Comparative transcriptome analysis of Rheum australe, an endangered medicinal herb, growing in its natural habitat and those grown in controlled growth chambers

Abstract

Rheum australe is an endangered medicinal herb of high altitude alpine region of Himalayas and is known to possess anti-cancerous properties. Unlike many herbs of the region, R. australe has broad leaves. The species thrives well under the environmental extremes in its niche habitat, therefore an understanding of transcriptome of R. australe to environmental cues was of significance. Since, temperature is one of the major environmental variables in the niche of R. australe, transcriptome was studied in the species growing in natural habitat and those grown in growth chambers maintained at 4 °C and 25 °C to understand genes associated with different temperatures. A total of 39,136 primarily assembled transcripts were obtained from 10,17,74,336 clean read, and 21,303 unigenes could match to public databases. An analysis of transcriptome by fragments per kilobase of transcript per million, followed by validation through qRT-PCR showed 22.4% up- and 22.5% down-regulated common differentially expressed genes in the species growing under natural habitat and at 4 °C as compared to those at 25 °C. These genes largely belonged to signaling pathway, transporters, secondary metabolites, phytohormones, and those associated with cellular protection, suggesting their importance in imparting adaptive advantage to R. australe in its niche.

DeepPlnc: Bi-modal Deep Learning for Highly Accurate Plant lncRNA Discovery

“…The assembled transcriptome of Rheum australe had reported a total of 35,679 transcriptome sequences, of which 23,569 sequences were having significant BLAST hits. As mentioned by Mala et al, 2021 [25], dissimilar sequence (DS) clustering was performed to identify the multiple representatives of the same gene which reduced the number of total unigenes from 23,569 to 21,303. These 21,303 unigene transcripts comprised well annotated protein coding RNAs (3,912), hypothetical (7,109) and predicted genes (10,282).…”

“…To demonstrate the applicability of DeepPlnc, it was run against the recently published transcriptome data of an endangered Himalayan medicinal plant, Rheum australe whose genome sequence is still not known and absolutely no information is there for lncRNAs (Mala et al, 2021).…”

“…Temperature is one of the major environmental factors in the niche of Rheum australe which determines its growth and development. To compare and understand the influence of temperature in terms of lncRNA transcripts response, the transcriptome profiling of the plant samples at 4°C and 25°C were retrieved studies (Mala et al, 2021). The study provided a total of 21,303 unigenes.…”

Regulation of the Bud Dormancy Development and Release in Micropropagated Rhubarb ‘Malinowy’

“…Obtained cDNA samples were used for the gene expression analysis performed using the quantitative real-time PCR (qRT-PCR) technique with specific primers [8,69]. Relative expression was based on expression of the GAPDH (glyceraldehyde-3-phosphate dehydrogenase) gene which was applied as a reference gene [70]. Quantitative RT-PCR was carried out in LightCycler ® 480 machine (Roche, Basel, Switzerland) using KAPA TM SybrFast qPCR Master Mix (Kapa Biosystems, Amsterdam, The Netherlands), according to manufacturer's instructions, in a total volume of 20 µL and 1/10 cDNA dilution for each tested sample.…”

Reprogramming plant specialized metabolism by manipulating protein kinases

“…Stilbenoids act as antioxidants that can undergo intramolecular cyclization under UV radiation (Chong et al 2009 ). Transcriptomic analysis reveals that the MAPK cascades, CDPKs, and WAKs are upregulated in the plants grown in natural conditions compared to those in growth chambers (Mala et al 2021 ).…”