Full-length transcriptome analysis provides new insights into the early bolting occurrence in medicinal Angelica sinensis

Gao, Xue Mei; Guo, Fengjing; Yuan, Chen; Bai, Gang; Liu, Yu-Xiao; Jin, Jianqin; Wang, Qing

doi:10.1038/s41598-021-92494-4

Cited by 13 publications

(12 citation statements)

References 56 publications

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“…To date, the gene regulatory mechanism of the flowering during the photoperiod has been shown, with upstream regulatory pathway genes (e.g., CONSTANS ( CO ), FLOWERING LOCUS C ( FLC ) and PHYOCHROME A ( PHYA )), downstream floral integrator genes (e.g., FLOWERING LOCUS T ( FT ), SUPPRESSOR OF OVEREXPRESSION OF CONSTANS 1 ( SOC1 ) and FT-interacting protein 1 ( FTIP1 )), downstream floral meristem identity genes (e.g., LEAFY ( LFY ), APETALA 1 ( AP1 ) and AP2 )), autonomous pathway genes (e.g., flowering time control protein FCA ( FCA ), flowering time control protein FPA ( FPA ) and FY ), sucrose metabolism genes (e.g., sucrose synthase ( SUS ), alpha-amylase ( AMY ) and glucan endo-1,3-b-glucosidase ( GLU )) and gibberellin (GA) pathway genes (e.g., gibberellin 2-β-dioxygenase 1 ( GA2OX1 ), gibberellin 20-oxidase 1 ( GA20OX1 ) and DELLA protein GAI ( GAI )) [ 15 , 16 , 17 , 18 ]. Although physiological changes (e.g., soluble sugar, protein and hormones) during vernalization and freezing storage have been investigated [ 19 , 20 ], gene-regulatory networks involved in the flowering of A. sinensis during vernalization have not been mapped.…”

Section: Introductionmentioning

confidence: 99%

Regulatory Networks of Flowering Genes in Angelica sinensis during Vernalization

Luo

Liu

et al. 2022

Plants

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Angelica sinensis is a low-temperature and long-day perennial herb that has been widely used for cardio-cerebrovascular diseases in recent years. In commercial cultivation, up to 40% of flowering decreases the officinal yield of roots and accumulation of bioactive compounds. Although the regulatory mechanism of flowering genes during the photoperiod has been revealed, the networks during vernalization have not been mapped. Here, transcriptomics profiles of A. sinensis with uncompleted (T1), completed (T2) and avoided vernalization (T3) were performed using RNA-seq, and genes expression was validated with qRT-PCR. A total of 61,241 isoforms were annotated on KEGG, KOG, Nr and Swiss-Prot databases; 4212 and 5301 differentially expressed genes (DEGs) were observed; and 151 and 155 genes involved in flowering were dug out at T2 vs. T1 and T3 vs. T1, respectively. According to functional annotation, 104 co-expressed genes were classified into six categories: FLC expression (22; e.g., VILs, FCA and FLK), sucrose metabolism (12; e.g., TPSs, SUS3 and SPSs), hormone response (18; e.g., GID1B, RAP2s and IAAs), circadian clock (2; i.e., ELF3 and COR27), downstream floral integrators and meristem identity (15; e.g., SOC1, AGL65 and SPLs) and cold response (35; e.g., PYLs, ERFs and CORs). The expression levels of candidate genes were almost consistent with FPKM values and changes in sugar and hormone contents. Based on their functions, four pathways that regulate flowering during vernalization were mapped, including the vernalization pathway, the autonomic pathway, the age pathway and the GA (hormone) pathway. This transcriptomic analysis provides new insights into the gene-regulatory networks of flowering in A. sinensis.

