De Novo Transcriptome Assembly and Characterization of the Synthesis Genes of Bioactive Constituents in Abelmoschus esculentus (L.) Moench

Zhang, Chenghao; Wang, Dong; Wei, Gen; Xu, Baoyu; Shen, Chenjia; Yu, Chenliang

doi:10.3390/genes9030130

Cited by 17 publications

(11 citation statements)

References 54 publications

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“…The comparative transcriptome analysis showed that the number and N50 sizes of the assembled unigenes from the present A. esculentus leaf transcriptome were larger than the previous reported transcriptome from Schafleitner, et al However, very recently Zhang, et al [52] reported A. esculentus transcriptome from root, stem, leaves, flowers, and fruits with 293,971 unigenes having N50 sizes of 1885 bp, which was better than our leaf transcriptome. The present, reported transcriptome assemblies along with precursors miRNA sequencing data [12] from A. esculentus can be merged to obtain comprehensive sequence information of this crop plant which will be useful for the functional genomics, host-pathogen interaction, and mRNA-miRNA network studies.…”

Section: Identification Of Simple Sequence Repeats (Ssrs) Of a Esculcontrasting

confidence: 76%

Comprehensive Leaf Transcriptome of a Non-model Plant, Abelmoschus esculentus for the Functional Genomics Studies

Padmanabhan¹,

Srikakulam²,

Kumar³

et al. 2018

J Genet Genome Res

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Abelmoschus esculentus is widely cultivated and consumed across the globe for its nutritional and medicinal purpose. In spite of the growing demand, its cultivation is massively affected by various insects, fungi, nematodes and viruses. Due to lack of genomic and limited transcriptomic resources, genetic manipulation studies concerning the crop improvement against various environmental factors is scarce for this crop. Thereby, the present study aims to develop high quality transcriptome of A. esculentus by employing the Next-Generation based RNA sequencing of four cDNA libraries generated from the leaf samples. Sequencing yielded a total of 206.3 million paired-end clean reads with 66,382 assembled unigenes having a total length of 71.35 Mb, an average length of 1,074 bp and an N50 of 1,408 bp. About 56% of the unigenes were successfully annotated in four public databases including Pfam, GO, COG, and KEGG. GO analysis revealed that the majority of the annotated unigenes were involved in key biological processes like ATP binding, DNA binding, transcription, DNA-templated, and integral component of membrane. KEGG pathway analysis showed that 16,307 unigenes were assigned to 143 pathways in which majority of secondary metabolites related transcripts involving in phenylpropanoids, flavonoid and terpenoid biosynthesis pathway were identified. In addition, transcription factor and simple sequence repeats (SSRs) analyses revealed 76 transcription factor families and 9,578 potential SSRs in the A. esculentus leaf transcriptome. Furthermore, de novo assembled leaf transcriptome generated in the present study had longer transcripts with better N50 sizes and the quality of assembly was ensured by qRT-PCR analysis. The A. esculentus sequence information presented in this study will be a valuable resource for further molecular genetics and functional genomics studies for the improvement of this crop plant.

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Section: Identification Of Simple Sequence Repeats (Ssrs) Of a Esculcontrasting

confidence: 76%

Comprehensive Leaf Transcriptome of a Non-model Plant, Abelmoschus esculentus for the Functional Genomics Studies

Padmanabhan¹,

Srikakulam²,

Kumar³

et al. 2018

J Genet Genome Res

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“…Previous work focused on identification and analysis glycosyltransferases (GTs) in polysaccharides biosynthesis 20 . Besides GTs, some metabolic pathways such as fructose and mannose metabolism may also participated in polysaccharides biosynthesis 21,22 . However, the biosynthesis mechanisms and metabolic pathways of polysaccharides have been not explored detailly in D. huoshanense.In China, the stem of Dendrobium is a traditional edible and medicinal part 2 .…”

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confidence: 99%

Transcriptome Analysis Reveals Biosynthesis of Important Bioactive Constituents and Mechanism of Stem Formation of Dendrobium huoshanense

