Browsing by Author "Hu, Yuchao"

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    Genome-Wide Identification of GASA Gene Family in Ten Cucurbitaceae Species and Expression Analysis in Cucumber
    (MDPI, 2022) Zhang, Kaijing; Hu, Yuchao; Yang, Dekun; Yan, Congsheng; Li, Nanyang; Li, Ziang; Njogu, Martin Kagiki; Wang, Xing; Jia, Li; ; ;
    Gibberellic acid-stimulated in Arabidopsis (GASA), a unique small molecular protein of plants, plays an essential role in plant growth and development. The GASA family genes have been identified and studied in many plants. However, the identification of GASA gene family in Cucurbitaceae species has not been reported yet. Therefore, in this study, based on the available genome information on the Cucurbitaceae species, the GASA family genes in 10 Cucurbitaceae species including cucumber (Cucumis sativus), watermelon (Citrullus lanatus), melon (Cucumis melo), pumpkin (Cucurbita moschata), wax gourd (Benincasa hispida), sponge gourd (Luffa cylindrica), bottle gourd (Lagenaria siceraria), bitter gourd (Momordica charantia), chayote (Sechium edule), and snake gourd (Trichosanthes anguina) were identified with bioinformatics methods. To understand the molecular functions of GASA genes, the expression pattern analysis of cucumber GASA family genes in different tissues and stress responses were also analyzed. The results showed that a total of 114 GASA genes were identified in the 10 Cucurbitaceae species, which were divided into three subfamilies. Synteny analysis of GASA genes among cucumber, Arabidopsis and rice showed that nine cucumber GASA genes were colinear with 12 Arabidopsis GASA genes, and six cucumber GASA genes were colinear with six rice GASA genes. The cis-acting elements analysis implied that the cucumber GASA genes contained many cis-elements associated with stress and hormone response. Tissue-specific expression analysis of cucumber GASA family genes revealed that only the CsaV3_2G029490 gene was lowly or not expressed in all tissues, the CsaV3_3G041480 gene was highly expressed in all tissues, and the other seven GASA genes showed tissue-specific expression patterns. Furthermore, nine cucumber GASA family genes exhibited different degrees of regulatory response under GA, abiotic and biotic stresses. Two cucumber GASA genes, CsaV3_3G042060 and CsaV3_3G041480, were differentially expressed under multiple biotic and abiotic stresses, which indicated that these two GASA genes play important roles in the growth and development of cucumber.
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    Genome-Wide Identification of GASA Gene Family in Ten Cucurbitaceae Species and Expression Analysis in Cucumber
    (MDPI, 2022-08-22) Zhang, Kaijing; Hu, Yuchao; Yang, Dekun; Yan, Congsheng; Li, Nanyang; Li, Ziang; Njogu, Martin Kagiki; Wang, Xing; Jia, Li
    Gibberellic acid-stimulated in Arabidopsis (GASA), a unique small molecular protein of plants, plays an essential role in plant growth and development. The GASA family genes have been identified and studied in many plants. However, the identification of GASA gene family in Cucurbitaceae species has not been reported yet. Therefore, in this study, based on the available genome information on the Cucurbitaceae species, the GASA family genes in 10 Cucurbitaceae species including cucumber (Cucumis sativus), watermelon (Citrullus lanatus), melon (Cucumis melo), pumpkin (Cucurbita moschata), wax gourd (Benincasa hispida), sponge gourd (Luffa cylindrica), bottle gourd (Lagenaria siceraria), bitter gourd (Momordica charantia), chayote (Sechium edule), and snake gourd (Trichosanthes anguina) were identified with bioinformatics methods. To understand the molecular functions of GASA genes, the expression pattern analysis of cucumber GASA family genes in different tissues and stress responses were also analyzed. The results showed that a total of 114 GASA genes were identified in the 10 Cucurbitaceae species, which were divided into three subfamilies. Synteny analysis of GASA genes among cucumber, Arabidopsis and rice showed that nine cucumber GASA genes were colinear with 12 Arabidopsis GASA genes, and six cucumber GASA genes were colinear with six rice GASA genes. The cis-acting elements analysis implied that the cucumber GASA genes contained many cis-elements associated with stress and hormone response. Tissue-specific expression analysis of cucumber GASA family genes revealed that only the CsaV3_2G029490 gene was lowly or not expressed in all tissues, the CsaV3_3G041480 gene was highly expressed in all tissues, and the other seven GASA genes showed tissue-specific expression patterns. Furthermore, nine cucumber GASA family genes exhibited different degrees of regulatory response under GA, abiotic and biotic stresses. Two cucumber GASA genes, CsaV3_3G042060 and CsaV3_3G041480, were differentially expressed under multiple biotic and abiotic stresses, which indicated that these two GASA genes play important roles in the growth and development of cucumber.
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    Genome-Wide Identification, Phylogenetic and Expression Pattern Analysis of GATA Family Genes in Cucumber (Cucumis sativus L.)
    (MDPI, 2021) Zhang, Kaijing; Jia, Li; Yang, Dekun; Hu, Yuchao; Njogu, Martin Kagiki; Wang, Panqiao; Lu, Xiaomin; Yan, Congsheng; ; ;
    GATA transcription factors are a class of transcriptional regulatory proteins that contain a characteristic type-IV zinc finger DNA-binding domain, which play important roles in plant growth and development. The GATA gene family has been characterized in various plant species. However, GATA family genes have not been identified in cucumber. In this study, 26 GATA family genes were identified in cucumber genome, whose physicochemical characteristics, chromosomal distributions, phylogenetic tree, gene structures conserved motifs, cis-regulatory elements in promoters, homologous gene pairs, downstream target genes were analyzed. Tissue expression profiles of cucumber GATA family genes exhibited that 17 GATA genes showed constitutive expression, and some GATA genes showed tissue-specific expression patterns. RNA-seq analysis of green and virescent leaves revealed that seven GATA genes might be involved in the chloroplast development and chlorophyll biosynthesis. Importantly, expression patterns analysis of GATA genes in response to abiotic and biotic stresses indicated that some GATA genes respond to either abiotic stress or biotic stress, some GATA genes such as Csa2G162660, Csa3G017200, Csa3G165640, Csa4G646060, Csa5G622830 and Csa6G312540 were simultaneously functional in resistance to abiotic and biotic stresses. Overall, this study will provide useful information for further analysis of the biological functions of GATA factors in cucumber