Genome-wide Identification and Expression of ARF Gene Family during Adventitious Root Development in Hot Pepper ( Capsicum annuum )

Zhang, Huanxin; Cao, Ning; Dong, C.Y.; Shang, Qingmao

doi:10.1016/j.hpj.2017.07.001

Cited by 36 publications

(29 citation statements)

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“…These results suggested that some ARF genes in pepper might be regulated in an auxin independent way. Recently, similar work has been published by Zhang et al [ 47 ]. The reason of the differences about the number (19 CaARF genes) and domain structure of the CaARF proteins obtained by Zhang et al (2017) might be that different databases were used in this study [ 47 ].…”

Section: Discussionsupporting

confidence: 61%

“…Recently, similar work has been published by Zhang et al [ 47 ]. The reason of the differences about the number (19 CaARF genes) and domain structure of the CaARF proteins obtained by Zhang et al (2017) might be that different databases were used in this study [ 47 ]. Zhang et al (2017) used the pepper genome database ( ), SMART, Motif Scan ( ) and the MEME web server, while the Pepper Genomics Database 2.0, SMART and MEME were used in our study.…”

Section: Discussionsupporting

confidence: 61%

“…These observations suggest that CaARF10 likely regulates auxin-induced leaf expansion. A clear increase in transcriptional level of most CaARF genes was observed in adventitious root growth [ 47 ].…”

Section: Discussionmentioning

confidence: 99%

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Identification and Expression Profiling of the Auxin Response Factors in Capsicum annuum L. under Abiotic Stress and Hormone Treatments

Zhan

Feng

et al. 2017

IJMS

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Auxin response factors (ARFs) play important roles in regulating plant growth and development and response to environmental stress. An exhaustive analysis of the CaARF family was performed using the latest publicly available genome for pepper (Capsicum annuum L.). In total, 22 non-redundant CaARF gene family members in six classes were analyzed, including chromosome locations, gene structures, conserved motifs of proteins, phylogenetic relationships and Subcellular localization. Phylogenetic analysis of the ARFs from pepper (Capsicum annuum L.), tomato (Solanum lycopersicum L.), Arabidopsis and rice (Oryza sativa L.) revealed both similarity and divergence between the four ARF families, and aided in predicting biological functions of the CaARFs. Furthermore, expression profiling of CaARFs was obtained in various organs and tissues using quantitative real-time RT-PCR (qRT-PCR). Expression analysis of these genes was also conducted with various hormones and abiotic treatments using qRT-PCR. Most CaARF genes were regulated by exogenous hormone treatments at the transcriptional level, and many CaARF genes were altered by abiotic stress. Systematic analysis of CaARF genes is imperative to elucidate the roles of CaARF family members in mediating auxin signaling in the adaptation of pepper to a challenging environment.

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Section: Discussionsupporting

confidence: 61%

Section: Discussionsupporting

confidence: 61%

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Identification and Expression Profiling of the Auxin Response Factors in Capsicum annuum L. under Abiotic Stress and Hormone Treatments

Zhan

Feng

et al. 2017

IJMS

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“…Duplicated genes are initially redundant, and consequently can adopt new functions [54]. The same phenomenon has been observed in other plants, such as Arabidopsis, canola, chick pea, hot pepper, rice, and tobacco [12,37,48,55,56].…”

Section: Discussionmentioning

confidence: 92%

Genomic Organization of the B3-Domain Transcription Factor Family in Grapevine (Vitis vinifera L.) and Expression during Seed Development in Seedless and Seeded Cultivars

Ahmad

Zhang

Yao

et al. 2019

IJMS

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Members of the plant-specific B3-domain transcription factor family have important and varied functions, especially with respect to vegetative and reproductive growth. Although B3 genes have been studied in many other plants, there is limited information on the genomic organization and expression of B3 genes in grapevine (Vitis vinifera L.). In this study, we identified 50 B3 genes in the grapevine genome and analyzed these genes in terms of chromosomal location and syntenic relationships, intron–exon organization, and promoter cis-element content. We also analyzed the presumed proteins in terms of domain structure and phylogenetic relationships. Based on the results, we classified these genes into five subfamilies. The syntenic relationships suggest that approximately half of the genes resulted from genome duplication, contributing to the expansion of the B3 family in grapevine. The analysis of cis-element composition suggested that most of these genes may function in response to hormones, light, and stress. We also analyzed expression of members of the B3 family in various structures of grapevine plants, including the seed during seed development. Many B3 genes were expressed preferentially in one or more structures of the developed plant, suggesting specific roles in growth and development. Furthermore, several of the genes were expressed differentially in early developing seeds from representative seeded and seedless cultivars, suggesting a role in seed development or abortion. The results of this study provide a foundation for functional analysis of B3 genes and new resources for future molecular breeding of grapevine.

