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Potentilla bifurca is widely distributed in Eurasia, including the Tibetan Plateau. It is a valuable medicinal plant in the Tibetan traditional medicine system, especially for the treatment of diabetes. This study investigated the functional gene profile of Potentilla bifurca at different altitudes by RNA-sequencing technology, including de novo as...
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... performed homology searches and functional annotation of all the unigenes in 5 databases, of which 128,327 (57.64%) had homologous genes retrieved in at least one database. Nr and KEGG matched the most homologous genes, 125,599 (56.42%) and 60,488 (27.17%), respectively (Table S2). The alignment of the Nr database showed that 82.7% of the sequence alignments had an E value of less than 1 × 10 15 . ...Context 2
... the Pfam analysis, the most abundant domain identified was the pentatricopeptide repeat (PPR) family. The top 20 most abundant Pfam domains contained gene families related to abiotic stress response, such as the protein kinase domain, Hsp70 protein, ubiquitin family, etc. (Table 2). ...Citations
... Apart from ample evidence on the plasticity in morphoanatomical or eco-physiological traits along the high-altitude gradients, recently, a few transcriptome-based investigations have been conducted to understand the molecular mechanisms of high-altitude adaptation in different plants species that assume higher altitudes were more stressful for plants compared to lower ones as per high-altitudinal stress gradient hypothesis (Jinqiu et al. 2021;Du et al. 2021;Tang et al. 2022;Nong et al. 2023;Wang et al. 2023;Ye et al. 2023;Zhao et al. 2024;Luo et al. 2024). The majority of these molecular studies have mainly focused on targeted metabolite accumulation or associated biosynthetic gene expression by just comparing high-altitude species with low-altitude species; however, studies with representatives distributed along continuous gradient or range covering all aspects/ layers of plant organization are scarce, particularly absent in the Himalayas. ...
Main conclusion
This study at high-altitude alpine environment reveals the molecular signatures associated with stress response and secondary metabolite accumulation, contributing to Picrorhiza kurroa adaptation, which is primarily regulated by a strong interplay of phytohormones.
Abstract
The high-altitude alpine environment is an extreme and variable environment with unique combinations of abiotic/biotic stresses. Despite progress about plant response to individual and combined abiotic stress in controlled conditions, our knowledge of plant adaptations to multifactorial stress combinations that typically occur in alpine environments is limiting. Here, we utilized the high-altitude medicinal herb Picrorhiza kurroa to investigate how multifactorial stress combinations prevailing along the high-altitude gradient at the western Himalayas affect gene expression and cellular pathways. Leaf transcriptional dynamics identified 7,388 differentially expressed unigenes (DEGs), highlighting unique gene expression patterns, specific pathways, and processes that play a crucial role in plant response to the complex micro-environment of high-altitude. Gene regulatory response largely relies on basic helix–loop–helix (bHLH), no apical meristem (NAC), and ethylene responsive factor (ERF) transcription factor families. Further, unigenes associated with secondary metabolism, multiple abiotic/biotic stress responses, and a variety of cellular and reproductive developmental processes were activated through complex cross-talk among plant hormonal signal transduction pathways. The weak correlation between gene expression and corresponding protein accumulation could predict stress-responsive protein abundance largely under different post-transcriptional/translational regulation. These findings recognize an array of new candidate genes for climate resilience, which would contribute to further our research on high-altitude alpine plant adaptations.
... With increasing altitude, salidroside phenol was accumulated extensively in the roots and rhizomes of Picrorhiza kurroa [16]. Additionally, differentially expressed genes (DEGs) associated with high-altitude adaptation in Potentilla bifurca were predominantly involved in the biosynthesis of secondary metabolites, including sesquiterpenoids, triterpenoids, and flavonoids [17]. In Herpetospermum pedunculosum, the secondary metabolite Tricetin was found to be significantly upregulated with the increasing altitude [18]. ...
