title: Transcriptome analyses provide insights into the phylogeny and adaptive evolution of the mangrove fern genus Acrostichum.
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 Khmethod) 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.
authors: State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources, Key Laboratory of Biodiversity Dynamics and Conservation of Guangdong Higher Education Institutes, Sun Yat-Sen University, Guangzhou, 510275, China.
authors: Zhang
authors: Z
authors: Zhang
authors: State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources, Key Laboratory of Biodiversity Dynamics and Conservation of Guangdong Higher Education Institutes, Sun Yat-Sen University, Guangzhou, 510275, China.
authors: Ziwen
authors: Z
authors: He
authors: State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources, Key Laboratory of Biodiversity Dynamics and Conservation of Guangdong Higher Education Institutes, Sun Yat-Sen University, Guangzhou, 510275, China.
authors: Shaohua
authors: S
authors: Xu
authors: State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources, Key Laboratory of Biodiversity Dynamics and Conservation of Guangdong Higher Education Institutes, Sun Yat-Sen University, Guangzhou, 510275, China.
authors: Xinnian
authors: X
authors: Li
authors: State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources, Key Laboratory of Biodiversity Dynamics and Conservation of Guangdong Higher Education Institutes, Sun Yat-Sen University, Guangzhou, 510275, China.
authors: Wuxia
authors: W
authors: Guo
authors: State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources, Key Laboratory of Biodiversity Dynamics and Conservation of Guangdong Higher Education Institutes, Sun Yat-Sen University, Guangzhou, 510275, China.
authors: Yuchen
authors: Y
authors: Yang
authors: Hainan Dongzhai Harbor National Nature Reserve, Haikou, 571129, China.
authors: Cairong
authors: C
authors: Zhong
authors: State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources, Key Laboratory of Biodiversity Dynamics and Conservation of Guangdong Higher Education Institutes, Sun Yat-Sen University, Guangzhou, 510275, China.
authors: Renchao
authors: R
authors: Zhou
authors: State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources, Key Laboratory of Biodiversity Dynamics and Conservation of Guangdong Higher Education Institutes, Sun Yat-Sen University, Guangzhou, 510275, China.
authors: Suhua
authors: S
authors: Shi
mesh_terms: D000222:Adaptation, Physiological / Q000235:genetics*; D001483:Base Sequence; D002736:Chloroplasts / Q000235:genetics; D057231:Climate Change; D018744:DNA, Plant / Q000235:genetics; D019143:Evolution, Molecular; D020869:Gene Expression Profiling; D010802:Phylogeny; D029621:Polypodiaceae / Q000235:genetics*; D055051:Salt-Tolerant Plants / Q000235:genetics*; D017422:Sequence Analysis, DNA; D059467:Transcriptome / Q000235:genetics*
chemical_list: D018744:DNA, Plant