Magnesium transporter Gene Family: Genome-Wide Identification and Characterization in Theobroma cacao, Corchorus capsularis, and Gossypium hirsutum of Family Malvaceae

Heidari, Parviz; Abdullah, Abdullah; Faraji, Sahar; Poczai, Péter

doi:10.3390/agronomy11081651

Cited by 51 publications

(34 citation statements)

References 87 publications

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“…3 C and 4 A). Those high variation in the sequence structure revealed that TIFY family members have acquired changes in their genome during evolution events that affected their functions [ 43 , 45 ].…”

Section: Discussionmentioning

confidence: 99%

Genome-wide identification and characterization of the TIFY gene family in kiwifruit

Tao

Jia

et al. 2022

BMC Genomics

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Background The TIFY gene family is a group of plant-specific transcription factors involved in regulation of plant growth and development and a variety of stress responses. However, the TIFY family has not yet been well characterized in kiwifruit, a popular fruit with important nutritional and economic value. Results A total of 27 and 21 TIFY genes were identified in the genomes of Actinidia eriantha and A. chinensis, respectively. Phylogenetic analyses showed that kiwifruit TIFY genes could be classified into four major groups, JAZ, ZML, TIFY and PPD, and the JAZ group could be further clustered into six subgroups (JAZ I to JAZ VI). Members within the same group or subgroup have similar exon-intron structures and conserved motif compositions. The kiwifruit TIFY genes are unevenly distributed on the chromosomes, and the segmental duplication events played a vital role in the expansion of the TIFY genes in kiwifruit. Syntenic analyses of TIFY genes between kiwifruit and other five plant species (including Arabidopsis thaliana, Camellia sinensis, Oryza sativa, Solanum lycopersicum and Vitis vinifera) and between the two kiwifruit species provided valuable clues for understanding the potential evolution of the kiwifruit TIFY family. Molecular evolutionary analysis showed that the evolution of kiwifruit TIFY genes was primarily constrained by intense purifying selection. Promoter cis-element analysis showed that most kiwifruit TIFY genes possess multiple cis-elements related to stress-response, phytohormone signal transduction and plant growth and development. The expression pattern analyses indicated that TIFY genes might play a role in different kiwifruit tissues, including fruit at specific development stages. In addition, several TIFY genes with high expression levels during Psa (Pseudomonas syringae pv. actinidiae) infection were identified, suggesting a role in the process of Pas infection. Conclusions In this study, the kiwifruit TIFY genes were identified from two assembled kiwifruit genomes. In addition, their basic physiochemical properties, chromosomal localization, phylogeny, gene structures and conserved motifs, synteny analyses, promoter cis-elements and expression patters were systematically examined. The results laid a foundation for further understanding the function of TIFY genes in kiwifruit, and provided a new potential approach for the prevention and treatment of Psa infection.

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Section: Discussionmentioning

confidence: 99%

Genome-wide identification and characterization of the TIFY gene family in kiwifruit

Tao

Jia

et al. 2022

BMC Genomics

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“…In addition to physiological data about hormones and plant growth promotion, we further analyzed the data at the molecular level by transcriptomic analysis experiment by using two kinds of samples, 100 ppm IBA-treated buds (T) and control buds (CK). In recent times, modern biotechnological, bioinformatics tools and big-data platforms have helped understand the functions of genes and gene families up to depth ( Hoang et al, 2017 ; Abdullah et al, 2021 ; Faraji et al, 2021 ; Heidari et al, 2021 ; Manechini et al, 2021 ). In this study, RNA-seq results revealed that The IBA treatment significantly influenced DEGs regulation.…”

Section: Discussionmentioning

confidence: 99%

Transcriptome Analysis Reveals a Gene Expression Pattern That Contributes to Sugarcane Bud Propagation Induced by Indole-3-Butyric Acid

Deng

et al. 2022

Front. Plant Sci.

