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.

scholarly journals In vitro ROOTING OF TENERA HYBRID OIL PALM (Elaeis guineensis Jacq.) PLANTS1

2018 ◽  
Vol 41 (4) ◽  
Author(s):  
Marlúcia Souza Pádua ◽  
Raíssa Silveira Santos ◽  
Luciano Vilela Paiva ◽  
Vanessa Cristina Stein ◽  
Luciano Coutinho Silva
Keyword(s):  
Somatic Embryogenesis ◽  
Growth Regulators ◽  
Oil Palm ◽  
Somatic Embryos ◽  
Large Scale ◽  
Elaeis Guineensis ◽  
Germination Percentage ◽  
Shoot Length ◽  
Indole Butyric Acid

ABSTRACT Oil palm is a woody monocot of economic importance due to high oil production from its fruits. Currently, the conventional method most used to propagate oil palm is seed germination, but success is limited by long time requirements and low germination percentage. An alternative for large-scale propagation of oil palm is the biotechnological technique of somatic embryogenesis. The rooting of plants germinated from somatic embryos is a difficult step, yet it is of great importance for later acclimatization and success in propagation. The aim of this study was to evaluate the effect of the auxins indole acetic acid (IAA) and indole butyric acid (IBA) on the rooting of somatic embryos of Tenera hybrid oil palm. Plants obtained by somatic embryogenesis were inoculated in modified MS medium with 10% sucrose and 0.6% agar and supplemented with IAA or IBA at concentrations of 5 µM, 10 µM, and 15 µM, and the absence of growth regulators. After 120 days, the presence of roots, root type, length of the longest root, number of roots, number of leaves, and shoot length were analyzed. Growth regulators were favorable to rooting; plants cultivated with IBA growth regulator at 15 µM showed higher rooting percentage (87%) and better results for the parameters of number of roots (1.33) and shoot length (9.83).

scholarly journals A Comprehensive Survey on the Terpene Synthase Gene Family Provides New Insight into Its Evolutionary Patterns

2019 ◽  
Vol 11 (8) ◽  
pp. 2078-2098 ◽  
Author(s):  
Shu-Ye Jiang ◽  
Jingjing Jin ◽  
Rajani Sarojam ◽  
Srinivasan Ramachandran
Keyword(s):  
Gene Family ◽  
Large Scale ◽  
Family Members ◽  
Terpene Synthase ◽  
Limited Information ◽  
Terpene Synthases ◽  
Genome Wide ◽  
A Genome ◽  
Family Expansion ◽  
Insight Into

Abstract Terpenes are organic compounds and play important roles in plant growth and development as well as in mediating interactions of plants with the environment. Terpene synthases (TPSs) are the key enzymes responsible for the biosynthesis of terpenes. Although some species were employed for the genome-wide identification and characterization of the TPS family, limited information is available regarding the evolution, expansion, and retention mechanisms occurring in this gene family. We performed a genome-wide identification of the TPS family members in 50 sequenced genomes. Additionally, we also characterized the TPS family from aromatic spearmint and basil plants using RNA-Seq data. No TPSs were identified in algae genomes but the remaining plant species encoded various numbers of the family members ranging from 2 to 79 full-length TPSs. Some species showed lineage-specific expansion of certain subfamilies, which might have contributed toward species or ecotype divergence or environmental adaptation. A large-scale family expansion was observed mainly in dicot and monocot plants, which was accompanied by frequent domain loss. Both tandem and segmental duplication significantly contributed toward family expansion and expression divergence and played important roles in the survival of these expanded genes. Our data provide new insight into the TPS family expansion and evolution and suggest that TPSs might have originated from isoprenyl diphosphate synthase genes.

scholarly journals Identification, Evolutionary and Expression Analysis of PYL-PP2C-SnRK2s Gene Families in Soybean

