Genome-Wide Identification and Characterization of SET Domain Family Genes in Brassica napus L.

Sarfraz, Sehrish; Wahid, Sumbal; Xie, Meili; Zhao, Chuanji; Zuo, Rong; Gao, Feng; S, Liu

doi:10.3390/ijms23041936

Cited by 12 publications

(7 citation statements)

References 68 publications

(118 reference statements)

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“…The seven clades of the SET family encode proteins with different physicochemical properties, functions, and regulatory mechanisms, and the physicochemical properties of these cotton SDG genes are shown in Table S1. Findings from subcellular localization demonstrated that the majority of GhSDG proteins localize to the nucleus, which coincides with the results of previous research, suggesting that SDG proteins mainly add methyl groups to histone lysine residues [56,57]. These results are consistent with GO analysis (Fig.…”

Section: Number and Characteristics Of Ghsdg Genessupporting

confidence: 92%

“…A total of 47 SDG proteins have been identi ed in A. thaliana [44], and 52 SDG proteins have been identi ed in G. raimondii [41]. Until now, the largest number of SDGs were detected in monocotyledon 6-ploid wheat (166), followed by B. napus (122) [54,55]. The seven clades of the SET family encode proteins with different physicochemical properties, functions, and regulatory mechanisms, and the physicochemical properties of these cotton SDG genes are shown in Table S1.…”

Section: Number and Characteristics Of Ghsdg Genesmentioning

confidence: 99%

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H3K36 methyltransferase GhKMT3;1a and GhKMT3;2a promote flowering in upland cotton

Ju,

Ling,

Luo

et al. 2023

Preprint

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Background SET DOMAIN GROUP (SDG) proteins act as histone lysine methyltransferases, which play pivotal roles in a variety of developmental processes, such as flowering determination, by modifying chromatin structure to regulate related gene transcription. Although there is extensive evidence that histone methylation plays a key role in plant growth and development, especially H3K36 methylation in Arabidopsis, little information is available for cotton. Results A total of 86 SDG genes were identified through genome-wide analysis of the Gossypium hirsutum genome. Subsequently, we thoroughly studied Arabidopsis, G. arboreum, and G. raimondii homologs and conducted a comprehensive analysis of their gene structure and conserved domain organization. A total of 12 conserved domains were detected in 86 GhSDGs and classified into seven main classes to clarify their evolutionary relationship, which was unevenly distributed across 25 chromosomes of G. hirsutum. Transcriptome data analysis of tissue and developmental stage expression showed that the GhSDG gene was expressed in different tissues, with high expression levels in the flowering stage and floral organs such as stamens and pistils, especially for KMT3 classes involved in activation of flowering, showing dramatically changed expression patterns. Subsequently, we performed reverse transcription-quantitative PCR for 8 KMT3 classes of GhSDGs in eight tissues (root, stem, leaf, sepal, petals, bud, stamens and pistils). In addition, two predicted GhSDG genes (GhKMT3;1a and GhKMT3;2a) were shown to regulate cotton development by virus-induced gene silencing. Budding and flowering were delayed in upland cotton plants with silenced GhKMT3;1a and GhKMT3;2a, and plant height was also lowered. We found that GhKMT3;1a and GhKMT3;2a-mediated H3K36 methylation regulates the expression of flowering-related genes and plays an important role in the flowering of upland cotton. Conclusion We comprehensively identified 86 GhSDG genes in upland cotton. Our data indicate that GhKMT3;1a and GhKMT3;2a-mediated H3K36 methylation regulate the expression of flowering-related genes and play an important role in the growth and development of cotton plants. These findings may also lay a foundation for breeding early-maturing cotton varieties in the future.

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Section: Number and Characteristics Of Ghsdg Genessupporting

confidence: 92%

Section: Number and Characteristics Of Ghsdg Genesmentioning

confidence: 99%

H3K36 methyltransferase GhKMT3;1a and GhKMT3;2a promote flowering in upland cotton

Ju,

Ling,

Luo

et al. 2023

Preprint

View full text Add to dashboard Cite

show abstract

“…We did not obtain any ortholog against two AtARI genes ( AtARI6 ( At1g63760 ), AtARI4 ( At3g27720 ) which were considered as pseudogenes [ 9 ]). Many studies showed that WGD or segmental duplication play a critical role during the expansion of gene families [ 44 , 45 , 46 ]. We obtained similar results in BnARI genes: all the genes were produced from the WGD or segmental duplication except four genes BnaAnng26970D , BnaAnng26980D , BnaC04g42500D , BnaA03g14710D and BnaC03g50620D , which were produced as a result of tandem duplication events ( Table 1 ).…”

