Abstract
Understanding how species adapt to extreme environments is an extension of the main goals of evolutionary biology. While alpine plants are an ideal system for investigating the genetic basis of high-altitude adaptation, genomic resources in these species are still limited. In the present study, we generated reference-level transcriptomic data of five Saussurea species through high-throughput sequencing and de novo assembly. Three of them are located in the highland of the Qinghai-Tibet Plateau (QTP), and the other two are close relatives distributed in the lowland. A series of comparative and evolutionary genomics analyses were conducted to explore the genetic signatures of adaptive evolution to high-altitude environments. Estimation of divergence time using single-copy orthologs revealed that Saussurea species diversified during the Miocene, a period with extensive tectonic movement and climatic fluctuation on the QTP. We characterized gene families specific to the alpine species, including genes involved in oxidoreductase activity, pectin catabolic process, lipid transport, and polysaccharide metabolic process, which may play important roles in defense of hypoxia and freezing temperatures of the QTP. Furthermore, in a phylogenetic context with the branch model, we identified hundreds of genes with signatures of positive selection. These genes are involved in DNA repair, membrane transport, response to UV-B and hypoxia, and reproductive processes, as well as some metabolic processes associated with nutrient intake, potentially responsible for Saussurea adaptation to the harsh environments of high altitude. Overall, our study provides valuable genomic resources for alpine species and gained helpful insights into the genomic basis of plants adapting to extreme environments.
Highlights
Understanding the genetic basis of species adapting to high altitude is a long-standing theme of evolutionary biology [1,2,3,4,5]
The median length of transcripts was 417 bp–611 bp, and the median length of unigenes was 353 bp–427 bp, with contig N50s ranging from 899 bp to 1562 bp for transcripts and from 787 bp to 1334 bp for unigenes (Table 1)
Five Saussurea species were sampled for RNA-seq, of which three (S. pachyneura, S. salwinensis, and S. velutina) were collected from the Qinghai-Tibet Plateau (QTP) alpine zone of Baima Snow
Summary
Understanding the genetic basis of species adapting to high altitude is a long-standing theme of evolutionary biology [1,2,3,4,5]. Species inhabiting high-altitude environments have to face a variety of abiotic stresses, such as reduced oxygen availability, rapid fluctuations in temperature, and high ultraviolet (UV) radiation [6,7,8]. These stresses present strong selective pressure and have driven striking phenotypic and genetic adaptations [9,10,11,12]. In the alpine screes of the QTP (usually elevation above 4500 m), characterized by freezing temperatures, high winds, strong UV rays, and poor soil quality, plants have evolved extraordinarily diverse traits for adaptation, such as leafy bracts, woolly trichomes and cushion plants [23,24,25]. Despite increased understanding of the ecological benefits of these adaptive traits [26,27], the genetic mechanisms underlying high-altitude adaptation are still poorly studied
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