De novo Assembly and Characterization of the Fruit Transcriptome of Idesia polycarpa Reveals Candidate Genes for Lipid Biosynthesis

Li, Rongjun; Gao, Xiang; Li, Lin-Mao; Liu, Xiulin; Wang, Zhou-Ya; Lü, Shiyou

doi:10.3389/fpls.2016.00801

Cited by 22 publications

(29 citation statements)

References 50 publications

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“…Therefore, we attempted to uncover the key genes and pathways of elm fruit. RNA-Seq has been used to accurately monitor gene expression in hundreds of fruiting plants, such as sweet orange (Citrus sinensis) [44], mango (Mangifera indica) [28], Cucumis melo [45], and Idesia polycarpa [46], to track gene expression trends during fruit development. The synchronous dysregulation of key regulators in pathways verified by RNA-Seq and/or qRT-PCR analyses is valuable for understanding transcriptomic dynamics during elm fruit development.…”

Section: Discussionmentioning

confidence: 99%

Transcriptome Analysis of Elm (Ulmus pumila) Fruit to Identify Phytonutrients Associated Genes and Pathways

Zhang¹,

Li²,

Wang³

et al. 2019

Forests

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Plant fruit is an important source of natural active phytonutrients that are profitable for human health. Elm (Ulmus pumila) fruit is considered as natural plant food in China that is rich in nutrients. In the present study, high-throughput RNA sequencing was performed in U. pumila edible fruits and leaves and 11,386 unigenes were filtered as dysregulated genes in fruit samples, including 5231 up- and 6155 downregulated genes. Hundreds of pathways were predicted to participate in seed development and phytonutrient biosynthesis in U. pumila by GO, MapMan, and KEGG enrichment analysis, including “seed maturation”, “glycine, serine, and threonine metabolism” and “phenylpropanoid biosynthesis”. ABA-mediated glucose response-related ethylene-activated signaling pathway (e.g., ABI4) were supposed to associate with elm fruit development; unsaturated fatty acids pathway (e.g., ACX2 and SAD) were predicted to participate in determination of fatty acid composition in elm fruit; flavonoid and coumarins biosynthesis (e.g., CYP98A3 and CCoAOMT1) were demonstrated to correlate with the bioactivity of elm fruits in human cancer and inflammation resistance. To provide more information about fruit developmental status, the qRT-PCR analysis for key genes of “phenylpropanoid biosynthesis” and “alpha-Linolenic acid metabolism” were conducted in samples of young fruits, ripe fruit, old fruit, and leaves. Two biosynthetic pathways for unsaturated fatty acid and Jasmonic acid (JA) were deduced to be involved in fruit development in U. pumila and the phenylpropanoid glycoside, syringin, was speculated to accumulate in the early development stages of elm fruit. Our transcriptome data supports molecular clues for seed development and biologically active substances in elm fruits.

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Section: Discussionmentioning

confidence: 99%

Transcriptome Analysis of Elm (Ulmus pumila) Fruit to Identify Phytonutrients Associated Genes and Pathways

Zhang¹,

Li²,

Wang³

et al. 2019

Forests

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“…Data analysis was performed as described previously (Li et al ., 2016b). RNA degradation and contamination were monitored on 1% agarose gels.…”

Section: Methodsmentioning

confidence: 99%

“…RNA-sequencing (RNA-Seq) analysis RNA of HepG2 cells stably expressing wild-type (WT) or P24A mutant HDGF was extracted for RNA-Seq analysis. Data analysis was performed as described previously (Li et al, 2016b). RNA degradation and contamination were monitored on 1% agarose gels.…”

Section: Coimmunoprecipitationmentioning

confidence: 99%

Role of hepatoma‐derived growth factor in promoting de novo lipogenesis and tumorigenesis in hepatocellular carcinoma

et al. 2018

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Although identified as a growth factor, the mechanism by which hepatoma‐derived growth factor (HDGF) promotes cancer development remains unclear. We found that nuclear but not cytoplasmic HDGF is closely associated with prognosis of hepatocellular carcinoma (HCC). RNA‐sequencing analysis further demonstrated that the nuclear role of HDGF involved regulation of transcription of lipid metabolism genes. HDGF‐induced expression of lipogenic genes was mainly associated with activation of sterol regulatory element binding protein (SREBP) transcription factor. Coexpression of SREBP‐1 and nuclear HDGF predicts poor prognosis for HCC. In addition, by changing the first amino acid of the PWWP domain from proline to alanine, the type of PWWP domain changed from P‐ to A‐type, resulting in inability to induce SREBP‐1‐mediated gene transcription. The type of PWWP domain affects the recruitment of the C‐terminal binding protein‐1 transcriptional repressor on the promoter of the lipogenic gene. Our data indicate that HDGF acts as a coactivator of SREBP1‐mediated transcription of lipogenic genes. The PWWP domain is crucial for HDGF to promote lipogenesis. Moreover, transcriptional regulation of nuclear HDGF plays important roles in the development of HCC.

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“…Chemicals produced by the family are varied. For example, the early modern medicine aspirin was first isolated from the bark of willows and poplars, while Idesia fruits synthesize an abundant oil containing unsaturated fatty acids (Li et al., ). In addition, poplars are among the keystone components of the temperate and boreal forest communities in the North Hemisphere and are widely cultivated worldwide, accounting for more than half of the planted forests in China used for the paper, pulp, and wood industries (Hamzeh & Dayanandan, ; Stettler, Bradshaw, Heilman, & Hinckley, ).…”

Section: Introductionmentioning

confidence: 99%

Plastome phylogeny and lineage diversification of Salicaceae with focus on poplars and willows

Zhang

Wang

et al. 2018

Ecology and Evolution

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Phylogenetic relationships and lineage diversification of the family Salicaceae sensu lato (s.l.) remain poorly understood. In this study, we examined phylogenetic relationships between 42 species from six genera based on the complete plastomes. Phylogenetic analyses of 77 protein coding genes of the plastomes produced good resolution of the interrelationships among most sampled species and the recovered clades. Of the sampled genera from the family, Flacourtia was identified as the most basal and the successive clades comprised both Itoa and Poliothyrsis, Idesia, two genera of the Salicaceae sensu stricto (s.s.) (Populus and Salix). Five major subclades were recovered within the Populus clade. These subclades and their interrelationships are largely inconsistent with morphological classifications and molecular phylogeny based on nuclear internal transcribed spacer sequence variations. Two major subclades were identified for the Salix clade. Molecular dating suggested that species diversification of the major subclades in the Populus and Salix clades occurred mainly within the recent Pliocene. In addition, we found that the rpl32 gene was lost and the rps7 gene evolved into a pseudogene multiple times in the sampled genera of the Salicaceae s.l. Compared with previous studies, our results provide a well‐resolved phylogeny from the perspective of the plastomes.

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De novo Assembly and Characterization of the Fruit Transcriptome of Idesia polycarpa Reveals Candidate Genes for Lipid Biosynthesis

Cited by 22 publications

References 50 publications

Transcriptome Analysis of Elm (Ulmus pumila) Fruit to Identify Phytonutrients Associated Genes and Pathways

Transcriptome Analysis of Elm (Ulmus pumila) Fruit to Identify Phytonutrients Associated Genes and Pathways

Role of hepatoma‐derived growth factor in promoting de novo lipogenesis and tumorigenesis in hepatocellular carcinoma

Plastome phylogeny and lineage diversification of Salicaceae with focus on poplars and willows

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