Dynamics of metabolites and key regulatory proteins in the developing seeds of Pongamia pinnata, a potential biofuel tree species

Singha, Kambam Tamna; Sreeharsha, Rachapudi Venkata; Mariboina, Sureshbabu; Reddy, A. Ramachandra

doi:10.1016/j.indcrop.2019.111621

Cited by 14 publications

(4 citation statements)

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“…Accumulation of unsaturated fatty acids is believed to be an ideal feature for biodiesel production with good cetane number. The FAMEs of pongamia oil belonging to different geographical locations have shown a sizeable portion of oleic acid and linoleic acid as the seed progresses to maturity by the end of the growing season ( Pavithra et al, 2012 ; Singha et al, 2019 ). The oil biosynthesis is highly regulated temporally through lipid biosynthetic and degradation pathways wherein crucial rate-limiting enzymes are involved.…”

Section: Discussionmentioning

confidence: 99%

“…Oil was extracted from 5 pongamia accessions (pooled seeds of ten replicative plants of each accession) by using the Soxhlet extraction method using hexane as the solvent according to Singha et al (2019) . Briefly, seeds (5 g) were grounded to fine powder, and oil was extracted with 150 ml of hexane at distillation temperature for 3 h in the Soxhlet extractor using a heating mantle.…”

Section: Methodsmentioning

confidence: 99%

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Genome sequencing and analysis uncover the regulatory elements involved in the development and oil biosynthesis of Pongamia pinnata (L.) – A potential biodiesel feedstock

Sreeharsha

Mudalkar²,

Reddy

2022

Front. Plant Sci.

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Due to rapid industrialization, the consumption of petro-products has increased, while fossil fuel resources have been gradually depleted. There has been a resurgence of interest in plant-derived biofuels as a sustainable alternative to fossil fuels for the purpose of reducing greenhouse gas emissions. Pongamia pinnata L., which is also known as Millettia pinnata is an oil-yielding, leguminous tree with a large and complex genome. Despite its multiple industrial applications, this orphan tree species has inconsistent yields and a limited understanding of its functional genomics. We assessed physiological and morphological characteristics of five high-yielding pongamia accessions and deduced important yield descriptors. Furthermore, we sequenced the genome of this potential biofuel feedstock using Illumina HiSeq, NextSeq, and MiSeq platforms to generate paired-end reads. Around 173 million processed reads amounting to 65.2 Gb were assembled into a 685 Mb genome, with a gap rate of 0.02%. The sequenced scaffolds were used to identify 30,000 gene models, 406,385 Simple-Sequence-Repeat (SSR) markers, and 43.6% of repetitive sequences. We further analyzed the structural information of genes belonging to certain key metabolic pathways, including lipid metabolism, photosynthesis, circadian rhythms, plant-pathogen interactions, and karanjin biosynthesis, all of which are commercially significant for pongamia. A total of 2,219 scaffolds corresponding to 29 transcription factor families provided valuable information about gene regulation in pongamia. Similarity studies and phylogenetic analysis revealed a monophyletic group of Fabaceae members wherein pongamia out-grouped from Glycine max and Cajanus cajan, revealing its unique ability to synthesize oil for biodiesel. This study is the first step toward completing the genome sequence of this imminent biofuel tree species. Further attempts at re-sequencing with different read chemistry will certainly improve the genetic resources at the chromosome level and accelerate the molecular breeding programs.

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Section: Discussionmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Genome sequencing and analysis uncover the regulatory elements involved in the development and oil biosynthesis of Pongamia pinnata (L.) – A potential biodiesel feedstock

Sreeharsha

Mudalkar²,

Reddy

2022

Front. Plant Sci.

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“…Although various oil, lipid, and flavonoid metabolites have been identified in Pongamia, the genes associated with the biosynthesis of these metabolites remain unclear. Previous studies have attempted to elucidate the mechanisms underlying oil and lipid accumulation in Pongamia seeds using transcriptomic and metabolomic techniques [ 12 , 23 , 24 ]. However, the absence of a high-quality reference genome for Pongamia has constrained comprehensive investigation of this mechanism at the whole-genome level.…”

Section: Introductionmentioning

confidence: 99%

Comparative analysis of lipid and flavonoid biosynthesis between Pongamia and soybean seeds: genomic, transcriptional, and metabolic perspectives

