scholarly journals Global scale transcriptome analysis reveals differentially expressed genes involve in early somatic embryogenesis in Dimocarpus longan Lour

BMC Genomics ◽  
2020 ◽  
Vol 21 (1) ◽  
Author(s):  
Yukun Chen ◽  
Xiaoping Xu ◽  
Zhuanxia Liu ◽  
Zihao Zhang ◽  
Xu XuHan ◽  
...  
Keyword(s):  
Somatic Embryogenesis ◽  
Fatty Acid ◽  
Plant Hormones ◽  
Transcriptome Analysis ◽  
Woody Plants ◽  
Fatty Acid Biosynthesis ◽  
Differentially Expressed ◽  
Rna Seq ◽  
Acid Biosynthesis ◽  
Qrt Pcr

Abstract Background Somatic embryogenesis (SE) is a process of somatic cells that dedifferentiate to totipotent embryonic stem cells and generate embryos in vitro. Longan SE has been established and wildly used as model system for studying embryogenesis in woody plants, SE-related genes had been characterized. In spite of that, a comprehensive overview of SE at a molecular level is still absent. To understand the molecular mechanisms during longan SE, we examined the transcriptome changes by using Illumina HiSeq from the four distinct developmental stages, including non-embryogenic callus (NEC), embryogenic callus (EC), incomplete compact pro-embryogenic cultures (ICpEC), globular embryos (GE). Results RNA-seq of the four samples generated a total of 243.78 million high quality reads, approximately 81.5% of the data were mapped to longan genome. The cDNA libraries of NEC, EC, ICpEC and GE, generated 22,743, 19,745, 21,144, 21,102 expressed transcripts, 1935, 1710, 1816, 1732 novel transcripts, 2645, 366, 505, 588 unique genes, respectively. Comparative transcriptome analysis showed that a total of 10,642, 4180, 5846 and 1785 genes were differentially expressed in the pairwise comparisons of NEC_vs_EC, EC_vs_ICpEC, EC_vs_GE, ICpEC_vs_GE, respectively. Among them, plant hormones signalling related genes were significantly enriched, especially the auxin and cytokinin signalling components. The transcripts of flavonoid biosynthesis related genes were mainly expressed in NEC, while fatty acid biosynthesis related genes mainly accumulated in early SE. In addition, the extracelluar protein encoding genes LTP, CHI, GLP, AGP, EP1 were related to longan SE. Combined with the FPKM value of longan nine tissues transcription, 27 SE specific or preferential genes (LEC1, LEC1-like, PDF1.3, GH3.6, AGL80, PIN1, BBM, WOX9, WOX2, ABI3, et al.) and 28 NEC preferential genes (LEA5, CNOT3, DC2.15, PR1–1, NsLTP2, DIR1, PIP1, PIP2.1, TIP2–1, POD-P7 and POD5 et al.) were characterized as molecular markers for longan early SE. qRT-PCR validation of SE-related genes showed a high correlation between RNA-seq and qRT-PCR data. Conclusion This study provides new insights into the role of the transcriptome during early SE in longan. Differentially expressed genes reveal that plant hormones signalling, flavonoid and fatty acid biosynthesis, and extracelluar protein related genes were involved in longan early SE. It could serve as a valuable platform resource for further functional studies addressing embryogenesis in woody plants.

scholarly journals Global scale transcriptome analysis reveals differentially expressed genes involve in early somatic embryogenesis in Dimocarpus longan Lour.

2019 ◽  
Author(s):  
Yukun Chen ◽  
Xiaoping Xu ◽  
Zhuanxia Liu ◽  
Zihao Zhang ◽  
XuHan Xu ◽  
...  
Keyword(s):  
Somatic Embryogenesis ◽  
Fatty Acid ◽  
Plant Hormones ◽  
Transcriptome Analysis ◽  
Woody Plants ◽  
Fatty Acid Biosynthesis ◽  
Differentially Expressed ◽  
Rna Seq ◽  
Acid Biosynthesis ◽  
Qrt Pcr

