Comprehensive Analysis for GRF Transcription Factors in Sacred Lotus (Nelumbo nucifera)

Chen, Gui-Zhen; Huang, Jie; Xiao-qin, Zhou; Yang, Hao; Chen, Jinliao; Zhou, Yuzhen; Ahmad, Sagheer; Lan, Siren; Liu, Zhong‐Jian; Peng, Donghui

doi:10.3390/ijms23126673

Cited by 8 publications

(11 citation statements)

References 44 publications

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“…They were first discovered in Oryza sativa in 2000 [ 1 ]. Recently, GRF family members have been studied in some plants, such as Zea mays [ 2 ], C. sinensis [ 3 ], Arabidopsis [ 4 ], Brassica rapa [ 5 ], Brassica napus [ 6 ], Solanu lycopersicum [ 7 ], Nicotiana tabacum [ 8 ], Manihot esculenta [ 9 ], Malus pumila [ 10 ], Cucurbitaceae [ 11 ], Brachypodium distachyon [ 12 ], Morus alba [ 13 ], Juglandaceae [ 14 ], and Nelumbo nucifera [ 15 ]. The GRF gene family plays an important role in the formation of tissues and organs in various plant biological processes, especially during the early growth period, such as leaf development [ 16 ], root growth [ 17 ], stem elongation [ 18 ], floral organ maturation [ 19 ], seed formation [ 20 ], and hormone signal transduction [ 21 ].…”

Section: Introductionmentioning

confidence: 99%

Genome-Wide Identification and Characterization of the GRF Gene Family in Melastoma dodecandrum

Huang

Chen

Ahmad

et al. 2023

IJMS

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Growth-regulating factor (GRF) is a kind of transcription factor unique to plants, playing an important role in the flowering regulation, growth, and development of plants. Melastoma dodecandrum is an important member of Melastomataceae, with ornamental, medicinal, and edible benefits. The identification of the GRF gene family in M. dodecandrum can help to improve their character of flavor and continuous flowering. The members of the GRF gene family were identified from the M. dodecandrum genome, and their bioinformatics, selective pressure, and expression patterns were analyzed. The results showed that there were 20 GRF genes in M. dodecandrum. Phylogenetic analysis showed that the 71 GRF genes from M. dodecandrum, Arabidopsis thaliana, Camellia sinensis, and Oryza sativa can be divided into three clades and six subclades. The 20 GRF genes of M. dodecandrum were distributed in twelve chromosomes and one contig. Furthermore, the gene structure and motif analysis showed that the intron and motif within each clade were very similar, but there were great differences among different clades. The promoter contained cis-acting elements related to hormone induction, stress, and growth and development. Different transcriptomic expression of MdGRFs indicated that MdGRFs may be involved in regulating the growth and development of M. dodecandrum. The results laid a foundation for further study on the function and molecular mechanism of the M. dodecandrum GRF gene family.

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Section: Introductionmentioning

confidence: 99%

Genome-Wide Identification and Characterization of the GRF Gene Family in Melastoma dodecandrum

Huang

Chen

Ahmad

et al. 2023

IJMS

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“…The qRT-PCR was performed by using Taq Pro Universal SYBR qPCR Master Mix kit (Vazyme, Nanjing, China). Finally, the 2 −∆Ct method was used to calculate the expression level [ 1 ].…”

Section: Methodsmentioning

confidence: 99%

“…Transcription factor (TF) is a DNA-binding protein that can specifically bind to cis-acting elements in the promoter and regulate plant growth and development, and response to stress [ 1 ]. The WOX gene family belongs to the Homeobox (HOX) super family, which plays a vital role in plant growth, development, and abiotic stress responses [ 2 , 3 , 4 , 5 , 6 ].…”

Section: Introductionmentioning

confidence: 99%

Genome-Wide Analysis of WUSCHEL-Related Homeobox Gene Family in Sacred Lotus (Nelumbo nucifera)

Chen,

Huang,

Lin

et al. 2023

IJMS

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WUSCHEL-related homeobox (WOX) is a plant-specific transcription factor (TF), which plays an essential role in the regulation of plant growth, development, and abiotic stress responses. However, little information is available on the specific roles of WOX TFs in sacred lotus (Nelumbo nucifera), which is a perennial aquatic plant with important edible, ornamental, and medicinal values. We identified 15 WOX TFs distributing on six chromosomes in the genome of N. nucifera. A total of 72 WOX genes from five species were divided into three clades and nine subclades based on the phylogenetic tree. NnWOXs in the same subclades had similar gene structures and conserved motifs. Cis-acting element analysis of the promoter regions of NnWOXs found many elements enriched in hormone induction, stress responses, and light responses, indicating their roles in growth and development. The Ka/Ks analysis showed that the WOX gene family had been intensely purified and selected in N. nucifera. The expression pattern analysis suggested that NnWOXs were involved in organ development and differentiation of N. nucifera. Furthermore, the protein–protein interaction analysis showed that NnWOXs might participate in the growth, development, and metabolic regulation of N. nucifera. Taken together, these findings laid a foundation for further analysis of NnWOX functions.

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“…The MdActin gene was used as an internal reference [ 32 ], and the biological repetition and technical repetition were performed three times. The expression level was calculated by the 2 −∆Ct method [ 1 , 32 ].…”

Section: Methodsmentioning

confidence: 99%

“…Transcription factors (TFs) are critical in regulating plant growth, development, and response to stress [ 1 ]. YABBY is a family of TFs belonging to the zinc finger protein superfamily [ 2 ].…”

Section: Introductionmentioning

confidence: 99%

Identification, Molecular Characteristics, and Evolution of YABBY Gene Family in Melastoma dodecandrum

Huang

Chen

Ahmad

et al. 2023

IJMS

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The YABBY gene family plays an important role in plant growth and development, such as response to abiotic stress and lateral organ development. YABBY TFs are well studied in numerous plant species, but no study has performed a genome-wide investigation of the YABBY gene family in Melastoma dodecandrum. Therefore, a genome-wide comparative analysis of the YABBY gene family was performed to study their sequence structures, cis-acting elements, phylogenetics, expression, chromosome locations, collinearity analysis, protein interaction, and subcellular localization analysis. A total of nine YABBY genes were found, and they were further divided into four subgroups based on the phylogenetic tree. The genes in the same clade of phylogenetic tree had the same structure. The cis-element analysis showed that MdYABBY genes were involved in various biological processes, such as cell cycle regulation, meristem expression, responses to low temperature, and hormone signaling. MdYABBYs were unevenly distributed on chromosomes. The transcriptomic data and real-time reverse transcription quantitative PCR (RT-qPCR) expression pattern analyses showed that MdYABBY genes were involved in organ development and differentiation of M. dodecandrum, and some MdYABBYs in the subfamily may have function differentiation. The RT-qPCR analysis showed high expression of flower bud and medium flower. Moreover, all MdYABBYs were localized in the nucleus. Therefore, this study provides a theoretical basis for the functional analysis of YABBY genes in M. dodecandrum.

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Comprehensive Analysis for GRF Transcription Factors in Sacred Lotus (Nelumbo nucifera)

Cited by 8 publications

References 44 publications

Genome-Wide Identification and Characterization of the GRF Gene Family in Melastoma dodecandrum

Genome-Wide Identification and Characterization of the GRF Gene Family in Melastoma dodecandrum

Genome-Wide Analysis of WUSCHEL-Related Homeobox Gene Family in Sacred Lotus (Nelumbo nucifera)

Identification, Molecular Characteristics, and Evolution of YABBY Gene Family in Melastoma dodecandrum

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