Characterization and expression profiling of MYB transcription factors against stresses and during male organ development in Chinese cabbage (Brassica rapa ssp. pekinensis)

Saha, Gopal; Park, Jong-In; Ahmed, Nasar Uddin; Kayum, Abdul; Kang, Kwon-Kyoo; Nou, Ill Sup

doi:10.1016/j.plaphy.2016.03.021

Cited by 38 publications

(30 citation statements)

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“…The number of MsMYBs is greater than that in L. japonicas (104 MYBs), M. truncatula (166 MYBs), O. sativa (155 MYBs), and A. thaliana (197 MYBs), but less than that in G. hirsutum (524 MYBs) and B. rapa ssp. Pekinensis (475 MYBs) (Katiyar et al, 2012;Saha et al, 2016;Salih et al, 2016;. Of these 265 MsMYBs, the R2R3-MYB family is the most abundant MYB TF, which is consistent with previous studies of many plants (Salih et al, 2016;Du et al, 2012).…”

Section: Discussionsupporting

confidence: 88%

“…A total of 104, 166, 155, 197, 524, and 475 MYB genes of all the types were identified and analyzed in Lotus japonicas, M. truncatula, Oryza sativa, A. thaliana, Gossypium hirsutum, and Brassica rapa ssp. Pekinensis, respectively (Katiyar et al, 2012;Saha et al, 2016;Salih et al, 2016;. Moreover, 244 and 155 R2R3-MYB genes were reported in Glycine max and M. truncatula (Du et al, 2012;Zheng et al, 2017), respectively.…”

Section: Introductionmentioning

confidence: 99%

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Peer Review #1 of "MYB transcription factors in alfalfa (Medicago sativa): genome-wide identification and expression analysis under abiotic stresses (v0.1)"

2019

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Background. Alfalfa is the most widely cultivated forage legume and one of the most economically valuable crops in the world. Its survival and production are often hampered by environmental changes. However, there are few studies on stress-resistance genes in alfalfa because of its incomplete genomic information and rare expression profile data. The MYB proteins are characterized by a highly conserved DNA-binding domain, which is large, functionally diverse, and represented in all eukaryotes. The role of MYB proteins in plant development is essential; they function in diverse biological processes, including stress and defense responses, and seed and floral development. Studies on the MYB gene family have been reported in several species, but they have not been comprehensively analyzed in alfalfa. Methods. To identify more comprehensive MYB transcription factor family genes, the sequences of 168 Arabidopsis thaliana, 430 Glycine max, 185 Medicago truncatula, and 130 Oryza sativa MYB proteins were downloaded from the Plant Transcription Factor Database. These sequences were used as queries in a BLAST search against the Medicago sativa proteome sequences provided by the Noble Research Institute. Results. In the present study, a total of 265 MsMYB proteins were obtained, including 50 R1-MYB, 186 R2R3-MYB, 26 R1R2R3-MYB, and three atypical-MYB proteins. These predicted MsMYB proteins were divided into 12 subgroups by phylogenetic analysis, and gene ontology (GO) analysis indicated that most of the MsMYB genes are involved in various biological processes. The expression profiles and quantitative real-time PCR analysis indicated that some MsMYB genes might play a crucial role in the response to abiotic stresses. Additionally, a total of 170 and 914 predicted protein-protein and protein-DNA interactions were obtained, respectively. The interactions between MsMYB043 and MSAD320162, MsMYB253 and MSAD320162, and MsMYB253 and MSAD308489 were confirmed by a yeast two-hybrid system. This work provides information on the MYB family in alfalfa that was previously lacking and might promotes the cultivation of stress-resistant alfalfa.

