Genome-Wide Identification and Analysis of the R2R3-MYB Gene Family in Theobroma cacao

Du, Junhong; Zhang, Qianqian; Hou, Sijia; Chen, Jing; Meng, Jianqiao; Liang, Dan; Wu, Rongling; Guo, Yunqian

doi:10.3390/genes13091572

Cited by 14 publications

(7 citation statements)

References 52 publications

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“…In our study, we identified 124 R2R3-CnMYB genes, which exhibited a range of exon numbers from 1 to 16 ( Figure 3 ). Most of the R2R3-CnMYBs, similar to those found in other plant species, consisted of three exons and two introns ( Liu et al., 2014 ; Chen et al., 2022 ; Du et al., 2022 ). It is worth noting that within the same subfamily, the exon/intron patterns of R2R3- CnMYB genes showed remarkable, with the majority of genes having no more than two introns.…”

Section: Discussionsupporting

confidence: 70%

Genome-wide identification, classification and expression analysis of MYB gene family in coconut (Cocos nucifera L.)

Li,

Guo,

Min Htwe

et al. 2024

Front. Plant Sci.

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MYB transcription factors regulate the growth, development, and secondary metabolism of plant species. To investigate the origin of color variations in coconut pericarp, we identified and analyzed the MYB gene family present in coconut. According to the sequence of MYB genes in Arabidopsis thaliana, homologous MYB gene sequences were found in the whole genome database of coconut, the conserved sequence motifs within MYB proteins were analyzed by Motif Elicitation (MEME) tool, and the sequences without conservative structure were eliminated. Additionally, we employed RNA-seq technology to generate gene expression signatures of the R2R3-MYB genes across distinctive coconut parts exhibiting diverse colors. To validate these profiles, we conducted quantitative PCR (qPCR). Through comprehensive genome-wide screening, we successfully identified a collection of 179 MYB genes in coconut. Subsequent phylogenetic analysis categorized these 179 coconut MYB genes into 4-subfamilies: 124 R2R3-MYB, 4 3R-MYB types, 4 4R-MYB type, and 47 unknown types. Furthermore, these genes were further divided into 34 subgroups, with 28 of these subgroups successfully classified into known subfamilies found in Arabidopsis thaliana. By mapping the CnMYB genes onto the 16 chromosomes of the coconut genome, we unveiled a collinearity association between them. Moreover, a preservation of gene structure and motif distribution was observed across the CnMYB genes. Our research encompassed a thorough investigation of the R2R3-MYB genes present in the coconut genome, including the chromosomal localization, gene assembly, conserved regions, phylogenetic associations, and promoter cis-acting elements of the studied genes. Our findings revealed a collection of 12 R2R3-MYB candidate genes, namely CnMYB8, CnMYB15, CnMYB27, CnMYB28, CnMYB61, CnMYB63, CnMYB68, CnMYB94, CnMYB101, CnMYB150, CnMYB153, and CnMYB164. These genes showed differential expressions in diverse tissues and developmental stages of four coconut species, such as CnMYB68, CnMYB101, and CnMYB28 exhibited high expression in majority of tissues and coconut species, while CnMYB94 and CnMYB164 showed lower expression. These findings shed light on the crucial functional divergence of CnMYB genes across various coconut tissues, suggesting these genes as promising candidate genes for facilitating color development in this important crop.

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Section: Discussionsupporting

confidence: 70%

Genome-wide identification, classification and expression analysis of MYB gene family in coconut (Cocos nucifera L.)

Li,

Guo,

Min Htwe

et al. 2024

Front. Plant Sci.

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“…The characteristic of PnTLPs, including protein length, isoelectric point (pI), molecular weight (MW) and grand average of hydropathicity (GRAVY) were predicted by ExPASy ProtParam (http://web.expasy.org/protparam/) (Liu, Cui, et al, 2020). The subcellular localization of proteins were predicted by the Bologna Uni ed Subcellular Component Annotator (BUSCA) website (http://busca.biocomp.unibo.it/) (Du, Zhang, et al, 2022).…”

Section: Identi Cation Of Pntlp Genes and Analysis Of Its Characteris...mentioning

confidence: 99%

“…The gene duplication of PnTLPs in P. notoginseng genome was performed by MCscanX with the default parameters, and circus was used to locate all the PnTLP genes on the P. notoginseng chromosome by Tbtools version 1.120 (Du, Zhang, et al, 2022). The syntenic relationships between the PnTLP genes and TLP genes from A. thaliana and O. sativa were obtained also using McscanX and both results visualized in Tbtools (Feng, Abubakar, et al, 2023).…”

