Gene expression profiling during seed-filling process in peanut with emphasis on oil biosynthesis networks

Gupta, Kapil; Kayam, Galya; Faigenboim-Doron, Adi; Clevenger, Josh; Ozias‐Akins, Peggy; Hovav, Ran

doi:10.1016/j.plantsci.2016.04.014

Cited by 25 publications

(23 citation statements)

References 43 publications

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“…In recent years, Illumina sequencing, one next-generation sequencing (NGS) technology, has been applied for the transcriptional expression studies in many oil plants [16, 31–38], but some short sequences are not so effective to get BLAST hits owing to lack of a characterized protein domain [32, 39]. The recently established 454 sequencing platform can provide the longer reads, and has been used to generate well-defined transcriptomes in many oil plants, such as Siberian apricot, oilseed rape, olive, and peanut [39–43].…”

Section: Introductionmentioning

confidence: 99%

Integrated analysis of 454 and Illumina transcriptomic sequencing characterizes carbon flux and energy source for fatty acid synthesis in developing Lindera glauca fruits for woody biodiesel

Lin

Wang

et al. 2017

Biotechnol Biofuels

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Background Lindera glauca fruit with high quality and quantity of oil has emerged as a novel potential source of biodiesel in China, but the molecular regulatory mechanism of carbon flux and energy source for oil biosynthesis in developing fruits is still unknown. To better develop fruit oils of L. glauca as woody biodiesel, a combination of two different sequencing platforms (454 and Illumina) and qRT-PCR analysis was used to define a minimal reference transcriptome of developing L. glauca fruits, and to construct carbon and energy metabolic model for regulation of carbon partitioning and energy supply for FA biosynthesis and oil accumulation.ResultsWe first analyzed the dynamic patterns of growth tendency, oil content, FA compositions, biodiesel properties, and the contents of ATP and pyridine nucleotide of L. glauca fruits from seven different developing stages. Comprehensive characterization of transcriptome of the developing L. glauca fruit was performed using a combination of two different next-generation sequencing platforms, of which three representative fruit samples (50, 125, and 150 DAF) and one mixed sample from seven developing stages were selected for Illumina and 454 sequencing, respectively. The unigenes separately obtained from long and short reads (201, and 259, respectively, in total) were reconciled using TGICL software, resulting in a total of 60,031 unigenes (mean length = 1061.95 bp) to describe a transcriptome for developing L. glauca fruits. Notably, 198 genes were annotated for photosynthesis, sucrose cleavage, carbon allocation, metabolite transport, acetyl-CoA formation, oil synthesis, and energy metabolism, among which some specific transporters, transcription factors, and enzymes were identified to be implicated in carbon partitioning and energy source for oil synthesis by an integrated analysis of transcriptomic sequencing and qRT-PCR. Importantly, the carbon and energy metabolic model was well established for oil biosynthesis of developing L. glauca fruits, which could help to reveal the molecular regulatory mechanism of the increased oil production in developing fruits.ConclusionsThis study presents for the first time the application of an integrated two different sequencing analyses (Illumina and 454) and qRT-PCR detection to define a minimal reference transcriptome for developing L. glauca fruits, and to elucidate the molecular regulatory mechanism of carbon flux control and energy provision for oil synthesis. Our results will provide a valuable resource for future fundamental and applied research on the woody biodiesel plants.Electronic supplementary materialThe online version of this article (doi:10.1186/s13068-017-0820-2) contains supplementary material, which is available to authorized users.

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Section: Introductionmentioning

confidence: 99%

Integrated analysis of 454 and Illumina transcriptomic sequencing characterizes carbon flux and energy source for fatty acid synthesis in developing Lindera glauca fruits for woody biodiesel

Lin

Wang

et al. 2017

Biotechnol Biofuels

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“…Understanding those specific lipid formation process is extremely important to unravel the unique lipid metabolism and regulation mechanisms [ 10 ]. Recently, transcriptome sequencing and characterization based on the Illumina second-generation sequencing technology has enabled the rapid identification and profiling of mechanisms involving oil content and FA composition in various oil plants, such as soybean [ 11 , 12 ], peanut [ 13 , 14 ], and palm oil [ 15 ]. Similarly with perilla, the flax [ 16 ], sea buckthorn [ 17 ], Camelina sativa [ 18 ], Plukenetia volubilis L. [ 19 ], and tree peony [ 20 ] also rich in ALA in seed oil.…”

Section: Introductionmentioning

confidence: 99%

“…Similarly with perilla, the flax [ 16 ], sea buckthorn [ 17 ], Camelina sativa [ 18 ], Plukenetia volubilis L. [ 19 ], and tree peony [ 20 ] also rich in ALA in seed oil. In sequencing of flax seed, the key embryogenesis regulators were mined [ 14 ]. And more biosynthesis genes contributing in ALA accumulation have been identified in those plant seeds [ 11 , 12 , 13 , 14 , 15 , 16 , 17 , 18 , 19 , 20 ].…”

