scholarly journals Evidence-based gene models for structural and functional annotations of the oil palm genome

2017 ◽  
Author(s):  
Chan Kuang Lim ◽  
Tatiana V. Tatarinova ◽  
Rozana Rosli ◽  
Nadzirah Amiruddin ◽  
Norazah Azizi ◽  
...  
Keyword(s):  
Fatty Acid ◽  
Oil Palm ◽  
Fatty Acid Biosynthesis ◽  
Gene Prediction ◽  
Biological Data ◽  
Acid Biosynthesis ◽  
Important Resource ◽  
Intronless Genes ◽  
Starting Point ◽  
And Function

AbstractThe advent of rapid and inexpensive DNA sequencing has led to an explosion of data that must be transformed into knowledge about genome organization and function. Gene prediction is customarily the starting point for genome analysis. This paper presents a bioinformatics study of the oil palm genome, including a comparative genomics analysis, database and tools development, and mining of biological data for genes of interest. We annotated 26,087 oil palm genes integrated from two gene-prediction pipelines, Fgenesh++ and Seqping. As case studies, we conducted comprehensive investigations on intronless, resistance and fatty acid biosynthesis genes, and demonstrated that the current gene prediction set is of high quality. 3,672 intronless genes were identified in the oil palm genome, an important resource for evolutionary study. Further scrutiny of the oil palm genes revealed 210 candidate resistance genes involved in pathogen defense. Fatty acids have diverse applications ranging from food to industrial feedstock, and we identified 42 key genes involved in fatty-acid biosynthesis in oil palm mesocarp and kernel. These results provide an important resource for studies on plant genomes and a theoretical foundation for marker-assisted breeding of oil palm and related crops.

scholarly journals Comparative genomic and transcriptomic analysis of selected fatty acid biosynthesis genes and CNL disease resistance genes in oil palm

PLoS ONE ◽  
2018 ◽  
Vol 13 (4) ◽  
pp. e0194792 ◽  
Author(s):  
Rozana Rosli ◽  
Nadzirah Amiruddin ◽  
Mohd Amin Ab Halim ◽  
Pek-Lan Chan ◽  
Kuang-Lim Chan ◽  
...  
Keyword(s):  
Disease Resistance ◽  
Fatty Acid ◽  
Resistance Genes ◽  
Oil Palm ◽  
Fatty Acid Biosynthesis ◽  
Disease Resistance Genes ◽  
Transcriptomic Analysis ◽  
Comparative Genomic ◽  
Acid Biosynthesis

scholarly journals Abscisic Acid Improves Linoleic Acid Accumulation Possibly by Promoting Expression of EgFAD2 and Other Fatty Acid Biosynthesis Genes in Oil Palm Mesocarp

2021 ◽  
Vol 12 ◽  
Author(s):  
Peng Shi ◽  
Wei Hua ◽  
Yin Min Htwe ◽  
Dapeng Zhang ◽  
Jun Li ◽  
...  
Keyword(s):  
Abscisic Acid ◽  
Fatty Acid ◽  
Linoleic Acid ◽  
Oil Palm ◽  
Fatty Acid Biosynthesis ◽  
Enrichment Analysis ◽  
Linoleic Acid Content ◽  
Pathway Enrichment Analysis ◽  
Acid Biosynthesis ◽  
Palm Fruit

Abscisic acid plays an important role in fruit development. However, the effect of ABA on fatty acid biosynthesis in oil palm is still unknown. In this study, ABA treatments (CK, A1–A4) were applied to oil palm fruit at 16 WAP (weeks after pollination), and fatty acids in the mesocarp at 24 WAP were analyzed by GC-MS. Results showed that linoleic acid content under treatment A2 (20 μM ABA) was significantly higher (slightly increased by 8.33%) than the control. Therefore, mesocarp samples of A2, and the control at 16, 20, and 24 WAP was sampled for RNA-Seq. KEGG pathway enrichment analysis showed that 43 genes were differentially expressed in the fatty acid biosynthesis pathway, of which expression of EgFAD2 (unigene 105050201) under 20 μM ABA treatment was 1.84-fold higher than in the control at 20 WAP. Further sequence analysis found that unigene 105050201 had more ABA-responsive elements (ABRE), complete conserved domains, and a C-terminal signaling motif among two FAD2 copies. Furthermore, WGCNA and correlation analysis showed co-expression of EgFAD2 (unigene 105050201) with transcription factors (TFs) (WRI1, AP2-EREBP, bZIP, bHLH, C2C2-Dof, MYB, NAC, and WRKY), ABA signaling genes (PYR, PP2C, SnRK, and ABI5), and other genes involved in fatty acid biosynthesis (FATA, FATB, LACS, SAD, Oleosins, and so on). These results indicated that ABA treatment promoted the expression of FAD2 and other genes involved in fatty acid biosynthesis, which possibly resulted in the accumulation of linoleic acid. This study will be helpful for understanding the possible mechanisms through which ABA affects fatty acid biosynthesis and their accumulation in the mesocarp of oil palm.