Zhou

Gui

et al. 2020

Sci Rep

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the stem of Dendrobium huoshanense c.Z. tang and S.J. cheng was widely used as a medicinal herb in health care products due to its broad pharmacological activities. However, the molecular regulation mechanism of stem development and biosynthetic pathways of important bioactive substances are still unclear in D. huoshanense. in this study, the bioactive compounds in leaves, stems and roots, and the identification of candidate genes involved in stem formation and biosynthesis of active compounds via transcriptome sequence were analyzed. The accumulation of total polysaccharides and flavonoids were varied significantly in different tissues. A comparative transcriptomic analysis revealed several differentially expressed genes (DEGs) involved in polysaccharides biosynthesis (103 genes), including fructose and mannose related genes (29 genes) and glycosyltransferase genes (74 genes), and flavonoids biosynthesis (15 genes). Some candidate genes that participated in photoperiod regulation (27 genes), starch and sucrose metabolism (46 genes), and hormone-induced activation of signaling pathways (38 genes) may be involved in stem formation. In sum, this study provides a foundation for investigating the molecular processes in the biosynthesis of active compounds and stem development. the transcriptome data presented here provides an important resource for the future studies of the molecular genetics and functional genomics in D. huoshanense and optimized control of the active compounds produced by D. huoshanense.Dendrobium huoshanense C.Z. Tang and S.J. Cheng is an edible and medicinal plant, and has been utilized as a tonic in Traditional Chinese Medicine for centuries 1 . Specifically, it is used for boosting immunity, slowing aging, and possesses anti-tumor properties 2,3 . At present, increased demands and over-exploration caused reduced yield of wild resource and the damage of D. huoshanense habitats. Although artificial cultivation is an efficient way to protect natural resources and develop a sustainable medicinal supply, it was still faced an important issue to ensure and improve the quality and yield of D. huoshanense under artificial conditions. Understanding the regulation mechanism of quality and production of D. huoshanense has huge commercial and health value.At present, several ingredients from D. huoshanense have been identified as therapeutic active components, such as polysaccharides 4,5 , flavonoids 6,7 , alkaloids 8,9 . Modern pharmacological researches have confirmed that polysaccharides can activate immune cells, modulate the immune responses in the intestines, spleen, and liver, and inhibit cell proliferation in tumors [10][11][12][13] . Alkaloids possessed the functions of anti-inflammatory, anti-diabetic effect and anticancer activity 14,15 . Flavonoids also possesses biological functions including anti-oxidant, anti-cancer, anti-aging, cardiovascular protection, and building of immunity [16][17][18][19] . The key genes associated with polysaccharides and alkaloids biosynthesis have been identified,...

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“…Okra is now widely cultivated all over the world [30]. Due to the complex allopolyploid genome of okra (probably, 2n = 130–140), little attention has been paid to the genetic improvement of this crop until recently [31]. In the present work, a TMT-based proteomic technique was employed to analyze the proteins differentially expressed between the control and NaCl-treated seedlings over the first 48 h. These results will enhance our understanding of the regulatory mechanisms involved in okra response to salt stress.…”

Section: Discussionmentioning

confidence: 99%

Comparative proteomic analysis of okra (Abelmoschus esculentus L.) seedlings under salt stress

Zhan

Tang

et al. 2019

BMC Genomics

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Background Salinization seriously threatens land use efficiency and crop yields across the world. Understanding the mechanisms plants use to protect against salt stress will help breeders develop salt-tolerant vegetable crops. Okra ( Abelmoschus esculentus L.) is an important vegetable crop of the mallow family, which is now cultivated in warm regions worldwide. To understand the effects of salt stress on the protein level of okra, a comparative proteomic analysis of okra seedlings grown in the presence of 0 or 300 mmol L − 1 NaCl treatment was performed using an integrated approach of Tandem Mass Tag labeling and LC-MS/MS integrated approach. Results A total of 7179 proteins were identified in this study, for which quantitative information was available for 5774 proteins. In the NaCl/control comparison group, there were 317 differentially expressed proteins (DEPs), of which 165 proteins were upregulated and 152 proteins downregulated in the presence of NaCl. Based on the above data, we carried out a systematic bioinformatics analysis of proteins with information, including protein annotation, domain characteristics, functional classification, and pathway enrichment. Enriched gene ontology and Kyoto Encyclopedia of Genes and Genomes pathway analysis showed that the DEPs were most strongly associated with “response to stress” and “protein processing in endoplasmic reticulum”. Furthermore, several heat shock proteins were identified as DEPs. Conclusions This information provides a reference direction for further research on the okra proteome in the downstream of the salt stress response, with our data revealing that the responses of okra to salt stress involves by various pathways. Electronic supplementary material The online version of this article (10.1186/s12864-019-5737-7) contains supplementary material, which is available to authorized users.

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De Novo Transcriptome Assembly and Characterization of the Synthesis Genes of Bioactive Constituents in Abelmoschus esculentus (L.) Moench

Cited by 17 publications

References 54 publications

Comprehensive Leaf Transcriptome of a Non-model Plant, Abelmoschus esculentus for the Functional Genomics Studies

Comprehensive Leaf Transcriptome of a Non-model Plant, Abelmoschus esculentus for the Functional Genomics Studies

Transcriptome Analysis Reveals Biosynthesis of Important Bioactive Constituents and Mechanism of Stem Formation of Dendrobium huoshanense

Comparative proteomic analysis of okra (Abelmoschus esculentus L.) seedlings under salt stress

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