Molecular evolution and diversification of the GRF transcription factor family

Fonini, Leila Spagnolo; Lazzarotto, Fernanda; Barros, Pedro M.; Cabreira-Cagliari, Caroline; Martins, Mario; Saibo, Nelson J. M.; Turchetto‐Zolet, Andreia Carina; Margis‐Pinheiro, Márcia

doi:10.1590/1678-4685-gmb-2020-0080

Cited by 16 publications

(8 citation statements)

References 71 publications

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“…QLQ domain is an important protein-protein interaction domain, whereas WRC domain is a kind of plant-specific motif, which is mainly responsible for the interaction between transcription factors and DNA [2]. Since the first GRF family gene, namely OsGRF1, is isolated and functionally studied in rice [3], many GRF genes have been identified and characterized in a variety of plant species such as tomato, soybean, rice, cotton, streptophyta and Arabidopsis [2,[4][5][6][7].…”

Section: Introductionmentioning

confidence: 99%

Genome-wide identification and expression analysis of the growth regulating factor (GRF) family in Jatropha curcas

et al. 2021

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GRF genes have been confirmed to have important regulatory functions in plant growth, development and response to abiotic stress. Although the genome of Jatropha curcas is sequenced, knowledge about the identification of the species’ GRF genes and their expression patterns is still lacking. In this study, we characterized the 10 JcGRF genes. A detailed investigation into the physic nut GRF gene family is performed, including analysis of the exon-intron structure, conserved domains, conserved motifs, phylogeny, chromosomal locations, potential small RNA targets and expression profiles under both normal growth and abiotic stress conditions. Phylogenetic analysis indicated that the 10 JcGRF genes were classified into five groups corresponding to group I, II, III, IV and V. The analysis of conserved domains showed that the motifs of JcGRF genes were highly conserved in Jatropha curcas. Expression analysis based on RNA-seq and qRT-PCR showed that almost all JcGRF genes had the highest expression in seeds, but very low expression was detected in the non-seed tissues tested, and four JcGRF genes responded to at least one abiotic stress at at least one treatment point. Our research will provide an important scientific basis for further research on the potential functions of JcGRF genes in Jatropha curcas growth and development, and response to abiotic stress, and will eventually provide candidate genes for the breeding of Jatropha curcas.

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Section: Introductionmentioning

confidence: 99%

Genome-wide identification and expression analysis of the growth regulating factor (GRF) family in Jatropha curcas

et al. 2021

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“…For example, three nuclear upregulated lncRNAs (MSTRG.26736.3, MSTRG.26737.1, and MSTRG.26740.1) are clustered downstream of the same submergence upregulated gene MtrunA17Chr7g0230071 (Figure 4b, (Supplemental Figure 4b). The translated ORF for this gene is annotated as a putative growth response factor (GRF) that lacks the canonical QLQ and WRC domains 47 . Upstream of this putative GRF gene there is a conserved SURF ( MtrunA17Chr7g0230061 ) coding for the putative syntenic ortholog of Arabidopsis Hypoxia Unknown Protein 6 (HUP6).…”

Section: Resultsmentioning

confidence: 99%

Nuclear and cytoplasmic lncRNAs in root tips of the model legume Medicago truncatula under control and submergence

2023

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In this study, we aimed to identify long noncoding RNAs (lncRNAs) in root tips of the model legume Medicago truncatula using previously generated nuclear, total polyA, ribosome‐associated polyA, and Riboseq RNA datasets, which might shed light on their localization and potential regulatory roles. RNA‐seq data were mapped to the version 5 of the M. truncatula A17 genome and analyzed to identify genome annotated lncRNAs and putative new root tip (NRT) lncRNAs. lncRNAs were classified according to their genomic location relative to chromatin accessible regions, protein‐coding genes and transposable elements (TE), finding differences between annotated lncRNAs and NRT lncRNAs, both in their genomic position as well as in the type of TEs in their vicinity. We investigated their response to submergence and found a set of regulated lncRNAs that were preferentially upregulated in the nucleus, some of which were located nearby genes of the conserved submergence upregulated gene families, and chromatin accessible regions suggesting a potential regulatory role. Finally, the accumulation of lncRNAs under submergence was validated by reverse transcription quantitative polymerase chain reaction on nuclear RNA, providing additional evidence of their localization, which could ultimately be required for their function.

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“…Evolutionary history analyzes of the GRF family in various species help to speculate on gene function [3]. According to the analysis of the phylogenetic relationships, the Saccharum GRF family members were categorized into six groups.…”

Section: Discussionmentioning

confidence: 99%

“…Growth-regulating factors (GRFs) are plant-specific transcription factors, which play an essential role in regulating plant growth and abiotic stress response [1][2][3]. There are two conserved domains involved in GRF proteins: QLQ (Gln, Leu, and Gln) and WRC (Trp, Arg, and Cys), and both of them are located in the N-terminal region [4,5].…”

Section: Introductionmentioning

confidence: 99%

Genome-wide characterization and expression analysis of the growth-regulating factor family in Saccharum

Chen

et al. 2022

BMC Plant Biol

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Background Growth regulating factors (GRFs) are transcription factors that regulate diverse biological and physiological processes in plants, including growth, development, and abiotic stress. Although GRF family genes have been studied in a variety of plant species, knowledge about the identification and expression patterns of GRFs in sugarcane (Saccharum spp.) is still lacking. Results In the present study, a comprehensive analysis was conducted in the genome of wild sugarcane (Saccharum spontaneum) and 10 SsGRF genes were identified and characterized. The phylogenetic relationship, gene structure, and expression profiling of these genes were analyzed entirely under both regular growth and low-nitrogen stress conditions. Phylogenetic analysis suggested that the 10 SsGRF members were categorized into six clusters. Gene structure analysis indicated that the SsGRF members in the same group were greatly conserved. Expression profiling demonstrated that most SsGRF genes were extremely expressed in immature tissues, implying their critical roles in sugarcane growth and development. Expression analysis based on transcriptome data and real-time quantitative PCR verification revealed that GRF1 and GRF3 were distinctly differentially expressed in response to low-nitrogen stress, which meant that they were additional participated in sugarcane stress tolerance. Conclusion Our study provides a scientific basis for the potential functional prediction of SsGRF and will be further scrutinized by examining their regulatory network in sugarcane development and abiotic stress response, and ultimately facilitating their application in cultivated sugarcane breeding.

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Molecular evolution and diversification of the GRF transcription factor family

Cited by 16 publications

References 71 publications

Genome-wide identification and expression analysis of the growth regulating factor (GRF) family in Jatropha curcas

Genome-wide identification and expression analysis of the growth regulating factor (GRF) family in Jatropha curcas

Nuclear and cytoplasmic lncRNAs in root tips of the model legume Medicago truncatula under control and submergence

Genome-wide characterization and expression analysis of the growth-regulating factor family in Saccharum

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