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Section: Discussionsupporting

confidence: 88%

Section: Introductionmentioning

confidence: 99%

Peer Review #1 of "MYB transcription factors in alfalfa (Medicago sativa): genome-wide identification and expression analysis under abiotic stresses (v0.1)"

2019

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“…The functions of R2R3-MYB TFs in animals are restricted to the control of cell division and differentiation, whereas those in plants are diverse and with superior specific determination [23]. A total of 126 R2R3-MYB members have been found in Arabidopsis thaliana [16,31], 88 in Oryza sativa [32], 158 in Zea mays [33], 192 in Populus tremula [34], 244 in Glycine max [35], 205 in Gossypium raimondii [36], 118 in Vitis vinifera [19], and 256 in Brassica rapa [37]. In the model system from A. thaliana, the AtR2R3MYB family members are divided into 25 subgroups [30].…”

Section: Introductionmentioning

confidence: 99%

Members of R2R3-type MYB transcription factors from subgroups 20 and 22 are involved in abiotic stress response in tea plants

Wang

Cui

Wang

et al. 2018

Biotechnology & Biotechnological Equipment

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Abiotic stresses, including extreme temperature, drought and salinity, seriously threaten the growth and development of tea plants. The tea plant fights against various threats to innate defensive systems by regulating the expression profiles of related anti-genes. R2R3-type MYB family transcription factors (TFs) contribute to plant defense against abiotic stresses. Five CsMYB TFs were identified from the tea plant according to the transcriptome database. Conserved motif analysis revealed that subgroups 20 and 22 were conserved in the N-terminus with two motifs. All five CsMYB TF sequence homologies had a flexible C-terminal region. Subcellular localization analysis indicated that the protein of CsMYB19 was specifically localized in the nucleus. The expression patterns of CsMYB genes under abiotic stress treatments were significantly higher than that of the control, and the members from subgroup 20 had higher response than those in subgroup 22. During hormonal treatment, CsMYB8 was selected as highly responsive to methyl jasmonate (MeJA) treatment. The expression level of CsMYB20 was highest under ABA treatment and lowest under SA treatment. Our study serves as a foundation for understanding the response mechanisms of MYB genes under abiotic stress in tea plants.

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“…MYB is a large family of transcription factors in plants and involved in many life activities such as plant secondary metabolism [42], hormone responses [43], leaf organ formation [44], ower development [45].…”

Section: Discussionmentioning

confidence: 99%

Screening and identification of miRNAs related to sexual differentiation of strobili in Ginkgo biloba by integration analysis of small RNA, mRNA, and degradome sequencing

Liu

Cheng

et al. 2020

Preprint

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Background: Ginkgo biloba, a typical dioecious plant, is a traditional medicinal plant widely planted. However, it has a long juvenile period, which severely affected the breeding and cultivation of superior ginkgo varieties.Results: In order to clarify the complex mechanism of sexual differentiation in G. biloba strobili. Here, a total of 3,293 miRNAs were identified in buds and strobili of G. biloba, including 1,085 conserved miRNAs and 2,208 novel miRNAs using the three sequencing approaches of transcriptome, small RNA, and degradome. Comparative transcriptome analysis screened 4,346 and 7,087 differentially expressed genes (DEGs) in MB _vs_ FB and MS _vs_ OS, respectively. A total of 6,032 target genes were predicted for differentially expressed miRNA. The combined analysis of both small RNA and transcriptome datasets identiﬁed 51 miRNA-mRNA interaction pairs that may be involved in the process of G. biloba strobili sexual differentiation, of which 15 pairs were verified in the analysis of degradome sequencing. Conclusions: The comprehensive analysis of the small RNA, RNA and degradome sequencing data in this study provided candidate genes and clarified the regulatory mechanism of sexual differentiation of G. biloba strobili from multiple perspectives.

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Characterization and expression profiling of MYB transcription factors against stresses and during male organ development in Chinese cabbage (Brassica rapa ssp. pekinensis)

Cited by 38 publications

References 58 publications

Peer Review #1 of "MYB transcription factors in alfalfa (Medicago sativa): genome-wide identification and expression analysis under abiotic stresses (v0.1)"

Peer Review #1 of "MYB transcription factors in alfalfa (Medicago sativa): genome-wide identification and expression analysis under abiotic stresses (v0.1)"

Members of R2R3-type MYB transcription factors from subgroups 20 and 22 are involved in abiotic stress response in tea plants

Screening and identification of miRNAs related to sexual differentiation of strobili in Ginkgo biloba by integration analysis of small RNA, mRNA, and degradome sequencing

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