Dataset Information

Identification, Evolution, and Expression Profiling of Histone Lysine Methylation Moderators in Brassica rapa.

ABSTRACT: Histone modifications, such as methylation and demethylation, are vital for regulating chromatin structure, thus affecting its expression patterns. The objective of this study is to understand the phylogenetic relationships, genomic organization, diversification of motif modules, gene duplications, co-regulatory network analysis, and expression dynamics of histone lysine methyltransferases and histone demethylase in Brassica rapa. We identified 60 SET (HKMTases), 53 JmjC, and 4 LSD (HDMases) genes in B. rapa. The domain composition analysis subcategorized them into seven and nine subgroups, respectively. Duplication analysis for paralogous pairs of SET and JmjC (eight and nine pairs, respectively) exhibited variation. Interestingly, three pairs of SET exhibited Ka/Ks > 1.00 values, signifying positive selection, whereas the remaining underwent purifying selection with values less than 1.00. Furthermore, RT-PCR validation analysis and RNA-sequence data acquired on six different tissues (i.e., leaf, stem, callus, silique, flower, and root) revealed dynamic expression patterns. This comprehensive study on the abundance, classification, co-regulatory network analysis, gene duplication, and responses to heat and cold stress of SET and JmjC provides insights into the structure and diversification of these family members in B. rapa. This study will be helpful to reveal functions of these putative SET and JmjC genes in B. rapa.

SUBMITTER: Liu G

PROVIDER: S-EPMC6963287 | biostudies-literature | 2019 Nov

REPOSITORIES: biostudies-literature

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Identification, Evolution, and Expression Profiling of Histone Lysine Methylation Moderators in Brassica rapa.

Liu Gaofeng G Khan Nadeem N Ma Xiaoqing X Hou Xilin X

Plants (Basel, Switzerland) 20191120 12

Histone modifications, such as methylation and demethylation, are vital for regulating chromatin structure, thus affecting its expression patterns. The objective of this study is to understand the phylogenetic relationships, genomic organization, diversification of motif modules, gene duplications, co-regulatory network analysis, and expression dynamics of histone lysine methyltransferases and histone demethylase in Brassica rapa. We identified 60 SET (HKMTases), 53 JmjC< ...[more]

PMID: 31756989

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Project description:BackgroundXyloglucan endotransglucosylase/hydrolase genes (XTHs) are a multigene family and play key roles in regulating cell wall extensibility in plant growth and development. Brassica rapa and Brassica oleracea contain XTHs, but detailed identification and characterization of the XTH family in these species, and analysis of their tissue expression profiles, have not previously been carried out.ResultsIn this study, 53 and 38 XTH genes were identified in B. rapa and B. oleracea respectively, which contained some novel members not observed in previous studies. All XTHs of B. rapa, B. oleracea and Arabidopsis thaliana could be classified into three groups, Group I/II, III and the Early diverging group, based on phylogenetic relationships. Gene structures and motif patterns were similar within each group. All XTHs in this study contained two characteristic conserved domains (Glyco_hydro and XET_C). XTHs are located mainly in the cell wall but some are also located in the cytoplasm. Analyses of the mechanisms of gene family expansion revealed that whole-genome triplication (WGT) events and tandem duplication (TD) may have been the major mechanisms accounting for the expansion of the XTH gene family. Interestingly, TD genes all belonged to Group I/II, suggesting that TD was the main reason for the largest number of genes being in these groups. B. oleracea had lost more of the XTH genes, the conserved domain XET_C and the conserved active-site motif EXDXE compared with B. rapa, consistent with asymmetrical evolution between the two Brassica genomes. A majority of XTH genes exhibited different tissue-specific expression patterns based on RNA-seq data analyses. Moreover, there was differential expression of duplicated XTH genes in the two species, indicating that their functional differentiation occurred after B. rapa and B. oleracea diverged from a common ancestor.ConclusionsWe carried out the first systematic analysis of XTH gene families in B. rapa and B. oleracea. The results of this investigation can be used for reference in further studies on the functions of XTH genes and the evolution of this multigene family.

Dataset Information

Identification, Evolution, and Expression Profiling of Histone Lysine Methylation Moderators in Brassica rapa.

Publications

Identification, Evolution, and Expression Profiling of Histone Lysine Methylation Moderators in <i>Brassica rapa</i>.

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