Genome wide characterization of R2R3 MYB transcription factor from Apocynum venetum revealed potential stress tolerance and flavonoid biosynthesis genes

Abubakar, Aminu Shehu; Feng, Xinkang; Gao, Gang; Yu, Chang Yeon; Chen, Jikang; Chen, Kunmei; Wang, Xiaofei; Mou, Pan; Shao, Deyi; Chen, Ping; Zhu, Aiguo

doi:10.1016/j.ygeno.2022.110275

Cited by 13 publications

(3 citation statements)

References 91 publications

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“…Ka/Ks represents the ratio between non-synonymous substitutions (Ka) and synonymous substitutions (Ks), which can determine whether the gene encoding the protein is under selection pressure. Ka/Ks >> 1 stands for positive selection, Ka/Ks ≈ 1 represents neutral selection, and Ka/Ks << 1 means purifying selection [ 21 , 23 ]. With the exception of BnERF-03/01 and BnERF-05/01 duplicated pairs, which have a higher sequence divergence degree and farther evolutionary distance, the Ka/Ks ratio of all duplicated gene pairs was less than one ( Supplementary Table S3 ).…”

Section: Resultsmentioning

confidence: 99%

Genome-Wide Analysis of AP2/ERF Gene Superfamily in Ramie (Boehmeria nivea L.) Revealed Their Synergistic Roles in Regulating Abiotic Stress Resistance and Ramet Development

Qiu

Zhao

Abubakar

et al. 2022

IJMS

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AP2/ERF transcription factors (TFs) are one of the largest superfamilies in plants, and play vital roles in growth and response to biotic/abiotic stresses. Although the AP2/ERF family has been extensively characterized in many species, very little is known about this family in ramie (Boehmeria nivea L.). In this study, 138 AP2/ERF TFs were identified from the ramie genome and were grouped into five subfamilies, including the AP2 (19), RAV (5), Soloist (1), ERF (77), and DREB (36). Unique motifs were found in the DREB/ERF subfamily members, implying significance to the AP2/ERF TF functions in these evolutionary branches. Segmental duplication events were found to play predominant roles in the BnAP2/ERF TF family expansion. Light-, stress-, and phytohormone-responsive elements were identified in the promoter region of BnAP2/ERF genes, with abscisic acid response elements (ABRE), methyl jasmonate response elements, and the dehydration response element (DRE) being dominant. The integrated transcriptome and quantitative real-time PCR (qPCR) revealed 12 key BnAP2/ERF genes positively responding to waterlogging. Five of the genes are also involved in ramet development, with two (BnERF-30 and BnERF-32) further showing multifunctional roles. The protein interaction prediction analysis further verified their crosstalk mechanism in coordinating waterlogging resistance and ramet development. Our study provides new insights into the presence of AP2/ERF TFs in ramie, and provides candidate AP2/ERF TFs for further studies on breeding varieties with coupling between water stress tolerance and high yield.

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Section: Resultsmentioning

confidence: 99%

Genome-Wide Analysis of AP2/ERF Gene Superfamily in Ramie (Boehmeria nivea L.) Revealed Their Synergistic Roles in Regulating Abiotic Stress Resistance and Ramet Development

Qiu

Zhao

Abubakar

et al. 2022

IJMS

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“…The paucity of gene sequence resources has limited in-depth molecular research onApocynum species (Li et al , 2019). Complete genome assembly is useful for comparative studies on the evolution of significant traits in plants, and may facilitate improvement and breeding to enhance quality (Abubakar, Feng, et al , 2022;Chenet al , 2021). High-quality genome and chromosome assembly data for the two species revealed significant differences in repeat sequences, with a higher number of DNA transposons in A. hendersonii compared to A. venetum .…”

Section: Discussionmentioning

confidence: 99%

Integrated multiomic study on the evolution and natural variation of flavonoid biosynthesis in Apocynum venetum and Apocynum hendersonii

Gao

Abubakar

Chen

et al. 2022

Preprint

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The genus Apocynum contains perennial bast fiber plants that are spread worldwide. Apocynum species have great application prospect in salt-alkali regions, are rich in flavonoids, and possess medicinal significance. Here, we report the draft genomes of two species, Apocynum venetum and Apocynum hendersonii, and elucidate their evolutionary relationship. The high synteny and collinearity between A. venetum and A. hendersonii suggested that the two species experienced the same WDG event, indicating that divergence might be more recent. Comparative analysis revealed that ApF3H and differentially evolved ApUFGT genes are critical for determining natural variation in flavonoid biosynthesis between relatives. ApF3H-1 enhanced the total flavonoid content and promoted the antioxidant capacity of transformed plants compared to the wild-type plant. ApUFGT5 and 6 explained the diversification of flavonoids or their derivatives. These data provide biochemical insight and knowledge on the genetic regulation of flavonoid biosynthesis, supporting the adoption of these genes in breeding programs aimed at the multipurpose use of plants.

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“…AtMYB115 and AtMYB118 in subgroup 25 play important roles in the regulation of embryogenesis [ 22 ]. Due to the important roles of MYB genes, we have identified a large number of MYB genes in various types of plants, including dicotyledonous plants (197 members in Arabidopsis thaliana [ 23 ], 55 members in Cucumis sativus [ 4 ], 129 members in Pyrus bretschneideri [ 24 ], 70 members in Beta vulgaris [ 25 ], 406 members in Gossypium hirsutum [ 26 ], 163 members in Apocynum venetu [ 27 ], 121 members in Solanum lycopersicum [ 28 ] and 111 members in Solanum tuberosum [ 29 ]) and monocotyledonous plants (155 members in Oryza sativa [ 23 ] and 157 members in Zea mays [ 30 ]). However, little is known about the R2R3-MYB gene family in Theobroma cacao (cacao).…”

Section: Introductionmentioning

confidence: 99%

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

Zhang

Hou

et al. 2022

Genes

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The MYB gene family is involved in the regulation of plant growth, development and stress responses. In this paper, to identify Theobroma cacao R2R3-MYB (TcMYB) genes involved in environmental stress and phytohormones, we conducted a genome-wide analysis of the R2R3-MYB gene family in Theobroma cacao (cacao). A total of 116 TcMYB genes were identified, and they were divided into 23 subgroups according to the phylogenetic analysis. Meanwhile, the conserved motifs, gene structures and cis-acting elements of promoters were analyzed. Moreover, these TcMYB genes were distributed on 10 chromosomes. We conducted a synteny analysis to understand the evolution of the cacao R2R3-MYB gene family. A total of 37 gene pairs of TcMYB genes were identified through tandem or segmental duplication events. Additionally, we also predicted the subcellular localization and physicochemical properties. All the studies showed that TcMYB genes have multiple functions, including responding to environmental stresses. The results provide an understanding of R2R3-MYB in Theobroma cacao and lay the foundation for a further functional analysis of TcMYB genes in the growth of cacao.

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Genome wide characterization of R2R3 MYB transcription factor from Apocynum venetum revealed potential stress tolerance and flavonoid biosynthesis genes

Cited by 13 publications

References 91 publications

Genome-Wide Analysis of AP2/ERF Gene Superfamily in Ramie (Boehmeria nivea L.) Revealed Their Synergistic Roles in Regulating Abiotic Stress Resistance and Ramet Development

Genome-Wide Analysis of AP2/ERF Gene Superfamily in Ramie (Boehmeria nivea L.) Revealed Their Synergistic Roles in Regulating Abiotic Stress Resistance and Ramet Development

Integrated multiomic study on the evolution and natural variation of flavonoid biosynthesis in Apocynum venetum and Apocynum hendersonii

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

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