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“…Despite the importance of pepper, genome-wide studies remain limited. The recent whole-genome sequencing of pepper 28 provided an excellent tool for genome-wide analysis for the identification and characterization of entire gene families present in this crop [30][31][32] . Recently, the ANK repeat domain was identified as one of the major markers linked to capsaicinoid synthesis in Capsicum annuum 33 and Capsicum chinense 34 .The present study aimed to analyze the gene locus and chromosome localization, protein length, number of ANK repeats, molecular weight (MW), isoelectric points (pI), gene structure and phylogenetic relationship of ANK genes in three Capsicum species: Capsicum baccatum, C. annuum and C. chinense.…”

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confidence: 99%

The ankyrin repeat gene family in Capsicum spp: Genome-wide survey, characterization and gene expression profile

Lopez-Ortiz

Peña-Garcia

Natarajan

et al. 2020

Sci Rep

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the ankyrin (AnK) repeat protein family is largely distributed across plants and has been found to participate in multiple processes such as plant growth and development, hormone response, response to biotic and abiotic stresses. it is considered as one of the major markers of capsaicin content in pepper fruits. In this study, we performed a genome-wide identification and expression analysis of genes encoding AnK proteins in three Capsicum species: Capsicum baccatum, Capsicum annuum and Capsicum chinense. We identified a total of 87, 85 and 96 ANK genes in C. baccatum, C. annuum and C. chinense genomes, respectively. next, we performed a comprehensive bioinformatics analysis of the Capsicum ANK gene family including gene chromosomal localization, Cis-elements, conserved motif identification, intron/exon structural patterns and gene ontology classification as well as profile expression. phylogenetic and domain organization analysis grouped the Capsicum ANK gene family into ten subfamilies distributed across all 12 pepper chromosomes at different densities. Analysis of the expression of ANK genes in leaf and pepper fruits suggested that the ANKs have specific expression patterns at various developmental stages in placenta tissue. our results provide valuable information for further studies of the evolution, classification and putative functions of ANK genes in pepper. open Scientific RepoRtS | (2020) 10:4044 | https://doi.drought tolerance 19 , ABA-mediated regulation of reactive oxygen species levels under salt-stress 20 , and several plant diseases 21 , including those generated by fungus such as rice blast 22 . The release of genomic data and the development of bioinformatics analyses have led to comprehensive research on the identification and characterization of the ANK gene family in plants such as Arabidopsis 23 , rice 18 , tomato 24 , maize 25 , Physcomitrella patens 26 and soybean 27 . The number of ANK repeats, genes, and proteins in plants varies considerably across diverse plant species. In Arabidopsis thaliana, 509 ANK repeats encoded by 105 genes were reported, whereas rice contains 175 ANK repeat genes 18,23 .Pepper (Capsicum spp.) is a member of the Solanaceae family and is closely related to potato, tomato, eggplant, tobacco and petunia. Pepper represents an economically important horticultural crop worldwide because of its wide variety of uses, as a food, coloring agent, and spice and in pharmaceuticals, cosmetics and ornamental products as well as for its nutrimental value 28,29 . Despite the importance of pepper, genome-wide studies remain limited. The recent whole-genome sequencing of pepper 28 provided an excellent tool for genome-wide analysis for the identification and characterization of entire gene families present in this crop [30][31][32] . Recently, the ANK repeat domain was identified as one of the major markers linked to capsaicinoid synthesis in Capsicum annuum 33 and Capsicum chinense 34 .The present study aimed to analyze the gene locus and chromosome localization, protein length, ...

show abstract

Genome-wide Identification and Expression of ARF Gene Family during Adventitious Root Development in Hot Pepper ( Capsicum annuum )

Cited by 36 publications

References 58 publications

Identification and Expression Profiling of the Auxin Response Factors in Capsicum annuum L. under Abiotic Stress and Hormone Treatments

Identification and Expression Profiling of the Auxin Response Factors in Capsicum annuum L. under Abiotic Stress and Hormone Treatments

Genomic Organization of the B3-Domain Transcription Factor Family in Grapevine (Vitis vinifera L.) and Expression during Seed Development in Seedless and Seeded Cultivars

The ankyrin repeat gene family in Capsicum spp: Genome-wide survey, characterization and gene expression profile

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