Diversification and evolution of the SDG gene family in Brassica rapa after the whole genome triplication

Dong, Heng; Liu, Dandan; Han, Tianyu; Zhao, Yayun; Sun, Ji Hua; Lin, Sue; Cao, Jiashu; Chen, Zhong‐Hua; Huang, Li

doi:10.1038/srep16851

Cited by 10 publications

(13 citation statements)

References 60 publications

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“… 5 In maize there is no orthologous gene of AtCMT2, and there is no strong correlation between CHG methylation and H3K9me2. 48 Although the putative orthologous genes of AtCMT2 , AtCMT3 , AtKYP/AtSUVH4 , AtSUVH5 , AtSUVH6 were confirmed in the B. rapa genome, 22 , 49 , 50 the basis of no strong association between CHG and H3K9me2 is that the interaction between cytosine methyltransferase and H3K9 methyltransferase in B. rapa may be different from that in A. thaliana , which may explain the smaller number of gbM genes in B. rapa .…”

Section: Discussionmentioning

confidence: 97%

Genome-wide characterization of DNA methylation, small RNA expression, and histone H3 lysine nine di-methylation in Brassica rapa L.

et al. 2018

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Epigenetic gene regulation is crucial to plant life and can involve dynamic interactions between various histone modifications, DNA methylation, and small RNAs. Detailed analysis of epigenome information is anticipated to reveal how the DNA sequence of the genome is translated into the plant’s phenotype. The aim of this study was to map the DNA methylation state at the whole genome level and to clarify the relationship between DNA methylation and transcription, small RNA expression, and histone H3 lysine 9 di-methylation (H3K9me2) in Brassica rapa. We performed whole genome bisulfite sequencing, small RNA sequencing, and chromatin immunoprecipitation sequencing using H3K9me2 antibody in a Chinese cabbage inbred line, RJKB-T24, and examined the impact of epigenetic states on transcription. Cytosine methylation in DNA was analysed in different sequence contexts (CG, CHG, and CHH) (where H could be A, C, or T) and position (promoter, exon, intron, terminator, interspersed repeat regions), and the H3K9me2 and 24 nucleotide small interfering RNAs (24 nt-siRNA) were overlaid onto the B. rapa reference genome. The epigenome was compared with that of Arabidopsis thaliana and the relationship between the position of DNA methylation and gene expression, and the involvement of 24 nt siRNAs and H3K9me2 are discussed.

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Section: Discussionmentioning

confidence: 97%

Genome-wide characterization of DNA methylation, small RNA expression, and histone H3 lysine nine di-methylation in Brassica rapa L.

et al. 2018

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“…For validating the expression of the putative lncRNAs, qRT‐PCR was performed using the total RNA extracted from the same samples with RNA‐seq. qRT‐PCR was achieved according to the process used in the previous study (Dong et al ., ) with the gene‐specific primer pairs (Table S14). BrUBC10 was used as the reference gene, and the results were calculated using the 2 −▵▵Ct method (Livak and Schmittgen, ).…”

Section: Methodsmentioning

confidence: 99%

Systematic identification of long non‐coding RNAs during pollen development and fertilization in Brassica rapa

et al. 2018

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The importance of long non-coding RNAs (lncRNAs) in plant development has been established, but a systematic analysis of lncRNAs expressed during pollen development and fertilization has been elusive. We performed a time series of RNA-seq experiments at five developmental stages during pollen development and three different time points after pollination in Brassica rapa and identified 12 051 putative lncRNAs. A comprehensive view of dynamic lncRNA expression networks underpinning pollen development and fertilization was provided. B. rapa lncRNAs share many common characteristics of lncRNAs: relatively short length, low expression but specific in narrow time windows, and low evolutionary conservation. Gene modules and key lncRNAs regulating reproductive development such as exine formation were uncovered. Forty-seven cis-acting lncRNAs and 451 trans-acting lncRNAs were revealed to be highly coexpressed with their target protein-coding genes. Of particular importance are the discoveries of 14 lncRNAs that were highly coexpressed with 10 function-known pollen-associated coding genes. Fifteen lncRNAs were predicted as endogenous target mimics for 13 miRNAs, and two lncRNAs were proved to be functional target mimics for miR160 after experimental verification and shown to function in pollen development. Our study provides the systematic identification of lncRNAs during pollen development and fertilization in B. rapa and forms the foundation for future genetic, genomic, and evolutionary studies.

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“…At present, the SET gene family has been analyzed in B. rapa [ 15 , 16 ], rice [ 17 ], bread wheat [ 18 ] and apple [ 19 ], etc. With the development of the research on the SET gene family, the role of the Su(var) 3-9 SET gene (SUV gene) family in DNA methylation is gradually revealed.…”

Section: Introductionmentioning

confidence: 99%

Comprehensive Analysis of the SUV Gene Family in Allopolyploid Brassica napus and Its Diploid Ancestors

Wang

2021

Genes

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SUV (the Suppressor of variegation [Su(var)] homologs and related) gene family is a subgroup of the SET gene family. According to the SRA domain and WIYLD domain distributions, it can be divided into two categories, namely SUVH (the Suppressor of variegation [Su(var)] homologs) and SUVR (the Suppressor of variegation [Su(var)] related). In this study, 139 SUV genes were identified in allopolyploid Brassica napus and its diploid ancestors, and their evolutionary relationships, protein properties, gene structures, motif distributions, transposable elements, cis-acting elements and gene expression patterns were analyzed. Our results showed that the SUV gene family of B. napus was amplified during allopolyploidization, in which the segmental duplication and TRD played critical roles. After the separation of Brassica and Arabidopsis lineages, orthologous gene analysis showed that many SUV genes were lost during the evolutionary process in B. rapa, B. oleracea and B. napus. The analysis of the gene and protein structures and expression patterns of 30 orthologous gene pairs which may have evolutionary relationships showed that most of them were conserved in gene structures and protein motifs, but only four gene pairs had the same expression patterns.

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Diversification and evolution of the SDG gene family in Brassica rapa after the whole genome triplication

Cited by 10 publications

References 60 publications

Genome-wide characterization of DNA methylation, small RNA expression, and histone H3 lysine nine di-methylation in Brassica rapa L.

Genome-wide characterization of DNA methylation, small RNA expression, and histone H3 lysine nine di-methylation in Brassica rapa L.

Systematic identification of long non‐coding RNAs during pollen development and fertilization in Brassica rapa

Comprehensive Analysis of the SUV Gene Family in Allopolyploid Brassica napus and Its Diploid Ancestors

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