Genome-wide identification and expression analysis of the JAZ gene family in turnip

Jia, Kai; Yan, Cunyao; Zhang, Jing; Cheng, Yunxia; Li, Wenwen; Yan, Huimin; Gao, Jie

doi:10.1038/s41598-021-99593-2

Cited by 12 publications

(8 citation statements)

References 51 publications

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“…Tandem and segmental replication events were observed in the MsOSCA gene family (Figure 4A), indicating that gene replication was also the driving force for the expansion of MsOSCA gene family members. Previous studies have shown that gene pairs with high homology in the gene family may have collinearity, which makes them have similar biological characteristics and expression patterns (Jia et al, 2021). In the present study, we found that MsOSCAs had collinearity with Medicago truncatula and Arabidopsis, suggesting that they might have similar functions, which requires further investigation.…”

Section: Discussionsupporting

confidence: 46%

Genome-wide investigation and expression analysis of OSCA gene family in response to abiotic stress in alfalfa

Li,

Wang,

et al. 2023

Front. Plant Sci.

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Alfalfa is an excellent leguminous forage crop that is widely cultivated worldwide, but its yield and quality are often affected by drought and soil salinization. Hyperosmolality-gated calcium-permeable channel (OSCA) proteins are hyperosmotic calcium ion (Ca2+) receptors that play an essential role in regulating plant growth, development, and abiotic stress responses. However, no systematic analysis of the OSCA gene family has been conducted in alfalfa. In this study, a total of 14 OSCA genes were identified from the alfalfa genome and classified into three groups based on their sequence composition and phylogenetic relationships. Gene structure, conserved motifs and functional domain prediction showed that all MsOSCA genes had the same functional domain DUF221. Cis-acting element analysis showed that MsOSCA genes had many cis-regulatory elements in response to abiotic or biotic stresses and hormones. Tissue expression pattern analysis demonstrated that the MsOSCA genes had tissue-specific expression; for example, MsOSCA12 was only expressed in roots and leaves but not in stem and petiole tissues. Furthermore, RT–qPCR results indicated that the expression of MsOSCA genes was induced by abiotic stress (drought and salt) and hormones (JA, SA, and ABA). In particular, the expression levels of MsOSCA3, MsOSCA5, MsOSCA12 and MsOSCA13 were significantly increased under drought and salt stress, and MsOSCA7, MsOSCA10, MsOSCA12 and MsOSCA13 genes exhibited significant upregulation under plant hormone treatments, indicating that these genes play a positive role in drought, salt and hormone responses. Subcellular localization results showed that the MsOSCA3 protein was localized on the plasma membrane. This study provides a basis for understanding the biological information and further functional analysis of the MsOSCA gene family and provides candidate genes for stress resistance breeding in alfalfa.

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Section: Discussionsupporting

confidence: 46%

Genome-wide investigation and expression analysis of OSCA gene family in response to abiotic stress in alfalfa

Li,

Wang,

et al. 2023

Front. Plant Sci.

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“…Multiple TIFY protein sequences were compared, and a phylogenetic tree was constructed using the maximum likelihood method. Based on the results of the phylogenetic tree and the classification of TIFY proteins in other species [ 23 – 25 ], the TIFY proteins were categorized into nine subfamilies, namely, JAZ I-VI, PPD, TIFY, and ZML (Fig. 2 ).…”

Section: Resultsmentioning

confidence: 99%

Genome-wide identification and expression analysis of the Eriobotrya japonica TIFY gene family reveals its functional diversity under abiotic stress conditions