Section: Discussionmentioning

confidence: 99%

Genome-Wide Identification and Analysis of Ariadne Gene Family Reveal Its Genetic Effects on Agronomic Traits of Brassica napus

Wahid¹,

Xie²,

Sarfraz³

et al. 2022

IJMS

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E3 ligases promote protein ubiquitination and degradation, which regulate every aspect of eukaryotic life. The Ariadne (ARI) proteins of RBR (ring between ring fingers) protein subfamily has been discovered as a group of potential E3 ubiquitin ligases. Only a few available research studies show their role in plant adaptations processes against the external environment. Presently, the functions of ARI proteins are largely unknown in plants. Therefore, in this study, we performed genome-wide analysis to identify the ARI gene family and explore their potential importance in B. napus. A total of 39 ARI genes were identified in the B. napus genome and were classified into three subfamilies (A, B and C) based on phylogenetic analysis. The protein–protein interaction networks and enrichment analysis indicated that BnARI genes could be involved in endoreduplication, DNA repair, proteasome assembly, ubiquitination, protein kinase activity and stress adaptation. The transcriptome data analysis in various tissues provided us an indication of some BnARI genes’ functional importance in tissue development. We also identified potential BnARI genes that were significantly responsive towards the abiotic stresses. Furthermore, eight BnARI genes were identified as candidate genes for multiple agronomic traits through association mapping analysis in B. napus; among them, BnaA02g12100D, which is the ortholog of AtARI8, was significantly associated with ten agronomic traits. This study provided useful information on BnARI genes, which could aid targeted functional research and genetic improvement for breeding in B. napus.

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“…The SYBR Green Ⅰ detection method and ABI Prism 7500 PCR system were used for qRT-PCR. Three biological replicates and three technical replicates were designed for each BvbZIP gene, the reference gene was 18S, and the relative expression level of the gene was calculated using the 2 −∆∆Ct method [ 86 ].…”

Section: Methodsmentioning

confidence: 99%

Genome-Wide Identification and Salt Stress Response Analysis of the bZIP Transcription Factor Family in Sugar Beet

Gong

Liu

Chen

et al. 2022

IJMS

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As one of the largest transcription factor families in plants, bZIP transcription factors play important regulatory roles in different biological processes, especially in the process of stress response. Salt stress inhibits the growth and yield of sugar beet. However, bZIP-related studies in sugar beet (Beta vulgaris L.) have not been reported. This study aimed to identify the bZIP transcription factors in sugar beet and analyze their biological functions and response patterns to salt stress. Using bioinformatics, 48 BvbZIP genes were identified in the genome of sugar beet, encoding 77 proteins with large structural differences. Collinearity analysis showed that three pairs of BvbZIP genes were fragment replication genes. The BvbZIP genes were grouped according to the phylogenetic tree topology and conserved structures, and the results are consistent with those reported in Arabidopsis. Under salt stress, the expression levels of most BvbZIP genes were decreased, and only eight genes were up-regulated. GO analysis showed that the BvbZIP genes were mainly negatively regulated in stress response. Protein interaction prediction showed that the BvbZIP genes were mainly involved in light signaling and ABA signal transduction, and also played a certain role in stress responses. In this study, the structures and biological functions of the BvbZIP genes were analyzed to provide foundational data for further mechanistic studies and for facilitating the efforts toward the molecular breeding of stress-resilient sugar beet.

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Genome-Wide Identification and Characterization of SET Domain Family Genes in Brassica napus L.

Cited by 12 publications

References 68 publications

H3K36 methyltransferase GhKMT3;1a and GhKMT3;2a promote flowering in upland cotton

H3K36 methyltransferase GhKMT3;1a and GhKMT3;2a promote flowering in upland cotton

Genome-Wide Identification and Analysis of Ariadne Gene Family Reveal Its Genetic Effects on Agronomic Traits of Brassica napus

Genome-Wide Identification and Salt Stress Response Analysis of the bZIP Transcription Factor Family in Sugar Beet

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