De novo transcriptome analysis of carotenoid and polyunsaturated fatty acid metabolism in Rhodomonas sp.

Rhodomonas spp. are often used in aquaculture as food for commercially reared invertebrates (e.g., shellfish and shrimp larva) and have thus received considerable research attention. Unfortunately, further molecular research is impeded by the lack of available genomic data. In this study, we sequenced and de novo assembled a complete Rhodomonas sp. transcriptome. A total of 18,070,504 clean reads were produced and assembled into 64,974 transcripts, with a mean size of 737.6 bp. Open reading frame (ORF) prediction indicated that 57,409 (88.36 %) transcripts possessed ORFs. BLASTX analyses allowed us to annotate 39,582 (60.92 %) of the transcripts with putative functions. At least one gene ontology term was assigned to all 26,462 (40.73 %) putative genes, and 28,075 (43.21 %) putative proteins were classified into 25 categories by Clusters of Orthologous Groups (COG) database analysis. Functional annotation from the Kyoto Encyclopedia of Genes and Genomes (KEGG) database assigned 12,200 (18.78 %) putative genes to 305 pathways. Furthermore, genes encoding putative enzymes that may be involved in the synthesis of alloxanthin and polyunsaturated fatty acids (mainly docosahexaenoic acid and eicosapentaenoic acid) were identified within the transcriptome. In conclusion, this is the most comprehensive transcriptomic resource currently available for Rhodomonas sp. and will accelerate research progress in the molecular biology of Rhodomonas.