Comparative identification, characterization, and expression analysis of bZIP gene family members in watermelon and melon genomes

Unel, Necdet Mehmet; Cetin, Fadime; Karaca, Yasin; Altunoğlu, Yasemin Çelik; Baloğlu, Mehmet Cengiz

doi:10.1007/s10725-018-0465-6

Cited by 18 publications

(18 citation statements)

References 64 publications

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“…Most OebZIP genes in the same subgroup possess the same features (Figure 2), as also reported for apple [35], melon [55], and cassava [33], i.e., the OebZIP genes in each S subgroup have one exon and the motif distribution is simple, just containing motif 1 (basic area) and motif 4 (Leu area). Some specific motifs (motif7, motif10) only exist in a specific subgroup (subgroup A).…”

Section: Evolutionary Analysis Of the Oebzip Gene Familysupporting

confidence: 73%

Genome-Wide Identification, Evolutionary Patterns, and Expression Analysis of bZIP Gene Family in Olive (Olea europaea L.)

Rong

Cheng

et al. 2020

Genes

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Olive (Olea europaea.L) is an economically important oleaginous crop and its fruit cold-pressed oil is used for edible oil all over the world. The basic region-leucine zipper (bZIP) family is one of the largest transcription factors families among eukaryotic organisms; its members play vital roles in environmental signaling, stress response, plant growth, seed maturation, and fruit development. However, a comprehensive report on the bZIP gene family in olive is lacking. In this study, 103 OebZIP genes from the olive genome were identified and divided into 12 subfamilies according to their genetic relationship with 78 bZIPs of A. thaliana. Most OebZIP genes are clustered in the subgroup that has a similar gene structure and conserved motif distribution. According to the characteristics of the leucine zipper region, the dimerization characteristics of 103 OebZIP proteins were predicted. Gene duplication analyses revealed that 22 OebZIP genes were involved in the expansion of the bZIP family. To evaluate the expression patterns of OebZIP genes, RNA-seq data available in public databases were analyzed. The highly expressed OebZIP genes and several lipid synthesis genes (LPGs) in fruits of two varieties with different oil contents during the fast oil accumulation stage were examined via qRT-PCR. By comparing the dynamic changes of oil accumulation, OebZIP1, OebZIP7, OebZIP22, and OebZIP99 were shown to have a close relationship with fruit development and lipid synthesis. Additionally, some OebZIP had a significant positive correlation with various LPG genes. This study gives insights into the structural features, evolutionary patterns, and expression analysis, laying a foundation to further reveal the function of the 103 OebZIP genes in olive.

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Section: Evolutionary Analysis Of the Oebzip Gene Familysupporting

confidence: 73%

Genome-Wide Identification, Evolutionary Patterns, and Expression Analysis of bZIP Gene Family in Olive (Olea europaea L.)

Rong

Cheng

et al. 2020

Genes

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“…Transcriptome sequencing (RNA-Seq) has strongly accelerated research on host-pathogen interactions in plants such as rice [31], maize [32], cucumber [33], watermelon [34] and strawberry [35]. Avr4/Cf-4and Avr9/Cf-9-dependent defense gene expression has been confirmed by cDNA-AFLP (cDNA-amplified fragment length polymorphism) analysis [36].…”

Section: Introductionmentioning

confidence: 99%

Comparative transcriptome analysis reveals the response mechanism of Cf-16-mediated resistance to Cladosporium fulvum infection in tomato

et al. 2020

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Background: Leaf mold disease caused by Cladosporium fulvum is a serious threat affecting the global production of tomato. Cf genes are associated with leaf mold resistance, including Cf-16, which confers effective resistance to leaf mold in tomato. However, the molecular mechanism of the Cf-16-mediated resistance response is largely unknown. Results: We performed a comparative transcriptome analysis of C. fulvum-resistant (cv. Ontario7816) and C. fulvumsusceptible (cv. Moneymaker) tomato cultivars to identify differentially expressed genes (DEGs) at 4 and 8 days post inoculation (dpi) with C. fulvum. In total, 1588 and 939 more DEGs were found in Cf-16 tomato than in Moneymaker at 4 and 8 dpi, respectively. Additionally, 1350 DEGs were shared between the 4-and 8-dpi Cf-16 groups, suggesting the existence of common core DEGs in response to C. fulvum infection. The up-regulated DEGs in Cf-16 tomato were primarily associated with defense processes and phytohormone signaling, including salicylic acid (SA) and jasmonic acid (JA). Moreover, SA and JA levels were significantly increased in Cf-16 tomato at the early stages of C. fulvum infection. Contrary to the previous study, the number of up-regulated genes in Cf-16 compared to Cf-10 and Cf-12 tomatoes was significantly higher at the early stages of C. fulvum infection. Conclusion: Our results provide new insight into the Cf-mediated mechanism of resistance to C. fulvum, especially the unique characteristics of Cf-16 tomato in response to this fungus.

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“…Our previous studies have shown that light (especially red light, RL) plays vital roles in the defense response of plants to the RKN M. incognita (Yang et al, 2015, 2018b), which may contribute to environment-friendly strategies to control RKNs in plants. A recent report has identified 59 bZIP genes in watermelon, and found that some of them may be involved in drought stress response (Unel et al, 2019). Although the chromosomal distributions, phylogenetic relationships, conserved motifs, and gene structures of the 59 ClabZIPs have been analyzed in a previous study (Unel et al, 2019), these analyses were insufficient to comprehensively reveal the information of the bZIP family genes in watermelon.…”

Section: Introductionmentioning

confidence: 99%

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

Yang

et al. 2019

PeerJ

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The basic leucine zipper (bZIP) family transcription factors play crucial roles in regulating plant development and stress response. In this study, we identified 62 ClabZIP genes from watermelon genome, which were unevenly distributed across the 11 chromosomes. These ClabZIP proteins could be classified into 13 groups based on the phylogenetic relationships, and members in the same group showed similar compositions of conserved motifs and gene structures. Transcriptome analysis revealed that a number of ClabZIP genes have important roles in the melatonin (MT) induction of cold tolerance. In addition, some ClabZIP genes were induced or repressed under red light (RL) or root-knot nematode infection according to the transcriptome data, and the expression patterns of several ClabZIP genes were further verified by quantitative real-time PCR, revealing their possible roles in RL induction of watermelon defense against nematode infection. Our results provide new insights into the functions of different ClabZIP genes in watermelon and their roles in response to cold stress and nematode infection.

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Comparative identification, characterization, and expression analysis of bZIP gene family members in watermelon and melon genomes

Cited by 18 publications

References 64 publications

Genome-Wide Identification, Evolutionary Patterns, and Expression Analysis of bZIP Gene Family in Olive (Olea europaea L.)

Genome-Wide Identification, Evolutionary Patterns, and Expression Analysis of bZIP Gene Family in Olive (Olea europaea L.)

Comparative transcriptome analysis reveals the response mechanism of Cf-16-mediated resistance to Cladosporium fulvum infection in tomato

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

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