Transcriptome Analysis Provides Insights into Potentilla bifurca Adaptation to High Altitude

Abstract

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 assembly of 222,619 unigenes from 405 million clean reads, 57.64% of which were annotated in Nr, GO, KEGG, Pfam, and Swiss-Prot databases. 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. Pathway analysis revealed that a large number of DEGs encode key enzymes involved in secondary metabolites, including phenylpropane and flavonoids. In addition, a total of 298 potential genomic SSRs were identified in this study, which provides information on the development of functional molecular markers for genetic diversity assessment. In conclusion, this study provides the first comprehensive assessment of the Potentilla bifurca transcriptome. This provides new insights into coping mechanisms for non-model organisms surviving in harsh environments at high altitudes, as well as molecular evidence for the selection of superior medicinal plants.

Keywords: Potentilla bifurca; de novo transcriptome sequencing; flavonoid metabolism; high altitude; secondary metabolism.

Figure 1

Potentilla bifurca plant. The red arrow shows its obovate-elliptic, apex 2-fid leaf type.

Figure 2

Unigene length distribution in P. bifurca.

Figure 3

Species classification of the homologous sequences of P. bifurca unigenes. (A) Frequency distribution of the unigene sequences, according to their E values (cut-off value = 1 × 10⁻⁵); (B) Species distribution of the homologous sequences.

Figure 4

Volcano map of differentially expressed unigenes.

Figure 5

Heatmap showing the top 50 up- and down-regulated genes in high-altitude and low-altitude in P. bifurca, with clear annotation.

Figure 6

Gene ontology classification of DEGs. (A) Up-regulated unigenes; (B) Down-regulated unigenes. All unigenes fall into three major functional categories. The Y-axis represents the number of genes in a category; red to yellow represents decreasing p-values.

Figure 7

SSR sequences identified in DEGs. (A) abundance of different types of SSRs; (B) the 10 most abundant SSRs.

Figure 8

Putative phenylpropanoid pathway in P. bifurca.

Figure 9

The bubble plot represents the top 20 KEGG pathways of DEGs under positive selection.

Figure 10

Polymethoxylated flavones and monolignol synthetic pathways. C3’H: 5-O-(4-coumaroyl)-D-quinate 3’-monooxygenase, C4H: cinnamate 4-hydroxylase, CCoAOMT: caffeoyl-CoA O-methyltransferase, CHS: chalcone synthase, HCT: shikimate O-hydroxycinnamoyl transferase.

Figure 11

Members interaction in polymethoxylated flavone and monolignol synthetic pathways. 4CL: 4-coumarate-CoA Ligase, C3’H: 5-O-(4-coumaroyl)-D-quinate 3’-monooxygenase, CAD: cinnamyl-alcohol dehydrogenase, CCoAOMT: caffeoyl-CoA O-methyltransferase, CCR: cinnamoyl-CoA reductase, CSE: caffeoylshikimate esterase, HCT: shikimate O-hydroxycinnamoyl transferase.