Genome-Wide Comparative Analysis of the R2R3-MYB Gene Family in Five Solanaceae Species and Identification of Members Regulating Carotenoid Biosynthesis in Wolfberry

Yin, Yue; Guo, Cong; Shi, Hongyan; Zhao, Jianhua; Ma, Fang; An, Wei; He, Xinru; Luo, Qing; Cao, Yang; Zhan, Xiangqiang

doi:10.3390/ijms23042259

Cited by 23 publications

(22 citation statements)

References 71 publications

(99 reference statements)

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“…WGD, TD, and DSD are the main events in eukaryotic genome evolution and drove the development of new functions and genetic evolutionary systems [ 39 ]. Gene families, such as R2R3-MYB and BAHD acyltransferase families, expanded primarily through WGD and DSD [ 24 , 40 ]. WGD and TD are the main duplication events in the PMEI gene family [ 41 ].…”

Section: Discussionmentioning

confidence: 99%

“…RNA extraction and qRT-PCR were performed as previously described [ 24 ]. The primers for LbaBBX genes were designed using Primer Premier 5 and are listed in Table S10 .…”

Section: Methodsmentioning

confidence: 99%

“…During the past few decades, many studies have identified TFs families with important roles in the regulation of carotenoid biosyntheses, such as SlMYB72 , SlWRKY35 , MdAP2 , and SlBBX20 [ 11 , 21 , 22 , 23 ]. Two R2R3-MYB family members, LbaMYB26 ( Lba02g01219 ) and LbaMYB123 ( Lba11g01830 ), are candidate genes involved in the regulation of carotenoid biosynthesis in L. barbarum fruits [ 24 ]. The BBX gene family has been identified and evaluated in many plant species, such as Solanum lycopersicum [ 25 ], Capsicum annuum [ 26 ], Iris germanica [ 27 ], Prunus avium [ 28 ], Vitis Vinifera [ 29 ], and Arabidopsis thaliana [ 30 ], and has diverse functions.…”

Section: Introductionmentioning

confidence: 99%

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Genome-Wide Identification and Analysis of the BBX Gene Family and Its Role in Carotenoid Biosynthesis in Wolfberry (Lycium barbarum L.)

Yin

Shi

et al. 2022

IJMS

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The B-box proteins (BBXs) are a family of zinc-finger transcription factors with one/two B-Box domain(s) and important roles in plant growth and development as well as stress responses. Wolfberry (Lycium barbarum L.) is an important traditional medicinal and food supplement in China, and its genome has recently been released. However, comprehensive studies of BBX genes in Lycium species are lacking. In this study, 28 LbaBBX genes were identified and classified into five clades by a phylogeny analysis with BBX proteins from Arabidopsis thaliana and the LbaBBXs have similar protein motifs and gene structures. Promoter cis-regulatory element prediction revealed that LbaBBXs might be highly responsive to light, phytohormone, and stress conditions. A synteny analysis indicated that 23, 20, 8, and 5 LbaBBX genes were orthologous to Solanum lycopersicum, Solanum melongena, Capsicum annuum, and Arabidopsis thaliana, respectively. The gene pairs encoding LbaBBX proteins evolved under strong purifying selection. In addition, the carotenoid content and expression patterns of selected LbaBBX genes were analyzed. LbaBBX2 and LbaBBX4 might play key roles in the regulation of zeaxanthin and antheraxanthin biosynthesis. Overall, this study improves our understanding of LbaBBX gene family characteristics and identifies genes involved in the regulation of carotenoid biosynthesis in wolfberry.

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Section: Discussionmentioning

confidence: 99%

“…RNA extraction and qRT-PCR were performed as previously described [ 24 ]. The primers for LbaBBX genes were designed using Primer Premier 5 and are listed in Table S10 .…”

Section: Methodsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Genome-Wide Identification and Analysis of the BBX Gene Family and Its Role in Carotenoid Biosynthesis in Wolfberry (Lycium barbarum L.)

Yin

Shi

et al. 2022

IJMS

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“…Accurate identification of R2R3-MYB genes throughout the genome is required to comprehensively analyze their functional roles in various abiotic stress responses. With the increasing number of flowering plant genomes being published, genome-wide identification of the R2R3-MYB gene family has been reported in many dicotyledonous species, such as Arabidopsis thaliana [ 19 ], Vitis vinifera [ 20 ], Eucalyptus grandis [ 21 ], Capsicum annuum [ 22 ], Pinus massoniana [ 23 ] and Lycium barbarum [ 24 ]. Genome-wide identification of the R2R3-MYB genes in the Populus trichocarpa genome (v3.0) has also been reported [ 25 , 26 , 27 , 28 ].…”

Section: Introductionmentioning

confidence: 99%

Comprehensive Genome-Wide Analyses of Poplar R2R3-MYB Transcription Factors and Tissue-Specific Expression Patterns under Drought Stress

