The <i>bZIP</i> gene family in watermelon: genome-wide identification and expression analysis under cold stress and root-knot nematode infection

Yang, Youxin; Li, Jingwen; Li, Hao; Yang, Yingui; Guang, Yelan; Zhou, Yong

doi:10.7717/peerj.7878

Cited by 50 publications

(46 citation statements)

References 87 publications

(130 reference statements)

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“…AtbZIP16 has been reported to regulate early development of seedling by integrating hormone and light signalling pathways thereby promoting germination as well elongation of hypocotyl 43 . Under RL (Red Light) treatment, ClabZIP6 and ClabZIP56 were significantly induced while ClabZIP37 and ClabZIP22 were repressed in leaves of Citrullus lanatus 44 . Figure 9 depicts that changes in expression of CtbZIPs under GA3 and light reveal that some of CtbZIP genes might be directly or indirectly affected by light intensity and hormones.…”

Section: Discussionmentioning

confidence: 99%

Genome-wide identification and expression analysis of bZIP gene family in Carthamus tinctorius L.

ShangGuan

et al. 2020

Sci Rep

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The basic leucine zipper (bZIP) is a widely known transcription factors family in eukaryotes. In plants, the role of bZIP proteins are crucial in various biological functions such as plant growth and development, seed maturation, response to light signal and environmental stress. To date, bZIP protein family has been comprehensively identified in Arabidopsis, castor, rice, ramie, soybean and other plant species, however, the complete genome-wide investigation of Carthamus tinctorius-bZIP family still remains unexplained. Here, we identified 52 putative bZIP genes from Carthamus tinctorius using a draft genome assembly and further analyzed their evolutionary classification, physicochemical properties, Conserved domain analysis, functional differentiation and the investigation of expression level in different tissues. Based on the common bZIP domain, CtbZIP family were clustered into 12 subfamilies renamed as (A–J, S, X), of which the X is a unique subfamily to Carthamus tinctorius. A total of 20 conserved protein motifs were found in CtbZIP proteins. The expression profiling of CtbZIP genes deciphered their tissue-specific pattern. Furthermore, the changes in CtbZIP transcript abundance suggested that their transcription regulation could be highly influenced by light intensity and hormones. Collectively, this study highlights all functional and regulatory elements of bZIP transcription factors family in Carthamus tinctorius which may serve as potential candidates for functional characterization in future.

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Section: Discussionmentioning

confidence: 99%

Genome-wide identification and expression analysis of bZIP gene family in Carthamus tinctorius L.

ShangGuan

et al. 2020

Sci Rep

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“…As one of the largest transcription factor families, basic leucine zipper (bZIP) family transcription factors play key roles in controlling plant development and stress responses [31]. bZIP genes have been reported to be involved in various flower developmental processes in plants, including pollen development, the floral transition and flower initiation [32,33].…”

Section: Many Transcription Factors Are Implicated In the Developmentmentioning

confidence: 99%

Pistils may be required for anthocyanin synthesis —— the whole-transcriptome analysis of mutant and normal capitula of Chrysanthemum morifolium

Liu

Luo

Chen

et al. 2020

Preprint

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Background Chrysanthemum morifolium is one of the most economically important and popular floricultural crops in Asteraceae. Chrysanthemums have many different flower colors and shapes. However, the molecular mechanism controlling the development of chrysanthemum floral colors and shapes is still an enigma. We obtained a cut chrysanthemum variety with mutant capitula in which the ray florets became green and the inside pistils became vegetative buds, while normal capitula have many rounds of purple ray florets and few disc florets. Results We conducted whole-transcriptome analysis of differentially expressed genes (DEGs) between the mutant and normal capitula using third-generation and second-generation sequencing techniques. We identified DEGs between the mutant and normal capitula to reveal important regulators underlying their differential development. Regulatory genes involved in the photoperiod pathway and the control of floral organ identification as well as important functional genes in the anthocyanin synthesis pathway were also identified. Therefore, a list of candidate genes for studying flower development and anthocyanin synthesis in chrysanthemums was generated. Qualitative analysis of pigments in the florets of normal and mutant capitula revealed anthocyanins were synthesized and accumulated in the florets of normal capitula, but not in the florets of mutant capitula. It was indicated that pistils may be required for anthocyanin synthesis in chrysanthemums. Conclusions These results will help to elucidate the molecular mechanisms of floral organ development and will contribute to the development of techniques for studying flower shape and color regulation to promote breeding in chrysanthemum.

