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

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.

Transcriptome analysis of the endangered Notopterygium incisum: Cold-tolerance gene discovery and identification of EST-SSR and SNP markers

“…Equal amounts of RNA purified from each of the three tissues were mixed together to construct cDNA libraries. The detailed transcriptome sequencing strategies were as followed by Jia et al., (2017).

Fig. 1Geographic distributions of the Notopterygium incisum samples.

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Evolutionary and ecological functional genomics, from lab to the wild

“…These ecological transcriptome studies allow a connection between genotypic variation into complex trait phenotypes as modulated by the prism of the natural environment. Such studies have now become increasingly popular, and have been undertaken in A. thaliana (Richards et al ., ; Tyagi et al ., ) and crops (Plessis et al ., ; Russell et al ., ; Zhao et al ., ), tree species (Philippe et al ., ; Verta et al ., ), lesser known plant species (Jia et al ., ; Yang et al ., ), and energy crops like switchgrass (Palmer et al ., ) and Miscanthus (Song et al ., ; Yan et al ., ; Xing et al ., ).…”

“…There has also been more work probing adaptation to harsh and unconventional environments including elevated mountain areas (Yang et al ., ; Jia et al ., ), inter‐tidal mangrove areas (Yang et al ., ; Guo et al ., ), and even the Antarctic (Cho et al ., ). In the case of biotic interactions, field transcriptomes have been sequenced from microbial plant colonizers and the plant host in tandem in a dual RNA‐seq approach (Hubbard et al ., ; Kamitani et al ., ).…”

Integrated physiological and transcriptomic analyses responses to altitude stress in oat (Avena sativa L.)

“…The Qinghai-Tibetan Plateau, the highest plateau in the world, plays an important role in climate changes in Asia and even the world [2]. In particular, the Qinghai-Tibetan Plateau environment is known for its harsh conditions, characterized by severe coldness, intensive ultraviolet radiations, hypoxia, poor soils and low CO 2 pressure [3,4]. Therefore, the survival in Qinghai-Tibetan Plateau is very challenging for most organisms.…”