Genome-wide identification of the ARF (auxin response factor) gene family in peach and their expression analysis

Diao, Donghui; Hu, Xiulin; Guan, Dan; Wang, Wei; Yang, Haiqing; Liu, Yueping

doi:10.1007/s11033-020-05525-0

Cited by 36 publications

(25 citation statements)

References 51 publications

(57 reference statements)

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Moreover, our in silico analyses revealed the presence of a conserved putative mono-partite nuclear localization signal (NLS) at the end of the DBD of all DzARFs which confirmed their localization to the nucleus ( Figure 1B ). Our observation is in line with previous studies which have well documented the occurrence of NLS in members of the ARF TF family ( Shen et al., 2010 ; Yu et al., 2014 ; Niu et al., 2018 ; Diao et al., 2020 ).…”

Section: Resultssupporting

confidence: 93%

Auxin Response Factor 2A Is Part of the Regulatory Network Mediating Fruit Ripening Through Auxin-Ethylene Crosstalk in Durian

Khaksar

Sirikantaramas

2020

Front. Plant Sci.

View full text Add to dashboard Cite

Fruit ripening is a highly coordinated developmental process driven by a complex hormonal network. Ethylene is the main regulator of climacteric fruit ripening. However, a putative role of other key phytohormones in this process cannot be excluded. We previously observed an increasing level of auxin during the post-harvest ripening of the durian fruit, which occurred concomitantly with the rise in the climacteric ethylene biosynthesis. Herein, we connect the key auxin signaling component, auxin response factors (ARFs), with the regulatory network that controls fruit ripening in durian through the identification and functional characterization of a candidate ripening-associated ARF. Our transcriptome-wide analysis identified 15 ARF members in durian (DzARFs), out of which 12 were expressed in the fruit pulp. Most of these DzARFs showed a differential expression, but DzARF2A had a marked ripening-associated expression pattern during post-harvest ripening in Monthong, a commercial durian cultivar from Thailand. Phylogenetic analysis of DzARF2A based on its tomato orthologue predicted a role in ripening through the regulation of ethylene biosynthesis. Transient expression of DzARF2A in Nicotiana benthamiana leaves significantly upregulated the expression levels of ethylene biosynthetic genes, pointing to a ripening-associated role of DzARF2A through the transcriptional regulation of ethylene biosynthesis. Dual-luciferase reporter assay determined that DzARF2A trans-activates durian ethylene biosynthetic genes. We previously reported significantly higher auxin level during post-harvest ripening in a fastripening cultivar (Chanee) compared to a slow-ripening one (Monthong). DzARF2A expression was significantly higher during post-harvest ripening in the fast-ripening cultivars (Chanee and Phuangmanee) compared to that of the slow-ripening ones (Monthong and Kanyao). Thus, higher auxin level could upregulate the expression of DzARF2A during ripening of a fast-ripening cultivar. The auxin-induced expression of DzARF2A confirmed its responsiveness to exogenous auxin treatment in a dosedependent manner, suggesting an auxin-mediated role of DzARF2A in fruit ripening. We suggest that high DzARF2A expression would activate ARF2A-mediated transcription of ethylene biosynthetic genes, leading to increased climacteric ethylene biosynthesis (auxin-ethylene crosstalk) and faster ripening. Hence, we demonstrated DzARF2A as a

show abstract

Section: Resultssupporting

confidence: 93%

Auxin Response Factor 2A Is Part of the Regulatory Network Mediating Fruit Ripening Through Auxin-Ethylene Crosstalk in Durian

Khaksar

Sirikantaramas

2020

Front. Plant Sci.

View full text Add to dashboard Cite

show abstract

“…Among stem formation, the gene expression levels of different 33 ZlARF genes clearly differed, and some of these genes were very highly and speci cally expressed. These results were similar to those obtained in peach [57] and sweet orange [58], suggesting that some ARF genes play important roles in stem developmental processes. The expression pro le of a gene is often related to its function.…”

Section: Relevant Functions and Expression Patterns Analysissupporting

confidence: 88%

Genome-Wide Identification Analysis of The Auxin Response Factor Gene Family (ARF) in Zizania Latifolia and its Role in Swelling Stem Formation After Ustilago Esculenta Infection