Plants ◽  
2020 ◽  
Vol 9 (10) ◽  
pp. 1356
Author(s):  
Zhaohan Zhang ◽  
Shahid Ali ◽  
Tianxu Zhang ◽  
Wanpeng Wang ◽  
Linan Xie
Keyword(s):  
Gene Family ◽  
Higher Plants ◽  
Expression Patterns ◽  
Family Members ◽  
Evolutionary Relationship ◽  
Gene Families ◽  
Class Iii ◽  
Sequencing Data ◽  
Entire Genome ◽  
Core Components

Abscisic acid (ABA) plays a crucial role in various aspects of plant growth and development, including fruit development and ripening, seed dormancy, and involvement in response to various environmental stresses. In almost all higher plants, ABA signal transduction requires three core components; namely, PYR/PYL/RCAR ABA receptors (PYLs), type 2C protein phosphatases (PP2Cs), and class III SNF-1-related protein kinase 2 (SnRK2s). The exploration of these three core components is not comprehensive in soybean. This study identified the GmPYL-PP2C-SnRK2s gene family members by using the JGI Phytozome and NCBI database. The gene family composition, conservation, gene structure, evolutionary relationship, cis-acting elements of promoter regions, and its coding protein domains were analyzed. In the entire genome of the soybean, there are 21 PYLs, 36 PP2Cs, and 21 SnRK2s genes; further, by phylogenetic and conservation analysis, 21 PYLs genes are classified into 3 groups, 36 PP2Cs genes are classified into seven groups, and 21 SnRK2s genes are classified into 3 groups. The conserved motifs and domain analysis showed that all the GmPYLs gene family members contain START-like domains, the GmPP2Cs gene family contains PP2Cc domains, and the GmSnRK2s gene family contains S_TK domains, respectively. Furthermore, based on the high-throughput transcriptome sequencing data, the results showed differences in the expression patterns of GmPYL-PP2C-SnRK2s gene families in different tissue parts of the same variety, and the same tissue part of different varieties. Our study provides a basis for further elucidation of the identification of GmPYL-PP2C-SnRK2s gene family members and analysis of their evolution and expression patterns, which helps to understand the molecular mechanism of soybean response to abiotic stress. In addition, this provides a conceptual basis for future studies of the soybean ABA core signal pathway.

OIL PALM BUD ROT IN LATIN AMERICA

2003 ◽  
Vol 39 (3) ◽  
pp. 225-240 ◽  
Author(s):  
H. DE FRANQUEVILLE
Keyword(s):  
Latin America ◽  
Oil Palm ◽  
Native Species ◽  
Large Scale ◽  
Elaeis Guineensis ◽  
Physiological Disorder ◽  
Elaeis Oleifera ◽  
Infectious Origin ◽  
Holding Back

In South and Central America, tens of thousands of hectares of oil palms (Elaeis guineensis Jacq.) are affected by bud-rot types of disease. Having destroyed entire estates in Panama, Colombia, Suriname, Brazil and Ecuador, they are holding back the development of oil palm cultivation in Latin America. The cause is unknown. Indeed, 30 years after these diseases first wreaked havoc on a large scale, it is still not known whether we are dealing with one or more diseases of infectious origin, or with a physiological disorder. Despite lengthy research launched in the early 1980s, no pathogens or insect vectors have been clearly identified. At present, genetics look likely to offer a solution in the medium- to long term, using traits of resistance transmitted by the native species on the American continent, Elaeis oleifera, to the interspecific hybrid E. oleifera×E. guineensis.

Identification and expression analysis of LEA gene family members in cucumber genome

2016 ◽  
Vol 80 (2) ◽  
pp. 225-241 ◽  
Author(s):  
Yasemin Celik Altunoglu ◽  
Pinar Baloglu ◽  
Esra Nurten Yer ◽  
Sefa Pekol ◽  
Mehmet Cengiz Baloglu
Keyword(s):  
Gene Family ◽  
Expression Analysis ◽  
Family Members ◽  
Lea Gene ◽  
Cucumber Genome
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