Abstract
BackgroundThe seagrass Zostera marina is a monocotyledonous angiosperm belonging to a polyphyletic group of plants that can live submerged in marine habitats. Zostera marina L. is one of the most common seagrasses and is considered a cornerstone of marine plant molecular ecology research and comparative studies. However, the mechanisms underlying its adaptation to the marine environment still remain poorly understood due to limited transcriptomic and genomic data.Principal FindingsHere we explored the transcriptome of Z. marina leaves under different environmental conditions using Illumina paired-end sequencing. Approximately 55 million sequencing reads were obtained, representing 58,457 transcripts that correspond to 24,216 unigenes. A total of 14,389 (59.41%) unigenes were annotated by blast searches against the NCBI non-redundant protein database. 45.18% and 46.91% of the unigenes had significant similarity with proteins in the Swiss-Prot database and Pfam database, respectively. Among these, 13,897 unigenes were assigned to 57 Gene Ontology (GO) terms and 4,745 unigenes were identified and mapped to 233 pathways via functional annotation against the Kyoto Encyclopedia of Genes and Genomes pathway database (KEGG). We compared the orthologous gene family of the Z. marina transcriptome to Oryza sativa and Pyropia yezoensis and 11,667 orthologous gene families are specific to Z. marina. Furthermore, we identified the photoreceptors sensing red/far-red light and blue light. Also, we identified a large number of genes that are involved in ion transporters and channels including Na+ efflux, K+ uptake, Cl− channels, and H+ pumping.ConclusionsOur study contains an extensive sequencing and gene-annotation analysis of Z. marina. This information represents a genetic resource for the discovery of genes related to light sensing and salt tolerance in this species. Our transcriptome can be further utilized in future studies on molecular adaptation to abiotic stress in Z. marina.
Highlights
Seagrasses are a polyphyletic group of plants that can live submerged in marine habitats [1]
To obtain a more comprehensive understanding of the functional genes from Z. marina adapted to different environment factors, we used the Illumina platform to sequence a pooled RNA sample covering the five abiotic stresses of temperature, salinity, light intensity, light quality, and pH
We identified the unigenes associated with the CLC family and this shows that Z. marina possesses a complicated and comprehensive salt tolerance system, which evolved as an adaptation to life in seawater
Summary
Seagrasses are a polyphyletic group of plants that can live submerged in marine habitats [1]. During the transition to a marine environment, seagrasses would have had to incorporate morphological and physiological mechanisms distinct from terrestrial angiosperms. Specific to the marine environment, seagrasses evolved the ability to tolerate high salt levels, short-term salinity fluctuations, low-intensity light, and a different light spectrum from that encountered by terrestrial angiosperms. These novel adaptations certainly involved specific genetic mechanisms, so developing the genes at a high throughput level will help generate an understanding of the adaptation mechanisms, evolutionary process, and parallel gene transfer events of seagrass. The seagrass Zostera marina is a monocotyledonous angiosperm belonging to a polyphyletic group of plants that can live submerged in marine habitats. We identified a large number of genes that are involved in ion transporters and channels including Na+ efflux, K+ uptake, Cl2 channels, and H+ pumping
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