Abstract
The extreme environment of the Qinghai-Tibet Plateau (QTP) provides an ideal natural laboratory for studies on adaptive evolution. Few genome/transcriptome based studies have been conducted on how plants adapt to the environments of QTP compared to numerous studies on vertebrates. Crucihimalaya himalaica is a close relative of Arabidopsis with typical QTP distribution, and is hoped to be a new model system to study speciation and ecological adaptation in extreme environment. In this study, we de novo generated a transcriptome sequence of C. himalaica, with a total of 49,438 unigenes. Compared to five relatives, 10,487 orthogroups were shared by all six species, and 4,286 orthogroups contain putative single copy gene. Further analysis identified 487 extremely significantly positively selected genes (PSGs) in C. himalaica transcriptome. Theses PSGs were enriched in functions related to specific adaptation traits, such as response to radiation, DNA repair, nitrogen metabolism, and stabilization of membrane. These functions are responsible for the adaptation of C. himalaica to the high radiation, soil depletion and low temperature environments on QTP. Our findings indicate that C. himalaica has evolved complex strategies for adapting to the extreme environments on QTP and provide novel insights into genetic mechanisms of highland adaptation in plants.
Highlights
Extreme environments provide an ideal natural laboratory for studies on adaptive evolution
Dated phylogenies indicated that the genus Crucihimalaya origin in about 5.2 Mya, and that C. himalaica split from C. lasiocarpa in about 3.56 Mya[20], which is in accordance with the time of Qinghai-Tibet Plateau (QTP) rapid uplift, 3.6 Mya[21]
The clean data were submitted to the NCBI Sequence Reads Archive (SRA) database
Summary
Extreme environments provide an ideal natural laboratory for studies on adaptive evolution. Relatives of Arabidopsis thaliana are important model systems to study evolutionary ecology and comparative genomics[9,10]. Dated phylogenies indicated that the genus Crucihimalaya origin in about 5.2 Mya, and that C. himalaica split from C. lasiocarpa in about 3.56 Mya[20], which is in accordance with the time of QTP rapid uplift, 3.6 Mya[21] This species must have undergone significant genetic changes to adapt to stress factors following the rapid uplift of QTP. Transcriptome analysis (RNA-seq) provides a rapid and effective approach to obtain massive protein-coding genes, which can be used for understanding ecological, comparative and evolutionary genomics questions for non-model organisms[22,23]. We aim to reveal how this Arabidopsis relative adapts to the complicated extreme environments on QTP at genome/ transcriptome level
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