Background: The accumulation of secondary metabolites in medicinal plants is often influenced by a variety of factors, and rhizosphere microorganisms typically engage in complex interactions with their host plants. Crepis napifera (Franch.) Babc., a regionally significant medicinal plant, contains a diverse array of terpenoids and demonstrates substantial potential for resource development and utilization. Methods: Transcriptome sequencing, metabolomic profiling, and 16S rRNA gene amplicon sequencing were employed to assess the transcriptional expression patterns, metabolic variations, and rhizosphere microbial community composition of C. napifera (Franch.) Babc. roots distributed across various regions. Results: A total of 3679, 8615, and 11,333 differentially expressed genes (DEGs) were identified in the pairwise comparisons between H1 vs. H2, H2 vs. H3, and H1 vs. H3, respectively. Notably, 497 DEGs were consistently detected across all three comparisons. Additionally, Weighted Gene Co-expression Network Analysis (WGCNA) revealed that the expression levels of genes within the turquoise and yellow modules exhibited a significant positive correlation with elevation. In total, 462 differentially expressed metabolites (DEMs) were identified across the same comparisons. Among these compounds, terpenoids, phenolic acids, amino acids and their derivatives, lipids, and alkaloids accounted for 62.98% of the total differential metabolite content. The accumulation patterns of DEMs varied significantly across different regions in the roots of C. napifera (Franch.) Babc. under the three altitude conditions. In response to environmental conditions and the survival strategy of C. napifera (Franch.) Babc. in alpine areas, an investigation into the rhizosphere microbial community was conducted. Four key microbial genera were identified as being correlated with terpenoid biosynthesis and plant nutritional metabolism. Specifically, Pedosphaera, Acidothermus, and Nevskia exhibited terpene biosynthesis capabilities. Additionally, Herbaspirillum, a common microorganism involved in plant nitrogen fixation, respiration, carbon metabolism, and cell wall metabolism, was also enriched in the rhizosphere of C. napifera (Franch.) Babc. These findings suggested that C. napifera (Franch.) Babc. might recruit these microorganisms to enhance its resistance to environmental stress in alpine areas. Conclusions: The accumulation of terpene in C. napifera (Franch.) Babc. across different regions was influenced by transcriptional changes. The rhizosphere microbial communities also changed during this process, showing a recruitment effect that enhances plant growth and offers potential value.
... In the application of this technique, a number of precedents were carried out to study non-model plants. For example, high-quality de novo assembly of Potentilla bifurca from two altitudes (1725 masl and 3215 masl) was reported for the first time, and pathway analysis revealed a large number of DEGs encoding key enzymes involved in secondary metabolites, including phenylpropane and flavonoids [76]. ...
... Sample selected from two altitude ranges −3215 and 1725 masl Transcriptomic Fifty differentially expressed genes (DEG), including peroxidase, superoxide dismutase protein, and the ubiquitin-conjugating enzyme responded to abiotic stresses; a large number of DEGs encode key enzymes involved in secondary metabolites, including phenylpropane and flavonoids; 298 potential genomic SSRs were identified for genetic diversity assessment. [76] Rhododendron sp. ...
High-altitude plants face extreme environments such as low temperature, low oxygen, low nutrient levels, and strong ultraviolet radiation, causing them to adopt complex adaptation mechanisms. Phenotypic variation is the core manifestation of ecological adaptation and evolution. Many plants have developed a series of adaptive strategies through long-term natural selection and evolution, enabling them to survive and reproduce under such harsh conditions. This article reviews the techniques and methods used in recent years to study the adaptive evolution of high-altitude plants, including transplantation techniques, genomics, transcriptomics, proteomics, and metabolomics techniques, and their applications in high-altitude plant adaptive evolution. Transplantation technology focuses on phenotypic variation, which refers to natural variations in morphological, physiological, and biochemical characteristics, exploring their key roles in nutrient utilization, photosynthesis optimization, and stress-resistance protection. Multiple omics technologies, including genomics, transcriptomics, proteomics, and metabolomics, have revealed genes, regulatory pathways, and metabolic networks associated with phenotypic variations at the genetic and molecular levels. At the same time, the limitations and deficiencies of current technologies used to study plant adaptation to high-altitude environments were discussed. In addition, we propose future improvements to existing technologies and advocate for the integration of different technologies at multiple levels to study the molecular mechanisms of plant adaptation to high-altitude environments, thus providing insights for future research in this field.
... When high-altitude plants face abiotic stresses like low oxygen, intense sunlight, and extreme temperature fluctuations, they are forced to adapt by undergoing a cascade of gene and RNA changes, including at the transcriptome level (Guo et al. 2021). The complete de novo transcriptome of Potentilla bifurca was reconstructed by Tang et al. (2022) from both low and high-altitude samples. Analysis of differential gene expression between samples collected at low and high altitudes for P. bifurca showed that the former strongly upregulated 3998 genes while the latter significantly downregulated 1886 genes. ...
... Along with variations in primary metabolites, there were also notable differences in organ-and altitude-specific SMs, indicating modifications in secondary metabolic pathways (Kumari et al. 2020;Tang et al. 2022;Satyakam et al. 2023). Numerous studies have shown a higher accumulation of SMs (phenolics and flavonoids) in organ and altitude-specific manners, possibly being linked to enhanced carbon allocation (Zhao et al. 2019;Kumari et al. 2020). ...