Section: Gene Duplication and Collinearity Analysis Of Pntlp Genesmentioning

confidence: 99%

Genome-wide identification of thaumatin-like protein family genes in Panax notoginseng and analysis of their responses to Fusarium solani infection

Yang,

Guan,

Wei

et al. 2023

Genet Resour Crop Evol

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Panax notoginseng is the most widely used Chinese medicinal herb, and one main challenge to the successful cultivation is root rot, which signi cantly reduces its yield and quality. Thaumatin-like proteins (TLPs) are a large and complex proteins of pathogenesis-related family 5 (PR-5), which play a important role in plant host defense and other physiological processes. The objective of this study is to identify the TLP gene family in P. notoginseng on a genome-wide scale and explore their response to Fusarium solani infection. In this study, a total of twenty PnTLP genes were identi ed in P. notoginseng genome and divided into ten subfamilies (Group I-X) by the phylogenetic analysis. Subcellular localization prediction showed that most of the PnTLP proteins were located in the extracellular, and few were distributed in chloroplast. Meanwhile, the gene structure and protein conserved domain were established by MEME Suite. Duplication analysis showed that segmental duplication, rather than tandem duplications promoting the expansion of the PnTLPs gene family. The analysis of collinear relationships re ected that there were 36 homologous genes between P. notoginseng and Arabidopsis and 9 between P. notoginseng and rice. Moreover, cis-acting elements of PnTLP gene promoters were predicted which indicated that PnTLPs are involved in biotic, abiotic stress, and hormone induction. Expression pro le analysis revealed the possible roles of TLPs in plant development and fungal stress response. Furthermore, qRT-PCR analyses revealed that the PnTLP members were up-regulated or down-regulated in response to F. solani stress. The results of this study provide insight into the PnTLP gene family, and their potential biological functions in plants' defenses against pathogenic fungi, which would provide candidate genes for future studies of their roles in disease resistance.

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“…Multiple sequence comparison of the EfR2R3-MYB proteins and 126 Arabidopsis thaliana AtR2R3-MYB proteins was carried out using MEGA 7.0 software with the neighbor-joining method (NJ method) and a bootstrap value of 1000 to construct the phylogenetic tree [27,28].…”

Section: Phylogenetic Tree Analysismentioning

confidence: 99%

Genome-Wide Identification and Expression Pattern of MYB Family Transcription Factors in Erianthus fulvus

Rao,

Qian,

Xie

et al. 2023

Genes

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MYB family genes have many functions and are widely involved in plant abiotic-stress responses. Erianthus fulvus is an important donor material for stress-resistance genes in sugarcane breeding. However, the MYB family genes in E. fulvus have not been systematically investigated. In this study, 133 EfMYB genes, including 48 Ef1R-MYB, 84 EfR2R3-MYB and 1 Ef3R-MYB genes, were identified in the E. fulvus genome. Among them, the EfR2R3-MYB genes were classified into 20 subgroups. In addition, these EfMYB genes were unevenly distributed across 10 chromosomes. A total of 4 pairs of tandemly duplicated EfMYB genes and 21 pairs of segmentally duplicated EfMYB genes were identified in the E. fulvus genome. Protein-interaction analysis predicted that 24 EfMYB proteins had potential interactions with 14 other family proteins. The EfMYB promoter mainly contains cis-acting elements related to the hormone response, stress response, and light response. Expression analysis showed that EfMYB39, EfMYB84, and EfMYB124 could be significantly induced using low-temperature stress. EfMYB30, EfMYB70, EfMYB81, and EfMYB101 responded positively to drought stress. ABA treatment significantly induced EfMYB1, EfMYB30, EfMYB39, EfMYB84, and EfMYB130. All nine genes were induced using MeJA treatment. These results provide comprehensive information on EfMYB genes and can serve as a reference for further studies of gene function.

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Genome-Wide Identification and Analysis of the R2R3-MYB Gene Family in Theobroma cacao

Cited by 14 publications

References 52 publications

Genome-wide identification, classification and expression analysis of MYB gene family in coconut (Cocos nucifera L.)

Genome-wide identification, classification and expression analysis of MYB gene family in coconut (Cocos nucifera L.)

Genome-wide identification of thaumatin-like protein family genes in Panax notoginseng and analysis of their responses to Fusarium solani infection

Genome-Wide Identification and Expression Pattern of MYB Family Transcription Factors in Erianthus fulvus

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