Inhibition of early steps of de novo fatty-acid biosynthesis by different xenobiotica

1991 ◽  
Vol 81 (2) ◽  
pp. 251-255
Author(s):  
Manfred Focke ◽  
Andrea Feld ◽  
Hartmut K. Lichtenthaler
Keyword(s):  
Fatty Acid ◽  
Fatty Acid Biosynthesis ◽  
De Novo ◽  
Acid Biosynthesis

Development of 'S', 'N’ Heterocycles as Antimycobacterials Targeting Fatty Acid Biosynthesis

2019 ◽  
Vol 15 ◽  
Author(s):  
L. K. Dahiwade ◽  
S. R. Rochlani ◽  
P. B. Choudhari ◽  
R. P. Dhavale ◽  
H. N. Moreira
Keyword(s):  
Fatty Acid ◽  
Fatty Acid Biosynthesis ◽  
Antimycobacterial Activity ◽  
Drug Candidate ◽  
Causative Organism ◽  
Present Communication ◽  
Acid Biosynthesis ◽  
Rational Development ◽  
After Cancer ◽  
Drug Resistant Strains

Background: Mycobacterium tuberculosis is a causative organism of tuberculosis, which is most deadly disease after cancer in a current decade. The development of multidrug and broadly drug- resistant strains making the tuberculosis problem more and more critical. In last 40 years, only one molecule is added to the treatment regimen. Generally, drug design and development programs are targeted proteins whose function is known to be essential to the bacterial cell. Objectives: Reported here are the development of 'S', 'N’ heterocycles as antimycobacterials targeting fatty acid biosynthesis. Material and Methods: In the present communication, rational development of anti-mycobacterial agent's targeting fatty acid biosynthesis has been done by integrating the pocket modelling and virtual analysis. Results: The identified potential 33 lead compounds were synthesized, characterized by physicochemical and spectroscopic methods like IR, NMR spectroscopy and further screened for antimycobacterial activity using isoniazid as standard. All the designed compounds have shown profound antimycobacterial activity. Conclusion: In this present communication, we found that 3c, 3f, 3l and 4k molecules had expressive desirable biological activity and specific interactions with fatty acids. Further optimization of these leads is necessary for the development of potential antimycobacterial drug candidate having less side effects.

scholarly journals Genome-Wide Mapping of Histone H3 Lysine 4 Trimethylation (H3K4me3) and Its Involvement in Fatty Acid Biosynthesis in Sunflower Developing Seeds

Plants ◽  
2021 ◽  
Vol 10 (4) ◽  
pp. 706
Author(s):  
Antonio J. Moreno-Pérez ◽  
Raquel Martins-Noguerol ◽  
Cristina DeAndrés-Gil ◽  
Mónica Venegas-Calerón ◽  
Rosario Sánchez ◽  
...  
Keyword(s):  
Fatty Acid ◽  
Chromatin Remodeling ◽  
Molecular Mechanisms ◽  
Acid Metabolism ◽  
Fatty Acid Biosynthesis ◽  
Acid Synthesis ◽  
Sunflower Seeds ◽  
Acid Biosynthesis ◽  
Functional Regions ◽  
Genome Wide

Histone modifications are of paramount importance during plant development. Investigating chromatin remodeling in developing oilseeds sheds light on the molecular mechanisms controlling fatty acid metabolism and facilitates the identification of new functional regions in oil crop genomes. The present study characterizes the epigenetic modifications H3K4me3 in relationship with the expression of fatty acid-related genes and transcription factors in developing sunflower seeds. Two master transcriptional regulators identified in this analysis, VIV1 (homologous to Arabidopsis ABI3) and FUS3, cooperate in the regulation of WRINKLED 1, a transcriptional factor regulating glycolysis, and fatty acid synthesis in developing oilseeds.

scholarly journals Serratia symbiotica Enhances Fatty Acid Metabolism of Pea Aphid to Promote Host Development

2021 ◽  
Vol 22 (11) ◽  
pp. 5951
Author(s):  
Xiaofei Zhou ◽  
Xiaoyu Ling ◽  
Huijuan Guo ◽  
Keyan Zhu-Salzman ◽  
Feng Ge ◽  
...  
Keyword(s):  
Body Weight ◽  
Fatty Acid ◽  
Myristic Acid ◽  
Fatty Acid Synthase ◽  
Fatty Acid Biosynthesis ◽  
Acid Biosynthesis ◽  
Pea Aphids ◽  
Serratia Symbiotica ◽  
Aphid Host ◽  
Host Development

Bacterial symbionts associated with insects are often involved in host development and ecological adaptation. Serratia symbiotica, a common facultative endosymbiont harbored in pea aphids, improves host fitness and heat tolerance, but studies concerning the nutritional metabolism and impact on the aphid host associated with carrying Serratia are limited. In the current study, we showed that Serratia-infected aphids had a shorter nymphal developmental time and higher body weight than Serratia-free aphids when fed on detached leaves. Genes connecting to fatty acid biosynthesis and elongation were up-regulated in Serratia-infected aphids. Specifically, elevated expression of fatty acid synthase 1 (FASN1) and diacylglycerol-o-acyltransferase 2 (DGAT2) could result in accumulation of myristic acid, palmitic acid, linoleic acid, and arachidic acid in fat bodies. Impairing fatty acid synthesis in Serratia-infected pea aphids either by a pharmacological inhibitor or through silencing FASN1 and DGAT2 expression prolonged the nymphal growth period and decreased the aphid body weight. Conversely, supplementation of myristic acid (C14:0) to these aphids restored their normal development and weight gain. Our results indicated that Serratia promoted development and growth of its aphid host through enhancing fatty acid biosynthesis. Our discovery has shed more light on nutritional effects underlying the symbiosis between aphids and facultative endosymbionts.

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