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Background   Stipagrostis pennata  is distributed in the mobile and semi-mobile sand dunes which can adapt well to extreme environments such as drought and high temperature. It is a pioneer plant species with potential for stabilizing sand dunes and ecological restoration. It can settle on moving sand dunes earlier than other desert plants. It can effectively improve the stability of sand dunes and help more plants settle down and increase plant diversity. However, despite its important ecological value, the genetic resources available for this species are limited.    Results  We used single-molecule real-time sequencing technology to obtain the complete full-length transcriptome of  Stipagrostis pennata , including 90,204 unigenes with an average length of 2624 bp. In addition, the 5436 transcription factors identified in these unigenes are rich in stress resistance genes, such as MYB-related, C3H, bHLH, GRAS and HSF,  etc ., which may play a role in adapting to desert drought and strong wind stress. Intron retention events are abundant alternative splicing events.  Stipagrostis pennata  has experienced stronger positive selection, accelerating the fixation of advantageous variants. Thirty-eight genes, such as CPP/TSO1-like gene, have evolved rapidly and may play a role in material transportation, flowering and seed formation.    Conclusions  The present study captures the complete full-length transcriptome of  Stipagrostis pennata  and reveals its rapid evolution. The desert adaptation in  Stipagrostis pennata  is reflected in the regulation of gene expression and the adaptability of gene function. Our findings provide a wealth of knowledge for the evolutionary adaptability of desert grass species.    Supplementary Information  The online version contains supplementary material available at 10.1186/s12864-021-08124-w.

Rapidly evolving genetic features for desert adaptations in Stipagrostis pennata