Abstract
Epiphytic ferns have been found to flourish after angiosperms dominated forest communities, and they play important roles in rainforest canopies. How do epiphytic ferns adapt to tropical rainforest canopy habitats? At present, we know little about the molecular mechanism underlying this adaptation. Asplenium nidus is a well-known epiphytic fern that is closely related to the terrestrial species Asplenium komarovii. Here, RNA-seq and comparative transcriptomic analyses were performed to explore the underlying basis of the adaptation of A. nidus to extreme environments. A total of 44.04 and 44.57 Mb clean reads were obtained from A. nidus and A. komarovii, respectively, and they were assembled into 89,741 and 77,912 unigenes. Functional annotation showed that 52,305 (58.28% of the total genes for A. nidus) and 45,938 (58.96% of the total genes for A. komarovii) unigenes were annotated in public databases. Genes involved in stress responses and photosynthesis were found to have undergone positive selection in A. nidus. Compared to A. komarovii, transcription factors related to stress response, leaf development, and root development were found to be considerably expanded in A. nidus, especially in the ANR1 subclade of MADS-box family genes which played roles in lateral root development. This study improves our understanding of the adaptation of A. nidus to epiphytic habitats by forming unique strategies.
Highlights
With 20,000-25,000 species, vascular epiphytes present widely in many families in ferns, gymnosperms, and angiosperms [1, 2]
Trinity was used for the de novo assembly of 173,229 and 142,138 contigs in A. nidus and A. komarovii transcriptomes (Table 1)
We used BUSCO to assess the completeness and quality of the transcriptome assemblies by using a eukaryotic species database containing 429 orthologroups as the reference. These transcriptomes showed high coverage rates of the orthologroups—68.3% in A. nidus and 77.7% in A. komarovii (Table 1)—indicating that the transcriptomes were relatively complete, and that the data was of high quality and could be used for subsequent analyses
Summary
With 20,000-25,000 species, vascular epiphytes present widely in many families in ferns, gymnosperms, and angiosperms [1, 2]. Epiphytes play important ecological roles in rainforests [3, 4]. Ferns are the second largest group of vascular plants, of which 2,800 species are epiphytic. Epiphytic ferns account for one-third of the leptosporangiate ferns, and they can endure severe drought stress, nutrient shortage, and intense sunlight, but not frost [1, 5]. Several epiphytic ferns, including some species in the genera Vittaria, Pyrrosia, Polypodium, and Platycerium, have been found to exhibit features typical of crassulacean acid metabolism (CAM) in photosynthesis [6,7,8]. Epiphytic plants utilize specialized ecological strategies to adapt to variable environments, especially drought stress during dry seasons
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