Abstract
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. To explore the phylogenetic relationships and molecular mechanisms underlying adaptations in this genus, we sequenced the transcriptomes of two species of Acrostichum, A. aureum and A. speciosum, as well as a species in the sister genus, Ceratopteris thalictroides. 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. 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. Two methods (the modified branch-site model and the Kh 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. Our study provides abundant transcriptome data and new insights into the evolution and adaptations of mangrove ferns in the inhospitable intertidal zone.
Highlights
Total number of raw reads Total number of clean reads Reads length Total number of contigs Total number of unigenes Mean length Median length N50 value Longest unigene GC content
We obtained 22–26 million raw reads for the three fern species, from which 17–21 million clean reads were retrieved after quality control (Table 1)
After the redundancies were removed, 47,517, 36,420 and 60,823 contigs with N50 values of 1,136 bp, 1,687 bp and 787 bp, respectively, were treated as unigenes in the downstream analyses (Table 1). These unigenes were deposited in the NCBI GenBank under accession numbers GEEI00000000 (A. aureum), GEEJ00000000 (A. speciosum) and GEEK00000000 (C. thalictroides)
Summary
Total number of raw reads Total number of clean reads Reads length (bp) Total number of contigs Total number of unigenes Mean length (bp) Median length (bp) N50 value (bp) Longest unigene (bp) GC content. By reconstructing the phylogeny of this genus and estimating divergence times, we can provide new insight on the origins of the genus. To resolve these evolutionary questions, large amounts of molecular resources, such as whole-genome sequences and transcriptome data, are needed. We sequenced, de novo assembled and annotated the transcriptomes of two mangrove fern species of Acrostichum (A. aureum and A. speciosum) and one species of its non-mangrove sister genus, Ceratopteris thalictroides. 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
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