De novo assembly and annotation of the Avicennia officinalis L. transcriptome

Avicennia officinalis L. is a typical mangrove species, inhabiting inhospitable environments in the interface between sea and land. In this study, we generated RNA-seq data to de novo assemble the A. officinalis transcriptome. Starting with 36.24 million 100 bp paired-end reads, 38,576 high-confidence transcripts with an average length of 834 bp were produced after filtration of weakly expressed and redundant transcripts. We found known protein homologs for 22,254 of these transcripts, and assigned them to at least one of 119 gene ontology (GO) terms. In addition, we identified different copies and isoforms of three candidate genes, AoPIP, AoTIP and AoDHN1, which might be involved in salt excretion via salt glands. All these genes were highly expressed in leaf tissue of A. officinalis, suggestive of a complicated mechanism of response to salt stress. We further identified 613 microsatellite markers for the assessment of genetic diversity and population differentiation in A. officinalis. Genomic resources generated in this study would be an important foundation for future research into molecular mechanisms underlying salt and other stress tolerance, as well as the evolutionary history of this mangrove species and its relatives.