ArticlePloS one2015
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.
Article in PloS one, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers.
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17 citing papers in PubMed, 29 citations in OpenAlex.
- Comprehensive Annotation of Olfactory and Gustatory Receptor Genes and Transposable Elements Revealed Their Evolutionary Dynamics in Aphids.Molecular biology and evolution · 2025Article
- Chromosome-scale Elaeis guineensis and E. oleifera assemblies: comparative genomics of oil palm and other Arecaceae.G3 (Bethesda, Md.) · 2024Article
- Genomic evidence for rediploidization and adaptive evolution following the whole-genome triplication.Nature communications · 2024Article
- Elucidating the Mesocarp Drupe Transcriptome of Açai (International journal of molecular sciences · 2023Article
- Expansion and adaptive evolution of theMarine life science & technology · 2023Article
- Article
- Genetic and molecular mechanisms underlying mangrove adaptations to intertidal environments.iScience · 2022Review
- Deep structured populations of geographically isolated nipa (Frontiers in plant science · 2022Article
- Chromosome identification in oil palm (Elaeis guineensis) using in situ hybridization with massive pools of single copy oligonucleotides and transferability across Arecaceae species.Chromosome research : an international journal on the molecular, supramolecular and evolutionary aspects of chromosome biology · 2021Article
- Coconut genome assembly enables evolutionary analysis of palms and highlights signaling pathways involved in salt tolerance.Communications biology · 2021Article
- An Improved Oil Palm Genome Assembly as a Valuable Resource for Crop Improvement and Comparative Genomics in thePlants (Basel, Switzerland) · 2020Article
- Ancient Polyploidy and Genome Evolution in Palms.Genome biology and evolution · 2019Article
- Evolution by duplication: paleopolyploidy events in plants reconstructed by deciphering the evolutionary history of VOZ transcription factors.BMC plant biology · 2018Article
- Comparative Analysis of Transcriptomes in Rhizophoraceae Provides Insights into the Origin and Adaptive Evolution of Mangrove Plants in Intertidal Environments.Frontiers in plant science · 2017Article
- Article
- Transcriptome analyses provide insights into the phylogeny and adaptive evolution of the mangrove fern genus Acrostichum.Scientific reports · 2016Article
- Article
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Authors and funding
6 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
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.
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