The polychaete, Perinereis nuntia ESTs and its use to uncover potential biomarker genes for molecular ecotoxicological studies.
The polychaete, Perinereis nuntia, has been used as an indicator species to assess the environmental condition of benthic communities in coastal marine environments. Recently, high-throughput sequencing technology has been proven to be a useful method for analyzing expressed sequence tags (ESTs) in non-model species. Thus, we have obtained extensive cDNA information by the pyrosequencing method, to utilize the polychaete species as a test organism for sediment quality monitoring studies. From the total RNA of P. nuntia, cDNA was reversely synthesized and randomly sequenced using a GS-FLX sequencer. In the assembly stage 1, 40,379 transcripts (13,666 contigs and 26,713 singletons) were acquired and showed 47% hitting rate compared with the GenBank non-redundant (NR) amino acid sequence database using BLASTX. After the stage-2 assembly, 21,657 transcripts were identified and showed 28% hitting rate. Finally, we obtained 6 064 unigenes that corresponded to the GenBank NR amino acid sequence database using BLASTX. Of the transcripts obtained in this species, we found a number of stress- and cell defense-related genes (e.g. heat shock protein family, antioxidant-related genes, cytochrome P450 genes) that are potentially useful for sediment monitoring at the molecular level, indicating that the pyrosequencing method is an effective approach to uncover gene families of potential biomarker genes simultaneously, and thus make transcriptomic studies possible. To confirm the usefulness of those potential biomarker genes, we analyzed the comparative profiling of P. nuntia mRNA transcripts between the samples collected from the polychaete aquaculture farm and the southern coast field of South Korea. In this paper, we summarize the expressed cDNA information of P. nuntia and discussed its potential use in environmental genomics and ecotoxicological studies for uncovering the potential molecular mechanisms of environmental stresses and chemical toxicity to the indicator species, P. nuntia in marine sediments.
Department of Molecular and Environmental Bioscience, Graduate School, Hanyang University, Seoul 133-791, South Korea.
Jae-Sung
JS
Rhee
Eun-Ji
EJ
Won
Ryeo-Ok
RO
Kim
Beom-Soon
BS
Choi
Ik-Young
IY
Choi
Gyung Soo
GS
Park
Kyung-Hoon
KH
Shin
Young-Mi
YM
Lee
Jae-Seong
JS
Lee
D000818:Animals; D018076:DNA, Complementary / Q000235:genetics; D030541:Databases, Genetic; D054750:Ecotoxicology; D004784:Environmental Monitoring; D020224:Expressed Sequence Tags; D015723:Gene Library; D005819:Genetic Markers; D019015:Geologic Sediments / Q000737:chemistry; D057166:High-Throughput Screening Assays; D011077:Polychaeta / Q000187:drug effects* / Q000235:genetics*; D012313:RNA / Q000235:genetics; D014874:Water Pollutants, Chemical / Q000633:toxicity*
D018076:DNA, Complementary; D005819:Genetic Markers; D014874:Water Pollutants, Chemical; D012313:RNA