De Novo Assembly and Characterization of the Transcriptome of Seagrass Zostera marina Using Illumina Paired-End Sequencing

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.

背景：Zostera marina（海草）是一种单子叶被子植物，隶属于一个多源性的植物类群，能够在海洋生境中生存。Zostera marina L. 是最常见的海草之一，被认为是海洋植物分子生态学和比较研究的基础。然而，由于转录组和基因组数据的有限，其适应海洋环境的机制仍未能得到充分理解。主要发现：本研究利用Illumina双端测序技术，探讨了在不同环境条件下Z. marina叶子的转录组。获得了约5500万个测序读数，代表58,457个转录本，对应24,216个非冗余基因。通过对NCBI非冗余蛋白质数据库的blast搜索，共14,389个（59.41%）非冗余基因得到了注释。其中，45.18%和46.91%的非冗余基因分别与Swiss-Prot数据库和Pfam数据库中的蛋白质具有显著相似性。在这其中，13,897个非冗余基因被分配到57个基因本体（GO）术语中，4,745个非冗余基因通过京都基因与基因组百科全书（KEGG）通路数据库的功能注释被识别并映射到233个通路中。我们将Z. marina转录组的直系同源基因家族与Oryza sativa和Pyropia yezoensis进行了比较，发现11,667个直系同源基因家族是Z. marina特有的。此外，我们还识别了感知红/远红光和蓝光的视紫红质受体。同时，我们还鉴定了大量参与离子转运子和通道的基因，包括Na+外排、K+摄取、Cl−通道和H+泵。结论：本研究对Z. marina进行了广泛测序和基因注释分析。这些信息为该物种中与光感应和盐耐受性相关的基因发现提供了遗传资源。Z. marina的转录组可以进一步用于未来关于该物种分子适应非生物胁迫的研究。