... As the altitude increased, salidroside phenol accumulated extensively in the root and rhizome of P. Kurroa. Tang et al. (2022) observed that DEGs upregulated in P. bifurca at high altitudes were most abundant in secondary metabolite syntheses, such as sesquiterpenoid, triterpenoid, wax biosynthesis, flavonoid biosynthesis, and phenylpropanoid biosynthesis. This suggests that the accumulation of these compounds was linked to P. bifurca adaptation to the highaltitude environment. ...
... Iljinsk [24]. The most significantly differentially expressed top 50 genes in the high-altitude samples were derived from plants that responded to abiotic stress, such as peroxidase, superoxide dismutase protein, and the ubiquitin-conjugating enzyme, and the KEGG pathway was related to secondary metabolites, including phenylpropane and flavonoids, in intraspecific adaptation to high altitude in Potentilla bifurca L. [25]. Compared to the above research, our findings showed a different picture of DEGs. ...
Kingdonia uniflora is an endangered alpine herb that is distributed along an altitudinal gradient. The unique traits and important phylogenetic position make K. uniflora an ideal model for exploring how endangered plants react to altitude variation. In this study, we sampled nine individuals from three representative locations and adopted RNA-seq technology to sequence 18 tissues, aiming to uncover how K. uniflora responded to different altitudes at the gene expression level. We revealed that genes that responded to light stimuli and circadian rhythm genes were significantly enriched in DEGs in the leaf tissue group, while genes that were related to root development and peroxidase activity or involved in the pathways of cutin, suberin, wax biosynthesis, and monoterpenoid biosynthesis were significantly enriched in DEGs in the flower bud tissue group. All of the above genes may play an important role in the response of K. uniflora to various stresses, such as low temperatures and hypoxia in high-altitude environments. Furthermore, we proved that the discrepancy in gene expression patterns between leaf and flower bud tissues varied along the altitudinal gradient. Overall, our findings provide new insights into the adaptation of endangered species to high-altitude environments and further encourage parallel research to focus on the molecular mechanisms of alpine plant evolution.
... When high-altitude plants face abiotic stresses like low oxygen, intense sunlight, and extreme temperature fluctuations, they are forced to adapt by undergoing a cascade of gene and RNA changes, including at the transcriptome level (Guo et al. 2021). The complete de novo transcriptome of Potentilla bifurca was reconstructed by Tang et al. (2022) from both low and high-altitude samples. Analysis of differential gene expression between samples collected at low and high altitudes for P. bifurca showed that the former strongly upregulated 3998 genes while the latter significantly downregulated 1886 genes. ...
... Along with variations in primary metabolites, there were also notable differences in organ-and altitude-specific SMs, indicating modifications in secondary metabolic pathways (Kumari et al. 2020;Tang et al. 2022;Satyakam et al. 2023). Numerous studies have shown a higher accumulation of SMs (phenolics and flavonoids) in organ and altitude-specific manners, possibly being linked to enhanced carbon allocation (Zhao et al. 2019;Kumari et al. 2020). ...
... As the altitude increased, salidroside phenol accumulated extensively in the root and rhizome of P. Kurroa. Tang et al. (2022) observed that DEGs upregulated in P. bifurca at high altitudes were most abundant in secondary metabolite syntheses, such as sesquiterpenoid, triterpenoid, wax biosynthesis, flavonoid biosynthesis, and phenylpropanoid biosynthesis. This suggests that the accumulation of these compounds was linked to P. bifurca adaptation to the highaltitude environment. ...
High-altitude climates are characterized by intense solar and UV (ultraviolet) stress, long periods of sunlight, low temperatures, and a significant temperature differential between day and night. These traits affect high-altitude plants’ physical structure and physiological and metabolic functions. Abiotic stress responses are critical for understanding how plants adapt to high altitudes. Thus, the adverse environment of mountainous areas makes organisms an ideal natural laboratory for examining speciation and adaptive evolution. Alpine plants employ morphological modifications to adapt to their high-altitude habitat, but the molecular and physiological mechanisms that underpin these adaptations remain unclear. According to recent plant climate adaptation findings, climate change may drive fresh selection and interfere with local adaptation. Genome/transcriptome sequencing has shown that energy consumption and positive selection response to various stresses depend on certain genes. RNA sequencing may also aid in the development of molecular markers such as co-dominant microsatellite markers and single-copy nuclear genes. Phytoconstituents are predominantly alkaloids, glycosides, polyphenols, and terpenes. Secondary metabolites from medicinal plants are plentiful and widely employed in traditional medicine. In drug development, huge datasets are analyzed using whole-genome sequencing and cellular protein expression patterns. Along with genomics, proteomics, and metabolomics, OMICs are used to find and characterize targeted drugs. Morphological statistics and high-throughput multi-omics have been widely employed to explore how plants adapt to high-altitude settings. These technologies can now capture images of a biological system’s underlying biology at a resolution never before possible. This review delves into the assessment of the transcriptome and metabolome in plant adaptation along altitude. The insights gained from this exploration can be of significant assistance to researchers engaged in the fields of medicinal plant biotechnology, chemical genetics, and adaption biology.