Li,

Wen,

Zhu

et al. 2024

BMC Genomics

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Background Plant-specific TIFY proteins are widely found in terrestrial plants and play important roles in plant adversity responses. Although the genome of loquat at the chromosome level has been published, studies on the TIFY family in loquat are lacking. Therefore, the EjTIFY gene family was bioinformatically analyzed by constructing a phylogenetic tree, chromosomal localization, gene structure, and adversity expression profiling in this study. Results Twenty-six EjTIFY genes were identified and categorized into four subfamilies (ZML, JAZ, PPD, and TIFY) based on their structural domains. Twenty-four EjTIFY genes were irregularly distributed on 11 of the 17 chromosomes, and the remaining two genes were distributed in fragments. We identified 15 covariate TIFY gene pairs in the loquat genome, 13 of which were involved in large-scale interchromosomal segmental duplication events, and two of which were involved in tandem duplication events. Many abiotic stress cis-elements were widely present in the promoter region. Analysis of the Ka/Ks ratio showed that the paralogous homologs of the EjTIFY family were mainly subjected to purifying selection. Analysis of the RNA-seq data revealed that a total of five differentially expressed genes (DEGs) were expressed in the shoots under gibberellin treatment, whereas only one gene was significantly differentially expressed in the leaves; under both low-temperature and high-temperature stresses, there were significantly differentially expressed genes, and the EjJAZ15 gene was significantly upregulated under both low- and high-temperature stress. RNA-seq and qRT-PCR expression analysis under salt stress conditions revealed that EjJAZ2, EjJAZ4, and EjJAZ9 responded to salt stress in loquat plants, which promoted resistance to salt stress through the JA pathway. The response model of the TIFY genes in the jasmonic acid pathway under salt stress in loquat was systematically summarized. Conclusions These results provide a theoretical basis for exploring the characteristics and functions of additional EjTIFY genes in the future. This study also provides a theoretical basis for further research on breeding for salt stress resistance in loquat. RT-qPCR analysis revealed that the expression of one of the three EjTIFY genes increased and the expression of two decreased under salt stress conditions, suggesting that EjTIFY exhibited different expression patterns under salt stress conditions.

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“…The JAZ gene family is present in a wide range of plants. There are 23 JAZs in A. thaliana [ 51 ], 15 in rice [ 52 ], 16 in maize [ 48 ], 36 in turnip [ 53 ], 30 in cotton [ 54 ], and 11 in grape [ 55 ]. We found that SLJAZ5 was located on chromosome 3; SLJAZ6 and SLJAZ7 on chromosome 6; SLJAZ8 on chromosome 7; SLJAZ9 , SLJAZ10 , SLJAZ11 , and SLJAZ12 on chromosome 8; SLJAZ13 on chromosome 9; SLJAZ14 on chromosome 11; and SLJAZ15 and SLJAZ16 on chromosome 12.…”

Section: Discussionmentioning

confidence: 99%

Jasmonate ZIM Domain Protein (JAZ) Gene SLJAZ15 Increases Resistance to Orobanche aegyptiaca in Tomato

Chen,

Zhang,

et al. 2024

Plants

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Orobanche aegyptiaca Pers. is a holoparasitic plant that severely reduces tomato (Solanum lycopersicum L.) production in China. However, there is a lack of effective control methods and few known sources of genetic resistance. In this study, we focused on key genes in the JAZ family, comparing the JAZ family in Arabidopsis thaliana (L. Heynh.) to the tomato genome. After identifying the JAZ family members in S. lycopersicum, we performed chromosomal localization and linear analysis with phylogenetic relationship analysis of the JAZ family. We also analyzed the gene structure of the JAZ gene family members in tomato and the homology of the JAZ genes among the different species to study their relatedness. The key genes for O. aegyptiaca resistance were identified using VIGS (virus-induced gene silencing), and the parasitization rate of silenced tomato plants against O. aegyptiaca increased by 47.23–91.13%. The genes were localized in the nucleus by subcellular localization. Heterologous overexpression in A. thaliana showed that the key gene had a strong effect on the parasitization process of O. aegyptiaca, and the overexpression of the key gene reduced the parasitization rate of O. aegyptiaca 1.69-fold. Finally, it was found that the SLJAZ15 gene can positively regulate the hormone content in tomato plants and affect plant growth and development, further elucidating the function of this gene.

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Genome-wide identification and expression analysis of the JAZ gene family in turnip

Cited by 12 publications

References 51 publications

Genome-wide investigation and expression analysis of OSCA gene family in response to abiotic stress in alfalfa

Genome-wide investigation and expression analysis of OSCA gene family in response to abiotic stress in alfalfa

Genome-wide identification and expression analysis of the Eriobotrya japonica TIFY gene family reveals its functional diversity under abiotic stress conditions

Jasmonate ZIM Domain Protein (JAZ) Gene SLJAZ15 Increases Resistance to Orobanche aegyptiaca in Tomato

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