De novo Sequencing and Transcriptome Analysis Reveal Key Genes Regulating Steroid Metabolism in Leaves, Roots, Adventitious Roots and Calli of Periploca sepium Bunge

Zhang, Jian; Li, Xinglin; Lu, Fuping; Wang, Shan-Ying; An, Yunhe; Su, Xiaoxing; Li, Xiankuan; Ma, Lin; Guang-jian, Han

doi:10.3389/fpls.2017.00594

Cited by 11 publications

(9 citation statements)

References 66 publications

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“…Triterpenoid saponins primarily undergo synthesis via the MVA and MEP pathways, with the MVA pathway metabolism taking place primarily in the cytoplasm, and the MEP pathway taking place primarily in the plastid [17]. Chloroplasts are abundant in leaf samples less in stem but not in root samples, this may explain why we found that MEP pathway-associated genes were primarily upregulated in leaf samples, as has also previously been observed in Periploca sepium Bunge and Cymbopogon winterianus [43,44]. This fact may also explain why we observed a higher abundance of triterpenoid saponins in the leaves of A. elata relative to the root and stem tissues.…”

Section: Discussionsupporting

confidence: 80%

Identification and analysis of CYP450 supergene family members from the transcriptome of Aralia elata (Miq.) Seem reveal candidate genes for triterpenoid saponins biosynthesis

Cheng

Liu

Tong

et al. 2020

Preprint

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BackgroundMembers of the cytochrome P450 (CYP450) gene superfamily have been shown to play essential roles in regulating secondary metabolites biosynthesis. However, the systematic identification and bioinformatics analysis of CYP450s have not been reported in Aralia elata (Miq.) Seem, a highly valued medicinal plant. ResultsIn the present study we conducted the RNA-sequencing (RNA-seq) analysis of the leaves, stems, and roots of A. elata, yielding 66,713 total unigenes. Following the annotation and classification of these unigenes, we were able to identify two pathways and 19 putative genes associated with the synthesis of triterpenoid saponins in these plants, with qRT-PCR subsequently being used to validate these gene expression patterns. Scanning with the CYP450 model from Pfam resulted in the identification of 111 full-length and 143 partial-length CYP450s, with the full-length CYP450s being further clustered into 7 clans and 36 families. Through phylogenetic and conserved motif analyses, we were further able to group these CYP450 proteins into two primary branches: A-type (53%) and non-A type (47%). We further conducted representative protein sequence alignment for these CYP450 family members, with secondary elements being assigned in light of the recently published Arabidopsis CYP90B1 structure. Using the available sequence information, we further identified predicted substrate recognition sites (SRSs) and substrate binding sites within these putative proteins.We further assessed the expression patterns of these 111 CYP450 genes across A. elata tissues, with 12 members of this gene family being selected at random for qRT-PCR validation. From these data, we identified CYP716A295 and CYP716A296 as the candidate genes most likely to be associated with oleanolic acid synthesis, while CYP72A763 was identified as being the most likely to play a role in hederagenin biosynthesis. Finally, we assessed the subcellular localization of these CYP450 proteins within Arabidopsis protoplasts, highlighting the fact that they localize to the endoplasmic reticulum.ConclusionsThis study presents a systematic analysis of the CYP450 gene family in A. elata and provided a foundation for further functional characterization of CYP450 genes.

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Section: Discussionsupporting

confidence: 80%

Identification and analysis of CYP450 supergene family members from the transcriptome of Aralia elata (Miq.) Seem reveal candidate genes for triterpenoid saponins biosynthesis

Cheng

Liu

Tong

et al. 2020

Preprint

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“…Triterpenoids and sesquiterpenoids are biosynthesized via the MVA pathway, that takes place primarily in the cytoplasm, whereas monoterpenoids, diterpenoid, and tetraterpenoids are biosynthesized via the MEP pathway, that takes place primarily in the plastid [23]. Chloroplasts are abundant in leaf samples less in stem but not in root samples, this may explain why we found that MEP pathway-associated genes were primarily upregulated in leaf samples, as has also previously been observed in Periploca sepium Bunge and Cymbopogon winterianus [44,45]. This fact may also explain why we observed a higher abundance of triterpenoid saponins in the leaves of A. elata relative to the root and stem tissues.…”

Section: Discussionsupporting

confidence: 80%

Identification and analysis of CYP450 supergene family members from the transcriptome of Aralia elata (Miq.) Seem reveal candidate genes for triterpenoid saponin biosynthesis

