Km cDNA pyrosequencing project
Krytolebias marmoratus cDNA GS20 pyrosequencing result
The self-fertilizing hermaphroditic fish, Kryptolebias marmoratus is considered a suitable model species in the fields of eco-biology, developmental biology, endocrinology, environmental genomics, aquatic toxicology, and molecular carcinogenesis. However, more extensive gene information is still needed to improve our understanding of the biology of this fish with respect to toxicological responses. We performed a transcriptomic study in this species using pyrosequencing. Liver and ovary mRNA was reverse synthesized into cDNA and randomly sequenced by a Roche 454, GS-20 sequencer. After quality assessment, the assembled expressed sequence tag (EST) translations were compared with the GenBank non-redundant (nr) amino acid sequence database using BLASTX. In the assembly stage 1, both 59,732 transcripts in liver and 103,526 transcripts in ovary were obtained. To identify the differently expressed genes in the ovary and liver tissue, all transcripts were sorted them out with an expect value threshold of 1.00E-05. Consequently, 7,168 contigs of ovary ESTs and 3,855 contigs of liver ESTs were not overlapped for expression in both tissues, whereas 3,763 contigs were commonly found in both tissues. Subsequently, we described the most highly represented genes in the liver and ovary of K. marmoratus. Isoforms of cytochrome P450 (CYP) and receptor-related genes showed tissue-preferential expressed patterns. To identify the potential biomarkers in this species, ovary and liver ESTs were assembled and annotated with the nr amino acid sequence database using BLASTX. Then, 35,471 transcripts were obtained, and 9,130 transcripts were hit (26%) at the assembly stage 2. Finally, we identified a number of stress-, antioxidant defense-, and DNA repair-related genes as potential molecular biomarkers for toxicological response using this species. We discuss the potential use for these markers in K. marmoratus for environmental genomics and eco-toxicological studies to uncover mechanisms of environmental stresses and chemical toxicities to K. marmoratus.