Abstract Background: Somatic embryogenesis (SE) is a process of somatic cells that dedifferentiate to totipotent embryonic stem cells and generate embryos in vitro. Longan SE has been established and wildly used as model system for studying embryogenesis in woody plants, SE-related genes had been characterized. In spite of that, a comprehensive overview of SE at a molecular level is still absent. To understand the molecular mechanisms during longan SE, we examined the transcriptome changes by using Illumina HiSeq from the four distinct developmental stages, including NEC, EC, ICpEC, GE. Results: RNA-seq of the four samples generated a total of 243.78 million high quality reads, approximately 81.5% of the data were mapped to longan genome. The cDNA libraries of NEC, EC, ICpEC and GE, generated 22743, 19745, 21144, 21102 expressed transcripts, 1935, 1710, 1816, 1732 novel transcripts, 2645, 366, 505, 588 unique genes, respectively. Comparative transcriptome analysis showed that a total of 10,642, 4,180, 5,846 and 1,785 genes were differentially expressed in the pairwise comparisons of NEC_vs_EC, EC_vs_ICpEC, EC_vs_GE, ICpEC_vs_GE, respectively. Among them, plant hormones signalling related genes were significantly enriched, especially the auxin and cytokinin signalling components. The transcripts of flavonoid biosynthesis related genes were mainly expressed in NEC, while fatty acid biosynthesis related genes mainly accumulated in early SE. In addition, the extracelluar protein encoding genes LTP, CHI, GLP, AGP, EP1 were related to longan SE. Combined with the FPKM of longan nine tissues transcription, 27 SE specific or preferential genes (LEC1, LEC1-like, PDF1.3, GH3.6, AGL80, PIN1, BBM, WOX9, WOX2, et al.) and 28 NEC preferential genes (LEA5, CNOT3, DC2.15, PR1-1, NsLTP2, DIR1, PIP1, PIP2.1 and POD5 et al.) were characterized as molecular markers for longan early SE. qRT-PCR validation of SE-related genes showed a high correlation between RNA-seq and qRT-PCR data. Conclusion: This study provides new insights into the role of the transcriptome during early SE in longan. Differentially expressed genes reveal that plant hormones signalling, flavonoid and fatty acid biosynthesis, and extracelluar protein related genes were involved in longan early SE. It could serve as a valuable platform resource for further functional studies addressing embryogenesis in woody plants.

scholarly journals Global scale transcriptome analysis reveals differentially expressed genes involve in early somatic embryogenesis in Dimocarpus longan Lour.

2019 ◽  
Author(s):  
Yukun Chen ◽  
Xiaoping Xu ◽  
Zhuanxia Liu ◽  
Zihao Zhang ◽  
XuHan Xu ◽  
...  
Keyword(s):  
Somatic Embryogenesis ◽  
Fatty Acid ◽  
Plant Hormones ◽  
Transcriptome Analysis ◽  
Woody Plants ◽  
Fatty Acid Biosynthesis ◽  
Differentially Expressed ◽  
Rna Seq ◽  
Acid Biosynthesis ◽  
Qrt Pcr

Abstract Background: Somatic embryogenesis (SE) is a process of somatic cells that dedifferentiate to totipotent embryonic stem cells and generate embryos in vitro. Longan SE has been established and wildly used as model system for studying embryogenesis in woody plants, SE-related genes had been characterized. In spite of that, a comprehensive overview of SE at a molecular level is still absent. To understand the molecular mechanisms during longan SE, we examined the transcriptome changes by using Illumina HiSeq from the four distinct developmental stages, including NEC, EC, ICpEC, GE.Results: RNA-seq of the four samples generated a total of 243.78 million high quality reads, approximately 81.5% of the data were mapped to longan genome. The cDNA libraries of NEC, EC, ICpEC and GE, generated 22743, 19745, 21144, 21102 expressed transcripts, 1935, 1710, 1816, 1732 novel transcripts, 2645, 366, 505, 588 unique genes, respectively. Comparative transcriptome analysis showed that a total of 10,642, 4,180, 5,846 and 1,785 genes were differentially expressed in the pairwise comparisons of NEC_vs_EC, EC_vs_ICpEC, EC_vs_GE, ICpEC_vs_GE, respectively. Among them, plant hormones signalling related genes were significantly enriched, especially the auxin and cytokinin signalling components. The transcripts of flavonoid biosynthesis related genes were mainly expressed in NEC, while fatty acid biosynthesis related genes mainly accumulated in early SE. In addition, the extracelluar protein encoding genes LTP, CHI, GLP, AGP, EP1 were related to longan SE. Combined with the FPKM of longan nine tissues transcription, 27 SE specific or preferential genes (LEC1, LEC1-like, PDF1.3, GH3.6, AGL80, PIN1, BBM, WOX9, WOX2, et al.) and 28 NEC preferential genes (LEA5, CNOT3, DC2.15, PR1-1, NsLTP2, DIR1, PIP1, PIP2.1 and POD5 et al.) were characterized as molecular markers for longan early SE. qRT-PCR validation of SE-related genes showed a high correlation between RNA-seq and qRT-PCR data.Conclusion: This study provides new insights into the role of the transcriptome during early SE in longan. Differentially expressed genes reveal that plant hormones signalling, flavonoid and fatty acid biosynthesis, and extracelluar protein related genes were involved in longan early SE. It could serve as a valuable platform resource for further functional studies addressing embryogenesis in woody plants.

scholarly journals Global scale transcriptome analysis reveal differentially expressed genes during early somatic embryogenesis in Dimocarpus longan Lour

