta and Mgamma groups based on phylogeny. Chromosomal localization of these genes reveals that 16 MADS-box genes, mostly MIKCc-type, are located within the duplicated segments of the rice genome, whereas most of the M-type genes, 20 in all, seem to have resulted from tandem duplications. Nine members belonging to the Mbeta group, which was considered absent in monocots, have also been identified. The expression profiles of all the MADS-box genes have been analyzed under 11 temporal stages of panicle and seed development, three abiotic stress conditions, along with three stages of vegetative development. Transcripts for 31 genes accumulate preferentially in the reproductive phase, of which, 12 genes are specifically expressed in seeds, and six genes show expression specific to panicle development. Differential expression of seven genes under stress conditions is also evident. An attempt has been made to gain insight into plausible functions of rice MADS-box genes by collating the expression data of functionally validated genes in rice and Arabidopsis.ConclusionOnly a limited number of MADS genes have been functionally validated in rice. A comprehensive annotation and transcriptome profiling undertaken in this investigation adds to our understanding of the involvement of MADS-box family genes during reproductive development and stress in rice and also provides the basis for selection of candidate genes for functional validation studies.

Dataset Information

Genome-Wide Identification and Characterization of the Potato IQD Family During Development and Stress.

Publications

Genome-Wide Identification and Characterization of the Potato <i>IQD</i> Family During Development and Stress.

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