![]() By combining the published chloroplast sequences and genomic data, we sought to 1) resolve the phylogenetic relationships in Acrostichum 2) estimate the divergence times between Acrostichum and its sister genus Ceratopteris, as well as within the Acrostichum genus and 3) detect candidate genes that are under positive selection in mangrove ferns. speciosum) and one species of its non-mangrove sister genus, Ceratopteris thalictroides. In this study, we sequenced, de novo assembled and annotated the transcriptomes of two mangrove fern species of Acrostichum ( A. A number of ferns have been studied using this strategy, such as the bracken fern Pteridium aquilinum 14, the fresh-water fern Ceratopteris richardii 15, the Japanese climbing fern Lygodium japonicum 16, as well as the fern species in the 1,000 Plants (1 KP) project 17. RNA-seq is a relatively convenient choice because a large number of sequences can be obtained at low cost 13. Because fern species usually have large chromosome numbers and genome sizes, whole-genome sequencing is difficult thus, complete genome sequences are not available for ferns, including Acrostichum 13. To resolve these evolutionary questions, large amounts of molecular resources, such as whole-genome sequences and transcriptome data, are needed. By reconstructing the phylogeny of this genus and estimating divergence times, we can provide new insight on the origins of the genus. Additionally, Acrostichum is the only fern genus that grows in the intertidal zone, occupying a special position in ferns. For example, identifying positively selected genes in the genomes of Acrostichum species could contribute to our understanding of molecular mechanisms of adaptive evolution 11, 12. Acrostichum displays markedly differential adaptations to heterogeneous habitats, thus offering an excellent system in which to study adaptive evolution. However, only F1 hybrids have been found in the wild, suggesting strong postzygotic isolation between these species 6. Although these plants prefer different environments, the two species can hybridize when their habitats overlap, especially in disturbed habitats 6. speciosum has papery fronds with a pointed tip 6. aureum has thickly coriaceous fronds with a broadly rounded end, whereas A. The differential adaptations of the two species to different light conditions are also reflected by their frond textures: A. aureum 9, which is corroborated by the differing Na + and Cl − levels in the roots and leaves of A. speciosum appears to have greater salt tolerance than A. speciosum is usually found in the shady mangrove understory, which is frequently flooded by tides 8. aureum is an upstream fern usually found in open, light-abundant habitats that are strongly influenced by fresh water, especially in mangrove forests that have been disturbed by human activities 7, whereas A. speciosum often occur sympatrically but occupy different habitats with respect to light and salinity 6. danaeifolium have chromosome numbers of 2n = 60 4, 5 ( Supplementary Information and Supplementary Fig. The three species of Acrostichum are all diploid, and A. aureum is the only species of mangroves that is widely distributed in both areas 3. speciosum are restricted within the Atlantic East-Pacific (AEP) area and Indo West-Pacific (IWP) area, respectively, whereas A. Therefore, these species are referred as “mangrove ferns” 2. They grow in the unstable marine intertidal zone, which is characterized by harsh conditions for plant growth, such as high salinity, tidal fluctuations and long-term climate changes 1, 2. (Pteridaceae) are important components of mangrove community. ![]() ![]() ![]() Our study provides abundant transcriptome data and new insights into the evolution and adaptations of mangrove ferns in the inhospitable intertidal zone. Two methods (the modified branch-site model and the K h method) were used to identify several positively selected genes, which may contribute to differential adaptation of the two Acrostichum species to different light and salt conditions. The estimated divergence time revealed that Acrostichum adapted to the coastal region during the late Cretaceous, whereas the two mangrove ferns from the Indo West-Pacific (IWP) area diverged more recently. We obtained 47,517, 36,420 and 60,823 unigenes for the three ferns, of which 24.39–45.63% were annotated using public databases. speciosum, as well as a species in the sister genus, Ceratopteris thalictroides. To explore the phylogenetic relationships and molecular mechanisms underlying adaptations in this genus, we sequenced the transcriptomes of two species of Acrostichum, A. The mangrove fern genus Acrostichum grows in the extremely unstable marine intertidal zone under harsh conditions, such as high salt concentrations, tidal rhythms and long-term climate changes. ![]()
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