The GASA Gene Family in Cacao (Theobroma cacao, Malvaceae): Genome Wide Identification and Expression Analysis

Abdullah, Abdullah; Faraji, Sahar; Mehmood, Furrukh; Malik, Hafiz Muhammad Talha; Ahmed, Ibrar; Heidari, Parviz; Poczai, Péter

doi:10.3390/agronomy11071425

Cited by 47 publications

(33 citation statements)

References 85 publications

(89 reference statements)

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“…These genes are lowered in number as compared to previous reports of the Rosaceae family, in which 69-141 genes were reported (Zhang et al, 2019;Liu et al, 2020a). However, the number of genes within a gene family can vary among species (Rezaee et al, 2020;Song et al, 2020;Abdullah et al, 2021a;Faraji et al, 2021). The identified tcBAHDs showed high diversity based on sequence structure, physicochemical properties, functions, and distribution across the chromosome, which is in agreement with previous reports of the BAHD gene family (Moglia et al, 2016;Zhang et al, 2019;Ahmad et al, 2020b;Liu et al, 2020a).…”

Section: Discussionsupporting

confidence: 88%

“…Previous studies also revealed that phylogenetic clustering in the same group is not an indication of the same function (Nawaz et al, 2019;Abdullah et al, 2021a). Interestingly, unlike G. raimondii, the BAHD genes of C. capsularis and T. cacao were closely related in each cluster of the tree.…”

Section: Discussionmentioning

confidence: 86%

“…The three-dimensional structure of BAHD proteins was estimated by the protein homology/analogy Recognition Engine Version 2.0 (Phyre2) server (Kelley et al, 2015). The predicted structure of proteins was validated using the Ramachandran plot (Lovell et al, 2003) following a previous study (Abdullah et al, 2021a). The Beta Cavity webserver (Kim et al, 2015) was used to estimate molecular voids and pockets in proteins.…”

Section: Three-dimensional Protein Modeling and Molecular Dockingmentioning

confidence: 99%

“…In particular, genome-wide studies of the BAHD family have been reported in various species, including Populus (Yu et al, 2009), Arabidopsis (Yu et al, 2009), soybean (Ahmad et al, 2020b), Cynara cardunculus (Moglia et al, 2016), and in some species of Rosaceae (Zhang et al, 2019;Liu et al, 2020a). The chromosome-level genome assembly of T. cacao (Motamayor et al, 2013;Argout et al, 2017) provides resources for the characterization of gene families, which has led to the identification and characterization of WRKY (Dayanne et al, 2017), NAC (Shen et al, 2020), GASA (Abdullah et al, 2021a), and MGT (Heidari et al, 2021a) in cacao. However, genome-wide characterization of the BAHD gene family has not been reported to date.…”

Section: Introductionmentioning

confidence: 99%

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The BAHD Gene Family in Cacao (Theobroma cacao, Malvaceae): Genome-Wide Identification and Expression Analysis

et al. 2021

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The benzyl alcohol O-acetyl transferase, anthocyanin O-hydroxycinnamoyl transferase, N-hydroxycinnamoyl anthranilate benzoyl transferase, and deacetylvindoline 4-O-acetyltransferase (BAHD) enzymes play a critical role in regulating plant metabolites and affecting cell stability. In the present study, members of the BAHD gene family were recognized in the genome of Theobroma cacao and characterized using various bioinformatics tools. We found 27 non-redundant putative tcBAHD genes in cacao for the first time. Our findings indicate that tcBAHD genes are diverse based on sequence structure, physiochemical properties, and function. When analyzed with BAHDs of Gossypium raimondii and Corchorus capsularis clustered into four main groups. According to phylogenetic analysis, BAHD genes probably evolved drastically after their divergence. The divergence time of duplication events with purifying selection pressure was predicted to range from 1.82 to 15.50 MYA. Pocket analysis revealed that serine amino acid is more common in the binding site than other residuals, reflecting its key role in regulating the activity of tcBAHDs. Furthermore, cis-acting elements related to the responsiveness of stress and hormone, particularly ABA and MeJA, were frequently observed in the promoter region of tcBAHD genes. RNA-seq analysis further illustrated that tcBAHD13 and tcBAHD26 are involved in response to Phytophthora megakarya fungi. In conclusion, it is likely that evolutionary processes, such as duplication events, have caused high diversity in the structure and function of tcBAHD genes.

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Section: Discussionsupporting

confidence: 88%

Section: Discussionmentioning

confidence: 86%

Section: Three-dimensional Protein Modeling and Molecular Dockingmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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The BAHD Gene Family in Cacao (Theobroma cacao, Malvaceae): Genome-Wide Identification and Expression Analysis

et al. 2021

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“…Gene duplication and loss were the main evolutionary driving forces for the expansion or contraction, and duplicated genes could lead to gene redundancy [ 42 ]. Duplication events in the critical sites such as the CDS, and the promoter sequence cause members of a gene family to receive new functions [ 43 , 44 ].…”

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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Unveiling the defensive role of Snakin-3, a member of the subfamily III of Snakin/GASA peptides in potatoes

Nahirñak,

Almasia,

Lia

et al. 2024

Plant Cell Rep

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The GASA Gene Family in Cacao (Theobroma cacao, Malvaceae): Genome Wide Identification and Expression Analysis

Cited by 47 publications

References 85 publications

The BAHD Gene Family in Cacao (Theobroma cacao, Malvaceae): Genome-Wide Identification and Expression Analysis

The BAHD Gene Family in Cacao (Theobroma cacao, Malvaceae): Genome-Wide Identification and Expression Analysis

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

Unveiling the defensive role of Snakin-3, a member of the subfamily III of Snakin/GASA peptides in potatoes

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