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Section: Introductionmentioning

confidence: 99%

Regulatory Networks of Flowering Genes in Angelica sinensis during Vernalization

Luo

Liu

et al. 2022

Plants

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“…For instance, 471 transcripts were predicted to be long non-coding RNAs (lncRNAs) in a rice seedling transcriptome (Zhang et al 2019 ). Transcription factors (TFs) are essential for turning on and off genes of many morphological and biological processes and functions in a coordinated fashion (Gao et al 2021 ). Our data reveal a slightly greater number of transcription factors belonging to CAMTA, HB-other, ARF, C3H, TALE, GATA, Co-like, and SBP TF family compared to the number of TFs previously reported in the annotated genome of rice (MSU_osa1r7) and available in the plant transcript factor database (PlantTFDB version 5.0) (Jin et al 2017 ).…”

Section: Discussionmentioning

confidence: 99%

The Long Read Transcriptome of Rice (Oryza sativa ssp. japonica var. Nipponbare) Reveals Novel Transcripts

Hasan

Huang

Liu

et al. 2022

Rice

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Background High-throughput next-generation sequencing technologies offer a powerful approach to characterizing the transcriptomes of plants. Long read sequencing has been shown to support the discovery of novel isoforms of transcripts. This approach enables the generation of full-length sequences revealing splice variants that may be important in regulating gene action. Investigation of the diversity of transcripts in the rice transcriptome including splice variants was conducted using PacBio long-read sequence data to improve the annotation of the rice genome. Results A cDNA library was prepared from RNA extracted from leaves, roots, seeds, inflorescences, and panicles of O. sativa ssp. japonica var Nipponbare and sequenced on a PacBio Sequel platform. This produced 346,190 non-redundant full-length non-chimeric reads (FLNC) resulting in 33,504 high-quality transcripts. Half of the transcripts were multi-exonic and entirely matched with the reference transcripts. However, 14,874 novel isoforms were also identified resulting predominantly from intron retention and at least one novel splice site. Intron retention was the prevalent alternative splicing event and exon skipping was the least observed. Of 73,659 splice junctions, 12,755 (17%) represented novel splice junctions with canonical and non-canonical intron boundaries. The complexity of the transcriptome was examined in detail for 19 starch synthesis-related genes, defining 276 spliced isoforms of which 94 splice variants were novel. Conclusion The data reveal the great complexity of the rice transcriptome. The novel transcripts provide new insights that may be a key input in future research to improve the annotation of the rice genome.

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“…Each qRT-PCR was implemented using the Power SYBR® Green PCR Master Mix (Roche) on a Quant-studioTM RealTime Detection System (Life Technologies, USA). The primers sequences, which were from other published articles 9,34,57 , can be found in Supplementary Table S4. The total volume of the reaction system was 20 μL, composed of 8 μL of sterile distilled deionized water, 10 uL of Power SYBR® Green Master Mix, 0.5 μL of the forward primer (10 μM), 0.5 μL of the reverse primer (10 μM), and 1 μL of cDNA.…”

Section: Methodsmentioning

confidence: 99%

Analysis of the difference between early-bolting and non-bolting roots of Angelica dahurica based on transcriptome sequencing

Wang

Guo

et al. 2022

Preprint

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Angelica dahurica（Fisch. ex Hoffm.）Benth.et Hook.f.var.formosana（Boiss.）Shan et Yuan (A. dahurica) is a famous traditional Chinese medicine commonly used in clinic, with anti-inflammatory, analgesic, anti-tumor, antibacterial, whitening and other pharmacological effects. However, early bolting of A. dahurica compromises the quality of the roots and hence is a major limitation for yield of medicinal materials. To date, the molecular factors of early bolting occurrenc and its effect on the growth of A. dahurica are unexplored. Hence, we commenced a transcriptome study by using the Illumina NovaSeq 6000 at two developmental types i.e. early-bolting and non-bolting (normal) roots of A. dahurica. Overall, 2,185 up and 1,414 down-regulated genes were obtained. A large number of identified transcripts were related to genes involved in early bolting. Gene ontology analysis highlighted differentially expressed genes that play a key role in various pathways. These pathways were mainly linked to cellular, molecular and biological processes. The morphological characteristics and coumarins content were also changed signifcantly in the early bolting roots of A. dahurica. This study lays a path towards understanding the transcriptomic control of early bolting in A. dahurica, which could be further applied to enhance the medicinal value.

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Full-length transcriptome analysis provides new insights into the early bolting occurrence in medicinal Angelica sinensis

Cited by 13 publications

References 56 publications

Regulatory Networks of Flowering Genes in Angelica sinensis during Vernalization

Regulatory Networks of Flowering Genes in Angelica sinensis during Vernalization

The Long Read Transcriptome of Rice (Oryza sativa ssp. japonica var. Nipponbare) Reveals Novel Transcripts

Analysis of the difference between early-bolting and non-bolting roots of Angelica dahurica based on transcriptome sequencing

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