Liu,

Huang,

Zhao

et al. 2024

Biotechnol Biofuels

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Background Soybean (Glycine max) is a vital oil-producing crop. Augmenting oleic acid (OA) levels in soybean oil enhances its oxidative stability and health benefits, representing a key objective in soybean breeding. Pongamia (Pongamia pinnata), known for its abundant oil, OA, and flavonoid in the seeds, holds promise as a biofuel and medicinal plant. A comparative analysis of the lipid and flavonoid biosynthesis pathways in Pongamia and soybean seeds would facilitate the assessment of the potential value of Pongamia seeds and advance the genetic improvements of seed traits in both species. Results The study employed multi-omics analysis to systematically compare differences in metabolite accumulation and associated biosynthetic genes between Pongamia seeds and soybean seeds at the transcriptional, metabolic, and genomic levels. The results revealed that OA is the predominant free fatty acid in Pongamia seeds, being 8.3 times more abundant than in soybean seeds. Lipidomics unveiled a notably higher accumulation of triacylglycerols (TAGs) in Pongamia seeds compared to soybean seeds, with 23 TAG species containing OA. Subsequently, we identified orthologous groups (OGs) involved in lipid biosynthesis across 25 gene families in the genomes of Pongamia and soybean, and compared the expression levels of these OGs in the seeds of the two species. Among the OGs with expression levels in Pongamia seeds more than twice as high as in soybean seeds, we identified one fatty acyl-ACP thioesterase A (FATA) and two stearoyl-ACP desaturases (SADs), responsible for OA biosynthesis, along with two phospholipid:diacylglycerol acyltransferases (PDATs) and three acyl-CoA:diacylglycerol acyltransferases (DGATs), responsible for TAG biosynthesis. Furthermore, we observed a significantly higher content of the flavonoid formononetin in Pongamia seeds compared to soybean seeds, by over 2000-fold. This difference may be attributed to the tandem duplication expansions of 2,7,4ʹ-trihydroxyisoflavanone 4ʹ-O-methyltransferases (HI4ʹOMTs) in the Pongamia genome, which are responsible for the final step of formononetin biosynthesis, combined with their high expression levels in Pongamia seeds. Conclusions This study extends beyond observations made in single-species research by offering novel insights into the molecular basis of differences in lipid and flavonoid biosynthetic pathways between Pongamia and soybean, from a cross-species comparative perspective.

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“…Pongamia pinnata ( Millettia pinnata ) is a medium-sized leguminous tree belonging to the Fabaceae family ( Marriboina et al, 2021 ). Pongamia seed oil with 50% oleic acid content can be used as potential feedstock for biofuel ( Calica, 2017 ; Singha et al, 2019 ). With nitrogen-fixing ability, Pongamia can fix 47.4 mg of nitrogen per plant under normal conditions ( Calica and Gresshoff, 2019 ).…”

Section: Introductionmentioning

confidence: 99%

Physiological, Biochemical, and Root Proteome Networks Revealed New Insights Into Salt Tolerance Mechanisms in Pongamia pinnata (L.) Pierre

et al. 2022

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Cultivation of potential biofuel tree species such as Pongamia pinnata would rehabilitate saline marginal lands toward economic gains. We carried out a physiological, biochemical, and proteomic analysis to identify key regulatory responses which are associated with salt tolerance mechanisms at the shoot and root levels. Pongamia seedlings were grown at 300 and 500 mM NaCl (∼3% NaCl; sea saline equivalent) concentrations for 15 and 30 days, gas exchange measurements including leaf net photosynthetic rate (Asat), stomatal conductance (gs), and transpiration rate (E), and varying chlorophyll a fluorescence kinetics were recorded. The whole root proteome was quantified using the free-labeled nanoLC-MS/MS technique to investigate crucial proteins involved in signaling pathways associated with salt tolerance. Pongamia showed no visible salt-induced morphological symptoms. However, Pongamia showed about 50% decline in gas exchange parameters including Asat, E, and gs 15 and 30 days after salt treatment (DAS). The maximum potential quantum efficiency of photosystem (PS) II (Fv/Fm) was maintained at approximately 0.8 in salt-treated plants. The thermal component of PSII (DIo) was increased by 1.6-fold in the salt-treated plants. A total of 1,062 protein species were identified with 130 commonly abundant protein species. Our results also elucidate high abundance of protein species related to flavonoid biosynthesis, seed storage protein species, and carbohydrate metabolism under salt stress. Overall, these analyses suggest that Pongamia exhibited sustained leaf morphology by lowering net photosynthetic rates and emitting most of its light energy as heat. Our root proteomic results indicated that these protein species were most likely recruited from secondary and anaerobic metabolism, which could provide defense for roots against Na+ toxicity under salt stress conditions.

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Dynamics of metabolites and key regulatory proteins in the developing seeds of Pongamia pinnata, a potential biofuel tree species

Cited by 14 publications

References 53 publications

Genome sequencing and analysis uncover the regulatory elements involved in the development and oil biosynthesis of Pongamia pinnata (L.) – A potential biodiesel feedstock

Genome sequencing and analysis uncover the regulatory elements involved in the development and oil biosynthesis of Pongamia pinnata (L.) – A potential biodiesel feedstock

Comparative analysis of lipid and flavonoid biosynthesis between Pongamia and soybean seeds: genomic, transcriptional, and metabolic perspectives

Physiological, Biochemical, and Root Proteome Networks Revealed New Insights Into Salt Tolerance Mechanisms in Pongamia pinnata (L.) Pierre

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