title: De Novo Assembly of Coding Sequences of the Mangrove Palm (Nypa fruticans) Using RNA-Seq and Discovery of Whole-Genome Duplications in the Ancestor of Palms.
abstract: Nypa fruticans (Arecaceae) is the only monocot species of true mangroves. This species represents the earliest mangrove fossil recorded. How N. fruticans adapts to the harsh and unstable intertidal zone is an interesting question. However, the 60 gene segments deposited in NCBI are insufficient for solving this question. In this study, we sequenced, assembled and annotated the transcriptome of N. fruticans using next-generation sequencing technology. A total of 19,918,800 clean paired-end reads were de novo assembled into 45,368 unigenes with a N50 length of 1,096 bp. A total of 41.35% unigenes were functionally annotated using Blast2GO. Many genes annotated to "response to stress" and 15 putative positively selected genes were identified. Simple sequence repeats were identified and compared with other palms. The divergence time between N. fruticans and other palms was estimated at 75 million years ago using the genomic data, which is consistent with the fossil record. After calculating the synonymous substitution rate between paralogs, we found that two whole-genome duplication events were shared by N. fruticans and other palms. These duplication events provided a large amount of raw material for the more than 2,000 later speciation events in Arecaceae. This study provides a high quality resource for further functional and evolutionary studies of N. fruticans and palms in general.
authors.affiliation: 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, Guangdong 510275, China.
authors.forename: Ziwen
authors.initials: Z
authors.lastname: He
authors.affiliation: 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, Guangdong 510275, China.
authors.forename: Zhang
authors.initials: Z
authors.lastname: Zhang
authors.affiliation: 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, Guangdong 510275, China.
authors.forename: Wuxia
authors.initials: W
authors.lastname: Guo
authors.affiliation: College of Life Sciences, Hainan Normal University, Haikou, Hainan 571158, China.
authors.forename: Ying
authors.initials: Y
authors.lastname: Zhang
authors.affiliation: 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, Guangdong 510275, China.
authors.forename: Renchao
authors.initials: R
authors.lastname: Zhou
authors.affiliation: 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, Guangdong 510275, China.
authors.forename: Suhua
authors.initials: S
authors.lastname: Shi
mesh_terms: D028023:Arecaceae / Q000235:genetics*; D019143:Evolution, Molecular; D020440:Gene Duplication; D063990:Gene Ontology; D049810:Genetic Speciation; D018745:Genome, Plant; D018895:Microsatellite Repeats; D058977:Molecular Sequence Annotation; D016366:Open Reading Frames; D010802:Phylogeny; D010940:Plant Proteins / Q000235:genetics; D018749:RNA, Plant / Q000235:genetics; D017423:Sequence Analysis, RNA
chemical_list: D010940:Plant Proteins; D018749:RNA, Plant