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

<div><p>Background</p><p>The seagrass <i>Zostera marina</i> is a monocotyledonous angiosperm belonging to a polyphyletic group of plants that can live submerged in marine habitats. <i>Zostera marina</i> 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.</p><p>Principal Findings</p><p>Here we explored the transcriptome of <i>Z. marina</i> 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 <i>Z. marina</i> transcriptome to <i>Oryza sativa</i> and <i>Pyropia yezoensis</i> and 11,667 orthologous gene families are specific to <i>Z. marina</i>. 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.</p><p>Conclusions</p><p>Our study contains an extensive sequencing and gene-annotation analysis of <i>Z. marina</i>. 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 <i>Z. marina</i>.</p></div

Summary of different environmental stressors designed in this research.

<p>Summary of different environmental stressors designed in this research.</p

Boletín de Segovia: Número 61 - 1892 mayo 19

Copia digital. Madrid : Ministerio de Cultura. Subdirección General de Coordinación Bibliotecaria, 200

GO comparison for the specific unigenes among the <i>Z. marina</i> and <i>P. yezoensis</i> and <i>O. sativa</i>.

<p>GO comparison for the specific unigenes among the <i>Z. marina</i> and <i>P. yezoensis</i> and <i>O. sativa</i>.</p

Pathway assignment based on KEGG for the <i>Z. marina</i> transcriptome.

<p>In total, 4,745 unigenes with Nr hits were grouped into 233 pathways.</p

Additional file 6: of Transcriptome-wide identification of optimal reference genes for expression analysis of Pyropia yezoensis responses to abiotic stress

Table S1. Pairwise variation (Vn/n + 1) analysis of 9 candidate. (XLSX 10 kb

Venn diagram of ortholog group distribution in <i>Z. marina</i>, <i>P. yezoensis</i> and <i>O. sativa</i>.

<p>Numbers shown in different sections indicate the numbers of ortholog groups and unigenes of <i>Z. marina</i>. The top numbers give the number of unigenes and the bottom numbers give the number of ortholog groups.</p

Comparison of transcripts detected using Illumina sequencing with the publicly available transciptome and ESTs.

<p>Comparison of transcripts detected using Illumina sequencing with the publicly available transciptome and ESTs.</p

Additional file 4: of Transcriptome-wide identification of optimal reference genes for expression analysis of Pyropia yezoensis responses to abiotic stress

Figure S4. Expression stability values(M) of nine candidate reference genes calculated geNorm under dehydration (A), temperature (B) and all conditions (C) respectively. (PDF 99 kb

Additional file 1: of Transcriptome-wide identification of optimal reference genes for expression analysis of Pyropia yezoensis responses to abiotic stress

Figure S1. Stability distribution of transcripts using PaGeFinder (PDF 8 kb