Hou

Lǚ

et al. 2021

Preprint

View full text Add to dashboard Cite

Background: Auxin signalling plays a crucial role in plant growth and development. Although the auxin response factor (ARF) gene family has been studied in some plant species, its structural features, molecular evolution, and expression profile in Zizania latifolia (Z. latifolia) are still not clear.Results: Our study identified 33 putative YSL genes from the whole Z. latifolia genome. Furthermore, a comprehensive overview of the ZlARFs was undertaken, including phylogenetic relationship, gene structures, conserved domains, synteny, Ka/Ks, motifs, and subcellular locations of the gene product. Synteny analyses and the calculation of Ka/Ks values suggested that all 57 orthologous/paralogous gene pairs between Z. latifolia and Z. latifolia, Z. latifolia and Oryza sativa have experienced strong purifying selection. The phylogenetic analysis of ARFs indicated that the ZlARFs can be divided into 6 classes and that most ZlARFs from Z. latifolia have closer relationships with Oryza sativa than with Arabidopsis. RNA-Seq data and qRT-PCR analyses showed that ZlARF genes were expressed in TDF treatment and U. esculenta infection, while some ZlARFs exhibited high expression levels only in U. esculenta infection. Meanwhile, the interaction networks and gene ontology (GO) term of the ZlARF genes were constructed and 23 ZlARF co-expressed genes were identified, most of which were down-regulated involve auxin-activated signalling pathway in after swelling stem formation. Transcriptome analysis results verified the relevant functions of ARF genes, and most ZlARF genes regulated physiological processes in response to differential cell expansion. Conclusion: Comprehensive bioinformation analysis of the auxin response factor gene family (ARF) in Z. latifolia and its association with swelling stem formation after U. esculenta infection. The bioinformatic and RNA-Seq analyses provided valuable information for further study on the regulation of the growth and development of swelling stem formation by ZlARFs in Z. latifolia.

show abstract

“…By 2015, around 1533 TFs were identified in P. persica [20], however just a few have been characterized and even less have been associated to the fruit ripening process. MADS-box PrupeSEP1 (Prupe.3G249400) [103], TCP PpTCP.A2 (Prupe.1G272500) [49], homeobox PpHB.G7 (Prupe.1G416800) [104], AP2/ERF PpERF2, PpERF3 and PpERF.E2 (Prupe.5G090800, Prupe.7G194400 and Prupe.3G032300) [54,105], ARFs PpARF5 (Prupe.1G368300) [106] and EIN3-like PpEIL1 to 5 (Prupe.6G018200, Prupe.2G058400, Prupe.2G058500, Prupe.6G181600, Prupe.2G070300) [105] are among those TFs already characterized and associated with peach fruit ripening. NAC domain TFs were enriched among the TFs that targeted the genes whose respective proteins were more abundant in mature compared to ripe fruit.…”

Section: Transcription Factors Assessmentmentioning

confidence: 99%

Shotgun proteomics of peach fruit reveals major metabolic pathways associated to ripening

et al. 2021

View full text Add to dashboard Cite

Background Fruit ripening in Prunus persica melting varieties involves several physiological changes that have a direct impact on the fruit organoleptic quality and storage potential. By studying the proteomic differences between the mesocarp of mature and ripe fruit, it would be possible to highlight critical molecular processes involved in the fruit ripening. Results To accomplish this goal, the proteome from mature and ripe fruit was assessed from the variety O’Henry through shotgun proteomics using 1D-gel (PAGE-SDS) as fractionation method followed by LC/MS-MS analysis. Data from the 131,435 spectra could be matched to 2740 proteins, using the peach genome reference v1. After data pre-treatment, 1663 proteins could be used for comparison with datasets assessed using transcriptomic approaches and for quantitative protein accumulation analysis. Close to 26% of the genes that code for the proteins assessed displayed higher expression at ripe fruit compared to other fruit developmental stages, based on published transcriptomic data. Differential accumulation analysis between mature and ripe fruit revealed that 15% of the proteins identified were modulated by the ripening process, with glycogen and isocitrate metabolism, and protein localization overrepresented in mature fruit, as well as cell wall modification in ripe fruit. Potential biomarkers for the ripening process, due to their differential accumulation and gene expression pattern, included a pectin methylesterase inhibitor, a gibbellerin 2-beta-dioxygenase, an omega-6 fatty acid desaturase, a homeobox-leucine zipper protein and an ACC oxidase. Transcription factors enriched in NAC and Myb protein domains would target preferentially the genes encoding proteins more abundant in mature and ripe fruit, respectively. Conclusions Shotgun proteomics is an unbiased approach to get deeper into the proteome allowing to detect differences in protein abundance between samples. This technique provided a resolution so that individual gene products could be identified. Many proteins likely involved in cell wall and sugar metabolism, aroma and color, change their abundance during the transition from mature to ripe fruit.

show abstract

Genome-wide identification of the ARF (auxin response factor) gene family in peach and their expression analysis

Cited by 36 publications

References 51 publications

Auxin Response Factor 2A Is Part of the Regulatory Network Mediating Fruit Ripening Through Auxin-Ethylene Crosstalk in Durian

Auxin Response Factor 2A Is Part of the Regulatory Network Mediating Fruit Ripening Through Auxin-Ethylene Crosstalk in Durian

Genome-Wide Identification Analysis of The Auxin Response Factor Gene Family (ARF) in Zizania Latifolia and its Role in Swelling Stem Formation After Ustilago Esculenta Infection

Shotgun proteomics of peach fruit reveals major metabolic pathways associated to ripening

Contact Info

Product

Resources

About