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Sugarcane is a cash crop that plays an integral part in the sugar industry. The Sustainable Sugarcane Initiative (SSI) has been adopted globally, ensuring enough and aiming for more yield, helping increase disease-free sugarcane cultivation. Single-bud seeds could be the best approach for sugarcane cultivation. Indole-3-butyric acid (IBA) is a rooting agent utilized significantly in seedling propagation. Greenhouse experiment results discovered the significant growth promotion in sugarcane seedlings and accumulation of plant hormones at 100 ppm IBA. Next, we performed transcriptomic analysis of sugarcane buds using RNA sequencing and compared their gene expression during root development due to affect of IBA (100 ppm). A total of 113,475 unigenes were annotated with an average length of 836 bp (N50 = 1,536). The comparative RNA-seq study between the control (CK) and IBA-treated (T) buds showed significant differentially expressed unigenes (494 upregulated and 2086 downregulated). The IBA influenced major biological processes including metabolic process, the cellular process, and single-organism process. For cellular component category, cell, cell part, organelle, membrane, and organelle part were mainly affected. In addition, catalytic activity and binding were primarily affected in the molecular function categories. Furthermore, the expression of genes related to plant hormones and signaling pathways was analyzed by qRT-PCR, which was consistent with the RNA-seq expression profile. This study provides new insights into the IBA response to the bud sprouting in sugarcane based on RNA sequencing, and generated information could help further research on breeding improvement of sugarcane.

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“…Magnesium (Mg) is a vital element for living cells involved in many critical cellular activities [1][2][3]. For instance, Mg as a cofactor is essential for the activity of many enzymes (> 300 enzymes) such as kinase, polymerase, and H + -ATPase [4][5][6].…”

Section: Introductionmentioning

confidence: 99%

“…Based on sequence structure, MGTs have been classified into three groups, including MRS2, CorA, and NIPA [10]. MRS2 and CorA proteins are recognized by a tripeptide conserved region, GMN (Glycine-Methionine-Asparagine), and two or three transmembrane (TM) domains in their C-terminal ends [11], while NIPAs contain several TMs in its structure [3,10]. However, our knowledge of NIPA class is limited.…”

Section: Introductionmentioning

confidence: 99%

Genome-Wide Identification, and Molecular Evolution of The Magnesium Transporter (MGT) Gene Family in <em>Citrullus Lanatus</em> and <em>Cucumis Sativus</em>

Heidari¹,

Puresmaeli²,

Mora‐Poblete³

2022

Preprint

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Magnesium transporters (MGTs) play a prominent role in the absorption, transport and storage of magnesium in plant cells. In the present study, MGT gene family members were identified and characterized in two species of cucurbitaceae, including C. sativus and C. lanatus. 20, 19, and 20 MGT genes were recognized in C. lanatus, C. sativus, and C. melo, respectively. According to physicochemical properties, the members of each sub-class of MGTs in the species of cucurbitaceae showed the close relationship. Proteins from NIPA were identified as hydrophilic proteins with high stability. Based on phylogenetic analysis, MGT family members were classified into three groups, and NIPAs showed more diversity. Besides, duplication events were not identified between the MGT members in C. lanatus, and C. sativus. According to pocket analysis, residues such as L, V, S, I, and A were frequently observed in the binding sites of MGT proteins in both species. The prediction of post-translation modifications revealed that MSR2 proteins have high phosphorylation potential than other sub-classes in both studied plants. The expression profile of MGTs showed that MGTs are more expressed in root tissues. In addition, MGTs showed differential expression in response to abiotic/biotic stresses as well as hormone application and NIPAs were more induced in response to stimuli in watermelon. The results of this study, as the primary work of MGT gene family, can be used in programs related to cucurbitaceae breeding.

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Magnesium transporter Gene Family: Genome-Wide Identification and Characterization in Theobroma cacao, Corchorus capsularis, and Gossypium hirsutum of Family Malvaceae

Cited by 51 publications

References 87 publications

Genome-wide identification and characterization of the TIFY gene family in kiwifruit

Genome-wide identification and characterization of the TIFY gene family in kiwifruit

Transcriptome Analysis Reveals a Gene Expression Pattern That Contributes to Sugarcane Bud Propagation Induced by Indole-3-Butyric Acid

Genome-Wide Identification, and Molecular Evolution of The Magnesium Transporter (MGT) Gene Family in <em>Citrullus Lanatus</em> and <em>Cucumis Sativus</em>

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