Genome-wide identification and expression analysis of extensin genes in tomato

Ding, Qiangqiang; Yang, Xinxin; Pi, Ying; Li, Zhifei; Xue, Juan; Chen, Hong; Li, Yang; Wu, Hongmiao

doi:10.1016/j.ygeno.2020.07.029

Cited by 19 publications

(10 citation statements)

References 31 publications

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“…The number of introns were variable in tcGASA within genes that cluster together in phylogeny. The loss and gain of introns occurs in the course of evolution within protein-coding genes of the plants and is also reported within the GASA of other plant species [13,18,[60][61][62].…”

Section: Discussionmentioning

confidence: 69%

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

et al. 2021

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The gibberellic acid-stimulated Arabidopsis (GASA/GAST) gene family is widely distributed in plants and involved in various physiological and biological processes. These genes also provide resistance to abiotic and biotic stresses, including antimicrobial, antiviral, and antifungal. We are interested in characterizing the GASA gene family and determining its role in various physiological and biological process in Theobroma cacao. Here, we report 17 tcGASA genes distributed on six chromosomes in T. cacao. The gene structure, promoter region, protein structure and biochemical properties, expression, and phylogenetics of all tcGASAs were analyzed. Phylogenetic analyses divided tcGASA proteins into five groups. Among 17 tcGASA genes, nine segmentally duplicating genes were identified which formed four pairs and cluster together in phylogenetic tree. Differential expression analyses revealed that most of the tcGASA genes showed elevated expression in the seeds (cacao food), implying their role in seed development. The differential expression of tcGASAs was recorded between the tolerant and susceptible cultivars of cacao, which indicating their possible role as fungal resistant. Our findings provide new insight into the function, evolution, and regulatory system of the GASA family genes in T. cacao and may suggest new target genes for development of fungi-resistant cacao varieties in breeding programs.

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Section: Discussionmentioning

confidence: 69%

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

et al. 2021

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Section: Discussionmentioning

confidence: 70%

The GASA Gene Family in Theobroma cacao: Genome wide Identification and Expression Analysis

Abdullah

Faraji

Mehmood

et al. 2021

Preprint

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The gibberellic acid-stimulated Arabidopsis (GASA/GAST) gene family is widely distributed in plants. The role of the GASA gene family has been reported previously in various physiological and biological processes, such as cell division, root and seed development, stem growth, and fruit ripening. These genes also provide resistance to abiotic and biotic stresses including antimicrobial, antiviral, and antifungal. Here, we report 17 tcGASA genes in Theobroma cacao L. distributed on six chromosomes. The gene structure, promoter-region sequences, protein structure, and biochemical properties, expression, and phylogenetics of all tcGASAs were analyzed. Phylogenetic analyses divided tcGASA proteins into five groups. The nine segmentally duplicating genes form four pairs and cluster together in phylogenetic tree. Purifying selection pressure was recorded on tcGASA, including duplicated genes. Several stress/hormone-responsive cis-regulatory elements were also recognized in the promoter region of tcGASAs. Differential expression analyses revealed that most of the tcGASA genes showed elevated expression in the seeds (cacao food), implying their role in seed development. The black rod disease of genus Phytophthora caused up to 20–25% loss (700,000 metric tons) in world cacao production. The role of tcGASA genes in conferring fungal resistance was also explored based on RNAseq data against Phytophthora megakarya. The differential expression of tcGASA genes was recorded between the tolerant and susceptible cultivars of cacao plants, which were inoculated with the fungus for 24h and 72h. This differential expression indicating possible role of tcGASA genes to fungal resistant in cacao. Our findings provide new insight into the function, evolution, and regulatory system of the GASA family genes in T. cacao and provide new target genes for development of fungi-resistant cacao varieties in breeding programs.

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“…Our results revealed two BAHD genes, tcBAHD13 (a vinorine synthase) and tcBAHD26 (an Omega-hydroxypalmitate Oferuloyl transferase) that were upregulated specifically in resistant cultivars, indicating that these two genes are potentially involved in the P. megakarya fungi response. Although, these results were not validated from qualitative PCR (qPCR), previous studies reported high consistency between the result of RNAseq and qPCR, i.e., in the GASA gene family in soybean (Ahmad et al, 2019) and apple (Fan et al, 2017), extensin genes in tomato (Ding et al, 2020), papain-like cysteine proteases in rice (Niño et al, 2020) and cotton (Zhang et al, 2019), and auxin/indole-3-acetic acid in pepper (Waseem et al, 2018). Nevertheless, a functional study is required to draw a complete conclusion.…”

Section: Discussionmentioning

confidence: 88%

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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Genome-wide identification and expression analysis of extensin genes in tomato

Cited by 19 publications

References 31 publications

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

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

The GASA Gene Family in Theobroma cacao: Genome wide Identification and Expression Analysis

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

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