... With the development of high-throughput sequencing technology, plant RNA-seq datasets can be obtained rapidly and comprehensively [24,25]. This technology is now widely used in transcriptome gene expression analysis [26], secondary metabolism studies of plants [27,28], disease resistance mechanisms [29], biocontrol [30,31], and so on. RNAseq datasets can also be used to study the molecular function of specific genes and to screen for internal reference genes [32,33]. ...
Lamiophlomis rotata (Benth.) Kudo is a perennial and unique medicinal plant of the Qinghai–Tibet Plateau. It has the effects of diminishing inflammation, activating blood circulation, removing blood stasis, reducing swelling, and relieving pain. However, thus far, reliable reference gene identifications have not been reported in wild L. rotata. In this study, we identified suitable reference genes for the analysis of gene expression related to the medicinal compound synthesis in wild L. rotata subjected to five different-altitude habitats. Based on the RNA-Seq data of wild L. rotata from five different regions, the stability of 15 candidate internal reference genes was analyzed using geNorm, NormFinder, BestKeeper, and RefFinder. TFIIS, EF-1α, and CYP22 were the most suitable internal reference genes in the leaves of L. rotata from different regions, while OBP, TFIIS, and CYP22 were the optimal reference genes in the roots of L. rotata. The reference genes identified here would be very useful for gene expression studies with different tissues in L. rotata from different habitats.
Background: Plants of Nitraria, belonging to the Zygophyllaceae family, are not only widely distributed at an altitude of about 1000 m but also at an altitude of about 3000 m, which is a rare phenomenon. However, little is known about the effect of altitude on the accumulation of metabolites in plants of Nitraria. Furthermore, the mechanism of the high–altitude adaptation of Nitraria has yet to be fully elucidated. Methods: In this study, metabolomics and transcriptomics were used to investigate the differential accumulation of metabolites of Nitraria berries and the regulatory mechanisms in different altitudes. Results: As a result, the biosynthesis of flavonoids is the most significant metabolic pathway in the process of adaptation to high altitude, and 5 Cyanidins, 1 Pelargonidin, 3 Petunidins, 1 Peonidin, and 4 Delphinidins are highly accumulated in high–altitude Nitraria. The results of transcriptomics showed that the structural genes C4H (2), F3H, 4CL (2), DFR (2), UFGT (2), and FLS (2) were highly expressed in high–altitude Nitraria. A network metabolism map of flavonoids was constructed, and the accumulation of differential metabolites and the expression of structural genes were analyzed for correlation. Conclusions: In summary, this study preliminarily offers a new understanding of metabolic differences and regulation mechanisms in plants of Nitraria from different altitudes.
High-altitude regions, characterized by unique climatic conditions and diverse ecosystems are home to an array of crops vital to the economic prosperity of local communities. The cultivation of high-altitude crops plays a significant role in ensuring food security, conserving biodiversity, and boosting the tourism sector. While traditional breeding methods have historically improved crop yield and resilience, recent years have witnessed a surge of interest in adopting multi-omics approaches, particularly genomics. High-throughput sequencing technologies have unveiled critical genes and pathways associated with key traits including stress resistance and tolerance, guiding innovative breeding strategies. Genomics has ushered in a new era for high-altitude crop cultivation, facilitating the development of crops adapted to extreme conditions, resistant to pests and diseases, and enriched with essential nutrients. In this chapter, we delve into the wealth of genomics resources available for high-altitude crops. We also discuss the current status and future prospects of various genomics techniques, including QTL mapping, genome-wide association mapping, marker-assisted selection, genomic selection, and genome editing, aiming to enhance crop yield, bolster climate resilience and stress tolerance, and elevate the nutritional value of high-altitude crops. This chapter offers a comprehensive overview of the latest advancements in high-altitude crop enhancement, the challenges associated with genomics, and sheds light on the future of agriculture in challenging landscapes.