Section: Introductionmentioning

confidence: 99%

“…In sequencing of flax seed, the key embryogenesis regulators were mined [ 14 ]. And more biosynthesis genes contributing in ALA accumulation have been identified in those plant seeds [ 11 , 12 , 13 , 14 , 15 , 16 , 17 , 18 , 19 , 20 ]. For perilla, 540 unique genes involved in acyl-lipid metabolism from four developmental stages in perilla seeds, and characterized the expression profiles of 43 genes involved in FA and triacylglycerol (TAG) synthesis [ 21 ].…”

Section: Introductionmentioning

confidence: 99%

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RNA Sequencing and Coexpression Analysis Reveal Key Genes Involved in α-Linolenic Acid Biosynthesis in Perilla frutescens Seed

Zhang

Song

et al. 2017

IJMS

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Perilla frutescen is used as traditional food and medicine in East Asia. Its seeds contain high levels of α-linolenic acid (ALA), which is important for health, but is scarce in our daily meals. Previous reports on RNA-seq of perilla seed had identified fatty acid (FA) and triacylglycerol (TAG) synthesis genes, but the underlying mechanism of ALA biosynthesis and its regulation still need to be further explored. So we conducted Illumina RNA-sequencing in seven temporal developmental stages of perilla seeds. Sequencing generated a total of 127 million clean reads, containing 15.88 Gb of valid data. The de novo assembly of sequence reads yielded 64,156 unigenes with an average length of 777 bp. A total of 39,760 unigenes were annotated and 11,693 unigenes were found to be differentially expressed in all samples. According to Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis, 486 unigenes were annotated in the “lipid metabolism” pathway. Of these, 150 unigenes were found to be involved in fatty acid (FA) biosynthesis and triacylglycerol (TAG) assembly in perilla seeds. A coexpression analysis showed that a total of 104 genes were highly coexpressed (r > 0.95). The coexpression network could be divided into two main subnetworks showing over expression in the medium or earlier and late phases, respectively. In order to identify the putative regulatory genes, a transcription factor (TF) analysis was performed. This led to the identification of 45 gene families, mainly including the AP2-EREBP, bHLH, MYB, and NAC families, etc. After coexpression analysis of TFs with highly expression of FAD2 and FAD3 genes, 162 TFs were found to be significantly associated with two FAD genes (r > 0.95). Those TFs were predicted to be the key regulatory factors in ALA biosynthesis in perilla seed. The qRT-PCR analysis also verified the relevance of expression pattern between two FAD genes and partial candidate TFs. Although it has been reported that some TFs are involved in seed development, more direct evidence is still needed to verify their function. However, these findings can provide clues to reveal the possible molecular mechanisms of ALA biosynthesis and its regulation in perilla seed.

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“…High-quality RNAseq data have allowed the identification and an accurate quantification of expression of transcription factors and key genes related with lipid metabolic pathways in soybean [20], Jatropha curcas [21], Arabidopsis [22], peanut [23] and castor bean [24]. In castor, comparison of expression between tissues allowed identification of candidate genes which may be important for triricinolein synthesis in seed in addition to the oleate-12 hydroxylase.…”

Section: Understanding Metabolic Routes In Oilseed Cropsmentioning

confidence: 99%

Genetic Improvement of Oilseed Crops Using Modern Biotechnology

Villanueva-Mejía¹,

Álvarez²

2017

Advances in Seed Biology

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In 2009, big challenges facing the agricultural sector in the twenty-first century were presented to the world. Human population growth, increased life expectancy, loss of biodiversity, climate change and accelerated land degradation are the main factors contributing to rethink agriculture system production. In that scenery, modern biotechnology has set a stage for the advancement of agricultural practices and it is clearly an important ally to apply a broad array of technologies and innovative systems where they are most needed, such as enhancing crop productivity, increasing yields, and ultimately ensuring food security. One of the biggest challenges is related to technify production systems, but with no doubt, developing genetic improvement toward getting an efficient and sustainable agriculture, generating new seed qualities (new traits), such as, among others, to upset fatty acids content in oilseed crops have been growing up significantly due to industry interest. In this study, a review about the main advances in genetic improvement of some oilseed crops, starting with omics to understand metabolic routes and to find out key genes in seed oil production, and also, getting in use of modern biotechnology to alter the production of fatty acids, and to face biotic challenges in oilseed crops is presented.

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Gene expression profiling during seed-filling process in peanut with emphasis on oil biosynthesis networks

Cited by 25 publications

References 43 publications

Integrated analysis of 454 and Illumina transcriptomic sequencing characterizes carbon flux and energy source for fatty acid synthesis in developing Lindera glauca fruits for woody biodiesel

Integrated analysis of 454 and Illumina transcriptomic sequencing characterizes carbon flux and energy source for fatty acid synthesis in developing Lindera glauca fruits for woody biodiesel

RNA Sequencing and Coexpression Analysis Reveal Key Genes Involved in α-Linolenic Acid Biosynthesis in Perilla frutescens Seed

Genetic Improvement of Oilseed Crops Using Modern Biotechnology

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