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“…To assess the expression profiles of watermelon CYP74 genes during RKN infection, the raw RNA-seq data under the treatments of CK (white light and water solution), RL (red light and water solution), RKN (white light and M. incognita infection), and RR (red light and M. incognita infection) were obtained and analyzed [23]. The expression levels of watermelon CYP74 genes were retrieved and estimated with FPKM (fragments per kilobase of exon per million fragments mapped) values as previously described [21]. The differentially expressed genes were identified with a cutoff of |fold change| ≥ 1.5.…”

Section: Expression Profiles Of Watermelon Cyp74 Genes Based On Rna-smentioning

confidence: 99%

“…Matsum. & Nakai) is an agricultural crop with high nutritional and economic values, but it is rather susceptible to various biotic and abiotic stresses during growth and development [21]. The root-knot nematodes (RKNs, Meloidogyne incognita) mainly infect the roots of host plants and increase susceptibility to other pathogenic diseases, and severely affect foliar growth and fruit yield of host plants [21,22].…”

mentioning

confidence: 99%

“…& Nakai) is an agricultural crop with high nutritional and economic values, but it is rather susceptible to various biotic and abiotic stresses during growth and development [21]. The root-knot nematodes (RKNs, Meloidogyne incognita) mainly infect the roots of host plants and increase susceptibility to other pathogenic diseases, and severely affect foliar growth and fruit yield of host plants [21,22]. In our previous report, red light (RL) exposure of watermelon leaves enhanced the systemic defense of the plant to RKN, which could be attributed to JAand salicylic acid (SA)-dependent signaling, antioxidant activity, and redox homeostasis [23].…”

mentioning

confidence: 99%

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The CYP74 Gene Family in Watermelon: Genome-Wide Identification and Expression Profiling Under Hormonal Stress and Root-Knot Nematode Infection

Zhou

Guang

et al. 2019

Agronomy

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Allene oxide synthase (AOS) and hydroperoxide lyase (HPL), members of the CYP74 gene family, are branches of the oxylipin pathway and play vital roles in plant responses to a number of stresses. In this study, four HPL genes and one AOS gene were identified in the watermelon genome, which were clustered into three subfamilies (CYP74A, CYP74B and CYP74C). Sequence analysis revealed that most HPL and AOS proteins from various plants contain representative domains, including Helix-I region, Helix-K region (ExxR) and Heme-binding domain. A number of development-, stress-, and hormone-related cis-elements were found in the promoter regions of the ClAOS and ClHPL genes, and the detected ClAOS and ClHPL genes were differentially expressed in different tissues and fruit development stages, as well as in response to various hormones. In addition, red light could enhance the expression of ClAOS in root-knot nematode-infected leaves and roots of watermelon, implying that ClAOS might play a primary role in red light-induced resistance against root-knot nematodes. These findings lay a foundation for understanding the specific function of CYP74 genes in watermelon.Agronomy 2019, 9, 872 2 of 17 isomerization or dehydration of fatty acid hydroperoxides and require neither molecular oxygen nor NAD(P)H-dependent cytochrome P450-reductase [1,2,6].CYP74 enzymes are broadly classified into four subfamilies (CYP74A, CYP74B, CYP74C, and CYP74D) based on their evolutionary heritage and relationship with the diversity of oxylipin structure [6]. AOS and DES members constitute the CYP74A and CYP74D subfamily, respectively, while CYP74B and CYP74C subfamilies contain enzymes with HPL activity [5,7]. In addition, AOS enzymes can be classified into three different types: The first two types can use either 13-hydroperoxide derivatives or 9-hydroperoxide derivatives as the substrate (13-AOS and 9-AOS, respectively), while the third type can use both of them (9/13-AOS) as the substrate [4,8]. Similarly, three types of HPL enzymes named as 13-HPL, 9-HPL, and 9/13-HPL were also reported in a number of plant species [9]. To date, AOS and HPL genes have been cloned and functionally characterized from a number of plant species, such as tomato (Solanum lycopersicum L. (Solanaceae)) [10,11], tobacco (Nicotiana attenuate Torr. ex S.Watson) [12], rice (Oryza sativa L.) [13,14], and barrel medic (Medicago truncatula Gaertn.) [15], whereas DES genes have been isolated in very few plants [16][17][18][19][20]. These findings reveal that plant CYP74 family genes are indispensable for oxylipin biosynthesis, and play important roles in plant growth and development, as well as in plant defense to various abiotic and biotic stresses.Watermelon (Citrullus lanatus (Thunb.) Matsum. & Nakai) is an agricultural crop with high nutritional and economic values, but it is rather susceptible to various biotic and abiotic stresses during growth and development [21]. The root-knot nematodes (RKNs, Meloidogyne incognita) mainly infect the roots of host plants and increase sus...

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The bZIP gene family in watermelon: genome-wide identification and expression analysis under cold stress and root-knot nematode infection

Cited by 50 publications

References 87 publications

Genome-wide identification and expression analysis of bZIP gene family in Carthamus tinctorius L.

Genome-wide identification and expression analysis of bZIP gene family in Carthamus tinctorius L.

Pistils may be required for anthocyanin synthesis —— the whole-transcriptome analysis of mutant and normal capitula of Chrysanthemum morifolium

The CYP74 Gene Family in Watermelon: Genome-Wide Identification and Expression Profiling Under Hormonal Stress and Root-Knot Nematode Infection

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