Cheng

Liu

Tong

et al. 2020

Preprint

View full text Add to dashboard Cite

Background: Members of the cytochrome P450 (CYP450) gene superfamily have been shown to play essential roles in regulating secondary metabolites biosynthesis. However, the systematic identification and bioinformatics analysis of CYP450s have not been reported in Aralia elata (Miq.) Seem , a highly valued medicinal plant. Results: In the present study we conducted the RNA-sequencing (RNA-seq) analysis of the leaves, stems, and roots of A. elata, yielding 66,713 total unigenes. Following the annotation and classification of these unigenes, we were able to identify two pathways and 19 putative genes associated with the synthesis of triterpenoid saponins in these plants, with qRT-PCR subsequently being used to validate these gene expression patterns. Scanning with the CYP450 model from Pfam resulted in the identification of 111 full-length and 143 partial-length CYP450s, with the full-length CYP450s being further clustered into 7 clans and 36 families. Through phylogenetic and conserved motif analyses, we were further able to group these CYP450 proteins into two primary branches: A-type (53%) and non-A type (47%). We further conducted representative protein sequence alignment for these CYP450 family members, with secondary elements being assigned in light of the recently published Arabidopsis CYP90B1 structure. Using the available sequence information, we further identified predicted substrate recognition sites (SRSs) and substrate binding sites within these putative proteins.We further assessed the expression patterns of these 111 CYP450 genes across A. elata tissues, with 12 members of this gene family being selected at random for qRT-PCR validation. From these data, we identified CYP716A295 and CYP716A296 as the candidate genes most likely to be associated with oleanolic acid synthesis, while CYP72A763 was identified as being the most likely to play a role in hederagenin biosynthesis. Finally, we assessed the subcellular localization of these CYP450 proteins within Arabidopsis protoplasts, highlighting the fact that they localize to the endoplasmic reticulum. Conclusions: This study presents a systematic analysis of the CYP450 gene family in A. elata and provided a foundation for further functional characterization of CYP450 genes.

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“…Due to its high throughput and cost-effectiveness, next-generation sequencing technology, such as Illumina sequencing technology, has been widely applied to determine the transcriptomes of nonmodel plants. In recent years, many transcriptome data on nonmodel plants, including Cunninghamia lanceolata ( Huang et al, 2012 ; Qiu et al, 2013 ), Camellia sinensis ( Shi et al, 2011 ), Chinese bayberry ( Feng et al, 2012 ), Calotropis gigantea ( Muriira et al, 2015 ) and Periploca sepium ( Zhang et al, 2017 ), have been generated using Illumina sequencing technology. These transcriptome data provide valuable resources for further studies in these plants.…”

Section: Discussionmentioning

confidence: 99%

RNA-Seq analysis of differential gene expression inBetula luminiferaxylem during the early stages of tension wood formation

Cai

Huang

et al. 2018

PeerJ

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Background Betula luminifera H. Winkler, which is widely distributed in southern China, is an economically important broadleaf tree species. However, little genomic information of B. luminifera is available, and little is known about the molecular mechanisms of wood formation in this species. Meanwhile, few efforts have focused on investigating the early transcriptional changes during tension wood formation in woody plants.ResultsA reference transcriptome dataset was first generated containing 45,700 Unigenes, and 35,135 (76.9%) Unigenes were annotated by a BLAST similarity search against four public databases. Then, based on an anatomical investigation, the global gene expression changes during the early stages of tension wood formation were analyzed. Gene expression profiling showed that a total of 13,273 Unigenes were differentially regulated during the early stages of tension wood formation. Most genes involved in cellulose and lignin biosynthesis were highlighted to reveal their biological importance in tension wood formation. In addition, the transcription levels of many genes involved in the auxin response pathway were significantly changed during the early stages of tension wood formation. Furthermore, 18 TFs co-expressed with key enzymes of cellulose synthesis were identified.ConclusionsOur results revealed the transcriptional changes associated with TW formation and identified potential key genes in the regulation of this process. These results will help to dissect the molecular mechanism of wood formation and provide key candidate genes for marker-assisted selection in B. luminifera.

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De novo Sequencing and Transcriptome Analysis Reveal Key Genes Regulating Steroid Metabolism in Leaves, Roots, Adventitious Roots and Calli of Periploca sepium Bunge

Cited by 11 publications

References 66 publications

Identification and analysis of CYP450 supergene family members from the transcriptome of Aralia elata (Miq.) Seem reveal candidate genes for triterpenoid saponins biosynthesis

Identification and analysis of CYP450 supergene family members from the transcriptome of Aralia elata (Miq.) Seem reveal candidate genes for triterpenoid saponins biosynthesis

Identification and analysis of CYP450 supergene family members from the transcriptome of Aralia elata (Miq.) Seem reveal candidate genes for triterpenoid saponin biosynthesis

RNA-Seq analysis of differential gene expression inBetula luminiferaxylem during the early stages of tension wood formation

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