Transcriptome analysis of unsaturated fatty acids biosynthesis shows essential genes in sprouting of Acer truncatum Bunge seeds

Chen, Dong-Ju; Luo, Xue‐Gang; Liu, Yan; Si, Chuanling; Wang, Nan; He, Hongbin; Zhang, Tongcun

doi:10.1016/j.fbio.2020.100739

Cited by 5 publications

(4 citation statements)

References 38 publications

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“…Among them, ABI3, FUS3, and WRI1 have been identified in many plants and can regulate the expression of functional genes involved in fatty acid synthesis, thereby regulating seed oil accumulation. Transcriptome analysis of walnut kernel development found that WRI1 was involved in lipid biosynthesis and polyunsaturated fatty acid metabolism [ 73 ]. In Torreya grandis, TgWRI1 and TgFUS3 are involved in the regulation of genes related to lipid biosynthesis during seed development [ 74 ].…”

Section: Discussionmentioning

confidence: 99%

The Manchurian Walnut Genome: Insights into Juglone and Lipid Biosynthesis

Cai

Zhang

et al. 2022

GigaScience

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Background Manchurian walnut (Juglans mandshurica Maxim.) is a tree with multiple industrial uses and medicinal properties in the Juglandaceae family (walnuts and hickories). J. mandshurica produces juglone, which is a toxic allelopathic agent and has potential utilization value. Furthermore, the seed of J. mandshurica is rich in various unsaturated fatty acids and has high nutritive value. Findings Here, we present a high-quality chromosome-scale reference genome assembly and annotation for J. mandshurica (n = 16) with a contig N50 of 21.4 Mb by combining PacBio high-fidelity reads with high-throughput chromosome conformation capture data. The assembled genome has an estimated sequence size of 548.7 Mb and consists of 657 contigs, 623 scaffolds, and 40,453 protein-coding genes. In total, 60.99% of the assembled genome consists of repetitive sequences. Sixteen super-scaffolds corresponding to the 16 chromosomes were assembled, with a scaffold N50 length of 33.7 Mb and a BUSCO complete gene percentage of 98.3%. J. mandshurica displays a close sequence relationship with Juglans cathayensis, with a divergence time of 13.8 million years ago. Combining the high-quality genome, transcriptome, and metabolomics data, we constructed a gene-to-metabolite network and identified 566 core and conserved differentially expressed genes, which may be involved in juglone biosynthesis. Five CYP450 genes were found that may contribute to juglone accumulation. NAC, bZip, NF-YA, and NF-YC are positively correlated with the juglone content. Some candidate regulators (e.g., FUS3, ABI3, LEC2, and WRI1 transcription factors) involved in the regulation of lipid biosynthesis were also identified. Conclusions Our genomic data provide new insights into the evolution of the walnut genome and create a new platform for accelerating molecular breeding and improving the comprehensive utilization of these economically important tree species.

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Section: Discussionmentioning

confidence: 99%

The Manchurian Walnut Genome: Insights into Juglone and Lipid Biosynthesis

Cai

Zhang

et al. 2022

GigaScience

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“…Due to its elite hardwood, it is widely used for timber production. Seeds and leaves are rich in oils, nervonic acid and tannins, which can also be used as raw materials for food processing and pharmaceutical development [ 25 , 26 , 27 ]. Therefore, increasing attention has been given to the various uses of A. truncatum , such as ornamental greening, medicinal value and ecological benefit, and research on A. truncatum has also increased.…”

Section: Introductionmentioning

confidence: 99%

Genome-Wide Identification and Analysis of the WRKY Gene Family and Cold Stress Response in Acer truncatum