Zhang

Wang

Chen

et al. 2023

IJMS

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R2R3-type MYB transcription factors are implicated in drought stress, which is a primary factor limiting the growth and development of woody plants. The identification of R2R3-MYB genes in the Populus trichocarpa genome has been previously reported. Nevertheless, the diversity and complexity of the conserved domain of the MYB gene caused inconsistencies in these identification results. There is still a lack of drought-responsive expression patterns and functional studies of R2R3-MYB transcription factors in Populus species. In this study, we identified a total of 210 R2R3-MYB genes in the P. trichocarpa genome, of which 207 genes were unevenly distributed across all 19 chromosomes. These poplar R2R3-MYB genes were phylogenetically divided into 23 subgroups. Collinear analysis demonstrated that the poplar R2R3-MYB genes underwent rapid expansion and that whole-genome duplication events were a dominant factor in the process of rapid gene expansion. Subcellular localization assays indicated that poplar R2R3-MYB TFs mainly played a transcriptional regulatory role in the nucleus. Ten R2R3-MYB genes were cloned from P. deltoides × P. euramericana cv. Nanlin895, and their expression patterns were tissue-specific. A majority of the genes showed similar drought-responsive expression patterns in two out of three tissues. This study provides a valid cue for further functional characterization of drought-responsive R2R3-MYB genes in poplar and provides support for the development of new poplar genotypes with elevated drought tolerance.

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“…In recent decades, the increasing availability of plant genome sequencing data has made comprehensively characterizing the genome-wide R2R3-MYB gene family in the plant kingdom successful. Currently, this gene family has been identified and characterized in more than 75 plant species [13,14], including Arabidopsis (Arabidopsis thaliana) [9], rice (Oryza sativa) [44], potato (Solanum tuberosum) [45], tomato (Solanum lycopersicum) [46], wolfberry (Lycium barbarum) [47], and pea (Pisum sativum) [48]. Nevertheless, little is known about the information of the genome-wide R2R3-MYB gene family in sweet potatoes.…”

Section: Introductionmentioning

confidence: 99%

Genome-Wide Comparative Analysis of the R2R3-MYB Gene Family in Six Ipomoea Species and the Identification of Anthocyanin-Related Members in Sweet Potatoes

Zhou

et al. 2023

Plants

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Sweet potatoes (Ipomoea batatas) are one of the important tuberous root crops cultivated worldwide, and thier storage roots are rich in antioxidants, such as anthocyanins. R2R3-MYB is a large gene family involved in various biological processes, including anthocyanin biosynthesis. However, few reports about the R2R3-MYB gene family of sweet potatoes have been released to date. In the present study, a total of 695 typical R2R3-MYB genes were identified in six Ipomoea species, including 131 R2R3-MYB genes in sweet potatoes. A maximum likelihood phylogenetic analysis divided these genes into 36 clades, referring to the classification of 126 R2R3-MYB proteins of Arabidopsis. Clade C25(S12) has no members in six Ipomoea species, whereas four clades (i.e., clade C21, C26, C30, and C36), including 102 members, had no members in Arabidopsis, and they were identified as Ipomoea-specific clades. The identified R2R3-MYB genes were unevenly distributed on all chromosomes in six Ipomoea species genomes, and the collinearity analysis among hexaploid I. batatas and another five diploid Ipomoea species suggested that the sweet potato genome might have undergone a larger chromosome rearrangement during the evolution process. Further analyses of gene duplication events showed that whole-genome duplication, transposed duplication, and dispersed duplication events were the primary forces driving the R2R3-MYB gene family expansion of Ipomoea plants, and these duplicated genes experienced strong purifying selection because of their Ka/Ks ratio, which is less than 1. Additionally, the genomic sequence length of 131 IbR2R3-MYBs varied from 923 bp to ~12.9 kb with a mean of ~2.6 kb, and most of them had more than three exons. The Motif 1, 2, 3, and 4 formed typical R2 and R3 domains and were identified in all IbR2R3-MYB proteins. Finally, based on multiple RNA-seq datasets, two IbR2R3-MYB genes (IbMYB1/g17138.t1 and IbMYB113/g17108.t1) were relatively highly expressed in pigmented leaves and tuberous root flesh and skin, respectively; thus, they were identified to regulate tissue-specific anthocyanin accumulation in sweet potato. This study provides a basis for the evolution and function of the R2R3-MYB gene family in sweet potatoes and five other Ipomoea species.

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Genome-Wide Comparative Analysis of the R2R3-MYB Gene Family in Five Solanaceae Species and Identification of Members Regulating Carotenoid Biosynthesis in Wolfberry

Cited by 23 publications

References 71 publications

Genome-Wide Identification and Analysis of the BBX Gene Family and Its Role in Carotenoid Biosynthesis in Wolfberry (Lycium barbarum L.)

Genome-Wide Identification and Analysis of the BBX Gene Family and Its Role in Carotenoid Biosynthesis in Wolfberry (Lycium barbarum L.)

Comprehensive Genome-Wide Analyses of Poplar R2R3-MYB Transcription Factors and Tissue-Specific Expression Patterns under Drought Stress

Genome-Wide Comparative Analysis of the R2R3-MYB Gene Family in Six Ipomoea Species and the Identification of Anthocyanin-Related Members in Sweet Potatoes

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