2019 ◽  
Author(s):  
Yukun Chen ◽  
Xiaoping Xu ◽  
Zhuanxia Liu ◽  
Zihao Zhang ◽  
XuHan Xu ◽  
...  
Keyword(s):  
Somatic Embryogenesis ◽  
Molecular Markers ◽  
Fatty Acid ◽  
Transcriptome Analysis ◽  
Embryogenic Callus ◽  
Molecular Mechanisms ◽  
Fatty Acid Biosynthesis ◽  
Acid Biosynthesis ◽  
Protein Encoding ◽  
Encoding Genes

Abstract Background Somatic embryogenesis (SE) is a process of somatic cells that dedifferentiate to the totipotent embryonic stem cells and generate embryos in vitro. Longan SE has been established and wildly used as a model system for studying embryogenesis in woody plants, and some SE-related genes had been characterized. In spite of that, a comprehensive overview of SE at a molecular level is still absent. With the aim of understanding the molecular mechanisms underlying SE in longan, we examined the transcriptome changes by using Illumina HiSeq platform from the four distinct developmental stages, including non-embryogenic callus (NEC), embryogenic callus (EC), incomplete compact pro-embryogenic cultures (ICpEC), globular embryos (GE). Results RNA-seq of the four samples generated a total of 243.78 million high quality reads, approximately 81.5% of the data were mapped to the reference genome. The cDNA libraries of NEC, EC, ICpEC and GE, generated 22743, 19745, 21144, 21102 expressed transcripts and 1935, 1710, 1816, 1732 novel transcripts, and 2645, 366, 505, 588 unique genes, respectively. Comparative transcriptome analysis revealed the important role of auxin and cytokinin during longan SE. The transcripts profiling of flavonoid and fatty acid biosynthesis related genes suggested that flavonoids were mainly accumulated in NEC, while fatty acid accumulated in early SE. In addition, the extracelluar protein encoding genes LTP, CHI, GLP, AGP, EP1 were related to longan SE. Transcript profiling combined with qRT-PCR performed on selected genes confirmed that 27 SE molecular markers (LEC1, LEC1-like, PDF1.3, GH3.6, AGL80, PIN1, BBM, WOX9, WOX2, ABI3, et al.) and 28 NEC markers (LEA5, CNOT3, DC2.15, PR1-1, NsLTP2, DIR1, PIP1, PIP2.1, TIP2-1, POD-P7 and POD5 et al.) were characterized as potential molecular markers for longan early SE, respectively. Conclusion Our transcriptome reveals the transcription regulation of auxin, cytokinin and other hormones signaling pathway, flavonoids biosynthesis, fatty acid biosynthesis, extracelluar protein encoding genes, and other SE-related genes during early SE. Furthermore, we characterizes the potential molecular markers to distinguish NEC and early SE of longan. The present work provides new insights into future functional studies, as a means of studying the molecular mechanisms in SE.

scholarly journals Transcriptome analysis and identification of genes associated with ω-3 fatty acid biosynthesis in Perilla frutescens (L.) var. frutescens

BMC Genomics ◽  
2016 ◽  
Vol 17 (1) ◽  
Author(s):  
Hyun Uk Kim ◽  
Kyeong-Ryeol Lee ◽  
Donghwan Shim ◽  
Jeong Hee Lee ◽  
Grace Q. Chen ◽  
...  
Keyword(s):  
Fatty Acid ◽  
Transcriptome Analysis ◽  
Fatty Acid Biosynthesis ◽  
Perilla Frutescens ◽  
Acid Biosynthesis

scholarly journals Functional Role of Linc-RNAs in Multiple Myeloma: Linc-MIR17HG Affects Fatty Acid Biosynthesis Via transcriptional Regulation of ACC1 with Potential Therapeutic Implications

Blood ◽  
2018 ◽  
Vol 132 (Supplement 1) ◽  
pp. 1925-1925
Author(s):  
Eugenio Morelli ◽  
Mariateresa Fulciniti ◽  
Mehmet Kemal Samur ◽  
Francesca Scionti ◽  
Annamaria Gulla ◽  
...  
Keyword(s):  
Fatty Acid ◽  
Cell Lines ◽  
Fatty Acid Biosynthesis ◽  
Newly Diagnosed ◽  
Rna Seq ◽  
Acid Biosynthesis ◽  
Transcriptional Regulatory ◽  
Equity Ownership ◽  
Regulatory Functions