Wei

et al. 2021

Genes

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WRKY transcription factors constitute one of the largest gene families in plants and are involved in many biological processes, including growth and development, physiological metabolism, and the stress response. In earlier studies, the WRKY gene family of proteins has been extensively studied and analyzed in many plant species. However, information on WRKY transcription factors in Acer truncatum has not been reported. In this study, we conducted genome-wide identification and analysis of the WRKY gene family in A. truncatum, 54 WRKY genes were unevenly located on all 13 chromosomes of A. truncatum, the highest number was found in chromosomes 5. Phylogenetic relationships, gene structure, and conserved motif identification were constructed, and the results affirmed 54 AtruWRKY genes were divided into nine subgroup groups. Tissue species analysis of AtruWRKY genes revealed which were differently exhibited upregulation in flower, leaf, root, seed and stem, and the upregulation number were 23, 14, 34, 18, and 8, respectively. In addition, the WRKY genes expression in leaf under cold stress showed that more genes were significantly expressed under 0, 6 and 12 h cold stress. The results of this study provide a new insight the regulatory function of WRKY genes under abiotic and biotic stresses.

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“…This study signified the presence of 106 unigenes involved in oil biosynthesis pathways ( Figure 9 ). In general, lipid and FA syntheses are initiated with the supply of acetyl-CoA substrate ( Wang et al, 2019 ), which is first converted to malonyl-CoA ( Chen et al, 2020 ), and carbon flux is initiated via FA synthase and most other enzymes associated with lipid and FA biosynthesis ( Huang, 1996 ). In this study, the initiation and acyl chain elongation of de novo FA biosynthesis were reported to be possibly regulated by 50 unigenes, and the latter showed apparent down-regulation of at least one isoform in S4 compared with S1, suggesting their functional involvement in the initiation of FA biosynthesis ( Figure 9 ).…”

Section: Discussionmentioning

confidence: 99%

“…From the previous studies, it can be speculated that the integration of transcriptomic and lipidomic studies can provide a comprehensive view of the dynamic processes regulating the seed development and oil biosynthesis in various plants ( Dossa et al, 2017 ; Wang et al, 2019 ; Chen et al, 2020 ). However, no such data have been collected for sesame seeds to date.…”

Section: Introductionmentioning

confidence: 99%

Integration of miRNAs, Degradome, and Transcriptome Omics Uncovers a Complex Regulatory Network and Provides Insights Into Lipid and Fatty Acid Synthesis During Sesame Seed Development

Zhang

Thakur

et al. 2021

Front. Plant Sci.

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Sesame (Sesamum indicum L.) has always been known as a health-promoting oilseed crop because of its nutrient-rich oil. In recent years, studies have focused on lipid and fatty acid (FA) biosynthesis in various plants by high-throughput sequencing. Here, we integrated transcriptomics, small RNAs, and the degradome to establish a comprehensive reserve intensive on key regulatory micro RNA (miRNA)-targeting circuits to better understand the transcriptional and translational regulation of the oil biosynthesis mechanism in sesame seed development. Deep sequencing was performed to differentially express 220 miRNAs, including 65 novel miRNAs, in different developmental periods of seeds. GO and integrated KEGG analysis revealed 32 pairs of miRNA targets with negatively correlated expression profiles, of which 12 miRNA-target pairs were further confirmed by RT-PCR. In addition, a regulatory co-expression network was constructed based on the differentially expressed gene (DEG) profiles. The FAD2, LOC10515945, LOC105161564, and LOC105162196 genes were clustered into groups that regulate the accumulation of unsaturated fatty acid (UFA) biosynthesis. The results provide a unique advanced molecular platform for the study of lipid and FA biosynthesis, and this study may serve as a new theoretical reference to obtain increased levels of UFA from higher-quality sesame seed cultivars and other plants.

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Transcriptome analysis of unsaturated fatty acids biosynthesis shows essential genes in sprouting of Acer truncatum Bunge seeds

Cited by 5 publications

References 38 publications

The Manchurian Walnut Genome: Insights into Juglone and Lipid Biosynthesis

The Manchurian Walnut Genome: Insights into Juglone and Lipid Biosynthesis

Genome-Wide Identification and Analysis of the WRKY Gene Family and Cold Stress Response in Acer truncatum

Integration of miRNAs, Degradome, and Transcriptome Omics Uncovers a Complex Regulatory Network and Provides Insights Into Lipid and Fatty Acid Synthesis During Sesame Seed Development

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