Genome-Wide Identification of WUSCHEL-Related Homeobox Gene Family and their Expression Analysis During Somatic Embryogenesis in Oil Palm (Elaeis guineensis)

2021 ◽  
Author(s):  
Anni Zhang ◽  
Yinchun Li ◽  
Rajesh Yarra ◽  
Rui Li ◽  
Hongxing Cao ◽  
...  
Keyword(s):  
Somatic Embryogenesis ◽  
Gene Family ◽  
Expression Analysis ◽  
Oil Palm ◽  
Elaeis Guineensis ◽  
Homeobox Gene ◽  
Genome Wide

scholarly journals Identification and expression analysis of histone modification gene (HM) family during somatic embryogenesis of oil palm

BMC Genomics ◽  
2022 ◽  
Vol 23 (1) ◽  
Author(s):  
Lixia Zhou ◽  
Rajesh Yarra ◽  
Longfei Jin ◽  
Yaodong Yang ◽  
Hongxing Cao ◽  
...  
Keyword(s):  
Somatic Embryogenesis ◽  
Histone Modification ◽  
Gene Family ◽  
Expression Analysis ◽  
Histone Modifications ◽  
Oil Palm ◽  
Large Scale ◽  
Elaeis Guineensis ◽  
Family Members ◽  
Evolutionary Relationship

Abstract Background Oil palm (Elaeis guineensis, Jacq.) is an important vegetable oil-yielding plant. Somatic embryogenesis is a promising method to produce large-scale elite clones to meet the demand for palm oil. The epigenetic mechanisms such as histone modifications have emerged as critical factors during somatic embryogenesis. These histone modifications are associated with the regulation of various genes controlling somatic embryogenesis. To date, none of the information is available on the histone modification gene (HM) family in oil palm. Results We reported the identification of 109 HM gene family members including 48 HMTs, 27 HDMs, 13 HATs, and 21 HDACs in the oil palm genome. Gene structural and motif analysis of EgHMs showed varied exon–intron organization and with conserved motifs among them. The identified 109 EgHMs were distributed unevenly across 16 chromosomes and displayed tandem duplication in oil palm genome. Furthermore, relative expression analysis showed the differential expressional pattern of 99 candidate EgHM genes at different stages (non-embryogenic, embryogenic, somatic embryo) of somatic embryogenesis process in oil palm, suggesting the EgHMs play vital roles in somatic embryogenesis. Our study laid a foundation to understand the regulatory roles of several EgHM genes during somatic embryogenesis. Conclusions A total of 109 histone modification gene family members were identified in the oil palm genome via genome-wide analysis. The present study provides insightful information regarding HM gene’s structure, their distribution, duplication in oil palm genome, and also their evolutionary relationship with other HM gene family members in Arabidopsis and rice. Finally, our study provided an essential role of oil palm HM genes during somatic embryogenesis process.

scholarly journals Identification and Expression Analysis of Histone Modification Gene (HM) Family During Somatic Embryogenesis of Oil Palm

2021 ◽  
Author(s):  
Lixia Zhou ◽  
Rajesh Yarra ◽  
Longfei Jin ◽  
Yaodong Yang ◽  
Hongxing Cao ◽  
...  
Keyword(s):  
Somatic Embryogenesis ◽  
Histone Modification ◽  
Gene Family ◽  
Expression Analysis ◽  
Histone Modifications ◽  
Oil Palm ◽  
Large Scale ◽  
Elaeis Guineensis ◽  
Family Members ◽  
Evolutionary Relationship

Abstract BackgroundOil palm (Elaeis guineensis, Jacq.) is an important vegetable oil yielding plant. Somatic embryogenesis is the promising method to produce large scale elite clones to meet the demand of palm oil. The epigenetic mechanisms such as histone modifications have emerged as critical factors during somatic embryogenesis. These histone modifications are associated with the regulation of various genes controlling the somatic embryogenesis. To date, none of the information is available on the histone modification gene (HM) family in oil palmResultsWe reported the identification of 109 HM gene family members including 48 HMTs, 27 HDMs, 13 HATs, and 21 HDACs in the oil palm genome. Gene structural and motif analysis of EgHMs showed varied exon-intron organization and with conserved motifs among them. The identified 109 EgHMs were distributed unevenly across 16 chromosomes and displayed tandem duplication in oil palm genome. Furthermore, relative expression analysis showed the differential expressional pattern of 99 candidate EgHM genes at different stages (non-embryogenic, embryogenic, somatic embryo) of somatic embryogenesis process in oil palm, suggesting the EgHMs play vital roles in somatic embryogenesis. Our study laid a foundation to understand the regulatory roles of several EgHM genes during somatic embryogenesis. ConclusionsA total of 109 histone modification gene family members were identified in the oil palm genome via genome wide analysis. The present study provide an insightful information regarding HM gene’s structure, their distribution, duplication in oil palm genome and also their evolutionary relationship with other HM gene family members in Arabidopsis and rice. Finally, our study provided an essential role of oil palm HM genes during somatic embryogenesis process.

The SAUR gene family in coffee: genome-wide identification and gene expression analysis during somatic embryogenesis

2022 ◽  
Author(s):  
Fabiana Couto Zanin ◽  
Natália Chagas Freitas ◽  
Renan Terassi Pinto ◽  
Wesley Pires Flausino Máximo ◽  
Leandro Eugenio Cardamone Diniz ◽  
...  
Keyword(s):  
Gene Expression ◽  
Somatic Embryogenesis ◽  
Gene Family ◽  
Expression Analysis ◽  
Gene Expression Analysis ◽  
Genome Wide

scholarly journals Genome-wide identification of cyclin-dependent kinase (CDK) genes affecting adipocyte differentiation in cattle

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Cuili Pan ◽  
Zhaoxiong Lei ◽  
Shuzhe Wang ◽  
Xingping Wang ◽  
Dawei Wei ◽  
...  
Keyword(s):  
Gene Family ◽  
Expression Analysis ◽  
Adipocyte Differentiation ◽  
Bos Taurus ◽  
Adipogenic Differentiation ◽  
Critical Role ◽  
Bos Indicus ◽  
Specific Expression ◽  
Genome Wide ◽  
A Genome

Abstract Background Cyclin-dependent kinases (CDKs) are protein kinases regulating important cellular processes such as cell cycle and transcription. Many CDK genes also play a critical role during adipogenic differentiation, but the role of CDK gene family in regulating bovine adipocyte differentiation has not been studied. Therefore, the present study aims to characterize the CDK gene family in bovine and study their expression pattern during adipocyte differentiation. Results We performed a genome-wide analysis and identified a number of CDK genes in several bovine species. The CDK genes were classified into 8 subfamilies through phylogenetic analysis. We found that 25 bovine CDK genes were distributed in 16 different chromosomes. Collinearity analysis revealed that the CDK gene family in Bos taurus is homologous with Bos indicus, Hybrid-Bos taurus, Hybrid Bos indicus, Bos grunniens and Bubalus bubalis. Several CDK genes had higher expression levels in preadipocytes than in differentiated adipocytes, as shown by RNA-seq analysis and qPCR, suggesting a role in the growth of emerging lipid droplets. Conclusion In this research, 185 CDK genes were identified and grouped into eight distinct clades in Bovidae, showing extensively homology. Global expression analysis of different bovine tissues and specific expression analysis during adipocytes differentiation revealed CDK4, CDK7, CDK8, CDK9 and CDK14 may be involved in bovine adipocyte differentiation. The results provide a basis for further study to determine the roles of CDK gene family in regulating adipocyte differentiation, which is beneficial for beef quality improvement.

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