Abstract Besides the well described function of RNA to produce proteins, a large volume of transcribed product has non-coding function. A recent analysis of RNA repertoire has identified a family of non-coding transcripts with sequence longer than 200 nucleotides, the long intergenic non-coding RNAs (lincRNAs). Although lincRNAs have been considered to provide regulatory functions, their precise role in cellular biology remains unclear. Using our RNA-seq data from 360 newly-diagnosed patients and 18 normal plasma cells, we have recently described the landscape of lincRNAs in multiple myeloma (MM) and reported their role as independent risk predictors for survival outcome. We have now studied the functional role of a lincRNA, the miR-17-92 primary precursor linc-MIR17HG, present in our lincRNA profile and highly correlated with overall survival in MM. We observe that inhibition of linc-MIR17HG by antisense LNA GapmeRs (n=2) leads to apoptosis in 12 genotypically distinct MM cell lines as well as in 13 primary patient MM cells. These effects are not fully rescued by expression of miR-17-92 microRNAs, suggesting a distinct biological function for linc-MIR17HG in MM. We therefore performed gene expression profile in 2 MM cell lines (AMO1 and NCI-H929) and in 2 primary patient MM cells after short-term suppression of linc-MIR17HG; and, at these early time points (18-36h), we found significant downregulation of a subset of genes (FC>2; p<0.05) including ACC1, EXT1, EPT1, ANO6, CCDC91 and KIA1109, but not miR-17-92 microRNAs. These transcriptional changes were validated by qRT-PCR in MM cell lines and primary MM cells exposed to different LNA GapmeRs targeting linc-MIR17HG with a non-overlapping spectrum of off-target effects. Importantly, our RNA-seq analysis of 360 newly-diagnosed MM patients from IFM/DFCI 2009 clinical study showed that expression of linc-MIR17HG strongly correlated with the expression of each of these genes (R2>0.4; p<0.01) in MM patients, further suggesting a regulatory function by linc-MIR17HG at transcriptional level. Using CRISPR interference (CRISPRi), we have also identified that the linc-MIR17HG with transcriptional regulatory functions is not produced from the canonical transcript isoforms MIR17HG-201/-203; these isoforms, rather, appear to be involved in production of microRNAs, leaving an alternative transcription start site usage as possible source for the transcriptional regulator isoform(s). We next investigated whether regulation of these early targets may contribute to the activity of linc-MIR17HG. We performed a RNAi-based screening in 2 MM cells lines (AMO1 and NCI-H929) by silencing each of the linc-MIR17HG downstream target genes with at least 2 different highly-specific siRNAs. This approach revealed that silencing of acetyl-CoA carboxylase 1 (ACC1, also known as ACACA), a gene encoding the limiting enzyme in the biosynthesis of fatty acids, significantly affects MM cell growth and viability. These results were validated using stable knock-down via shRNAs, confirming ACC1 as a novel vulnerability in MM. These results provide a molecular basis for reported role of fatty acid metabolism in MM cell growth and survival. We have now evaluated two orally available inhibitors of ACC1 activity, ND-630 and ND-646, in a panel of 10 MM cell lines, an report a potent time- and dose-dependent anti-proliferative effect. The activity of these inhibitors and linc-MIR17HG on fatty acid biosynthesis in MM cells is under investigation and will be presented. We have also begun to investigate molecular pathway used by linc-MIR17HG to modulate ACC1 function. Our preliminary data suggest that linc-MIR17HG may function as a scaffold between MYC and the E-box motifs present on ACC1 intronic sequences, facilitating MYC binding and its transcriptional activity. In conclusion, we highlight a transcriptional regulatory activity of a lincRNA in MM with significant functional impact that can be therapeutically translated. Disclosures Anderson: Bristol Myers Squibb: Consultancy; Millennium Takeda: Consultancy; Gilead: Membership on an entity's Board of Directors or advisory committees; OncoPep: Equity Ownership, Other: Scientific founder; C4 Therapeutics: Equity Ownership, Other: Scientific founder; Celgene: Consultancy. Munshi:OncoPep: Other: Board of director.

scholarly journals Pan-transcriptomic analysis identified common differentially expressed genes of Acinetobacter baumannii in response to polymyxin treatments

2020 ◽  
Vol 16 (4) ◽  
pp. 327-338
Author(s):  
Mengyao Li ◽  
Su Mon Aye ◽  
Maizbha Uddin Ahmed ◽  
Mei-Ling Han ◽  
Chen Li ◽  
...  
Keyword(s):  
Fatty Acid ◽  
Acinetobacter Baumannii ◽  
Outer Membrane ◽  
Differentially Expressed Genes ◽  
Fatty Acid Biosynthesis ◽  
Efflux Pumps ◽  
Transcriptomic Analysis ◽  
Differentially Expressed ◽  
Acid Biosynthesis

Our pan-transcriptomic study for polymyxin-treated A. baumannii identified that the remodelled outer membrane, up-regulated efflux pumps and down-regulated fatty acid biosynthesis might be essential for early responses to polymyxins in A. baumannii.

Sign in / Sign up

Export Citation Format

Share Document