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We characterized the Ammopiptanthus nanus transcriptome, identified a large number of orthologs and predicted the divergence time between A. nanus and A. mongolicus, the only two species in genus Ammopiptanthus.

Plants in the genus Ammopiptanthus are relic trees of the Tertiary period that have survived dramatic climate change in the Central Asia dryland. Currently, the only two remaining Ammopiptanthus species, A. nanus and A. mongolicus, are distributed in distinct arid regions. Comparative analysis between the two species will facilitate our understanding of speciation and their different adaptation mechanisms. However, lack of nucleotide sequence data hindered the functional genomics research on A. nanus and comparative transcriptome analysis between the two Ammopiptanthus species. Here, we utilized RNA-Seq to characterize the A. nanus transcriptome and then performed a comparative transcriptome analysis between the two species. A total of 69,990 transcripts were assembled from 93 million clean reads of A. nanus, and more than 78% of these transcripts were annotated. A batch of miRNA precursors was predicted and thousands of potential simple sequence repeats were identified. A total of 6606 pairs of putative orthologs with full-length coding sequences were obtained using reciprocal blast. Based on the rates of nonsynonymous (Ka) to synonymous (Ks) substitutions, the divergence time between A. nanus and A. mongolicus was calculated to be approximately 0.70 +/- 0.62 Mya. We identified 15 rapidly evolved genes that likely experienced positive selection; these genes are mainly involved in plant defense, epigenetic regulation, and plant development. Our results provide a comprehensive transcriptomic dataset for A. nanus and advance understanding on the evolutionary adaptation of the two species to their individual arid habitats.