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Comparative Study
. 2017 Jul 11;22(7):1158.
doi: 10.3390/molecules22071158.

Comparative Transcriptome Analysis Reveals Adaptive Evolution of Notopterygium Incisum and Notopterygium Franchetii, Two High-Alpine Herbal Species Endemic to China

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Free PMC article
Comparative Study

Comparative Transcriptome Analysis Reveals Adaptive Evolution of Notopterygium Incisum and Notopterygium Franchetii, Two High-Alpine Herbal Species Endemic to China

Yun Jia et al. Molecules. .
Free PMC article

Abstract

The extreme conditions (e.g., cold, low oxygen, and strong ultraviolet radiation) of the high mountains provide an ideal natural laboratory for studies on speciation and the adaptive evolution of organisms. Up to now, few genome/transcriptome-based studies have been carried out on how plants adapt to conditions at extremely high altitudes. Notopterygium incisum and Notopterygium franchetii (Notopterygium, Apiaceae) are two endangered high-alpine herbal plants endemic to China. To explore the molecular genetic mechanisms of adaptation to high altitudes, we performed high-throughput RNA sequencing (RNA-seq) to characterize the transcriptomes of the two species. In total, more than 130 million sequence reads, 81,446 and 63,153 unigenes with total lengths of 86,924,837 and 62,615,693 bp, were generated for the two herbal species, respectively. OrthoMCL analysis identified 6375 single-copy orthologous genes between N. incisum and N. franchetii. In total, 381 positively-selected candidate genes were identified for both plants by using estimations of the non-synonymous to synonymous substitution rate. At least 18 of these genes potentially participate in RNA splicing, DNA repair, glutathione metabolism and the plant-pathogen interaction pathway, which were further enriched in various functional gene categories possibly responsible for environment adaptation in high mountains. Meanwhile, we detected various transcription factors that regulated the material and energy metabolism in N. incisum and N. franchetii, which probably play vital roles in the tolerance to stress in surroundings. In addition, 60 primer pairs based on orthologous microsatellite-containing sequences between the both Notopterygium species were determined. Finally, 17 polymorphic microsatellite markers (SSR) were successfully characterized for the two endangered species. Based on these candidate orthologous and SSR markers, we detected that the adaptive evolution and species divergence of N. incisum and N. franchetii were significantly associated with the extremely heterogeneous environments and climatic oscillations in high-altitude areas. This work provides important insights into the molecular mechanisms of adaptation to high-altitudes in alpine herbal plants.

Keywords: Notopterygium; adaptive evolution; microsatellite marker; positive selection; transcriptome.

Conflict of interest statement

The authors declare no conflict of interest. The founding sponsors had no role in the design of the study; in the collection, analyses, or interpretation of data; in the writing of the manuscript, and in the decision to publish the results.

Figures

Figure 1
Figure 1
Overview of Notopterygium incisum and Notopterygium franchetii assemblies and annotations.
Figure 2
Figure 2
Gene Ontology (GO) distributions of unigenes.
Figure 3
Figure 3
The Ks distribution of orthologs between Notopterygium incisum and Notopterygium franchetii; their divergence is shown by the peak of Ks at 0.011 ± 0.021.
Figure 4
Figure 4
The glutathione-to-glutamate pathway and the plant–pathogen interaction pathway was adapted from the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway available online (http://www.genome.jp/kegg/pathway.html) [28]. (A) Many genes identified by KEGG as encoding the glutathione S-transferase (EC.2.5.1.18) and glutathione peroxidase (EC:1.11.1.9) are enriched in Notopterygium incisum and Notopterygium franchetii; (B) Many genes identified by KEGG as encoding the cyclic nucleotide gated channel (CNGC); CML (CaM/CML), calcium-binding protein, and pathogenesis-related protein 1 (PR1) are enriched in Notopterygium incisum and Notopterygium franchetii.
Figure 5
Figure 5
Transcript distribution in various transcription factor (TF) families.

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