Application of HiCEP to screening of radiation stress-responsive genes in the soil microarthropod Folsomia candida (Collembola).
The field of ecotoxicogenomics has received increasing attention for its potential to provide insight into pressing ecological issues. However, its applications are limited due to a lack of genetic sequence information for organisms used in ecotoxicological studies. We used high-coverage expression profiling (HiCEP), a method that requires no prior sequence knowledge, to examine stress-responsive genes and their dose dependence in the springtail Folsomia candida using gamma radiation as the stressor. Radiation-responsive genes and their dose dependency were detected at effective doses for reproduction, and 16 up-regulated transcript-derived fragments (TDFs) were sequenced. Quantitative PCR analysis also found that most of the TDFs were up-regulated. The sequences of the TDFs showed resemblance to known genes, such as glutathione S-transferase and poly(ADP-ribose) polymerase, but most showed no similarity to any genes in the gene databases. These results suggest that HiCEP is effective for discovering differently expressed genes and their dose dependence, even in organisms for which few sequence data are available. The limited length of the TDFs, however, may impede functional annotation of the genes. In conclusion, HiCEP is useful for ecotoxicogenomic studies in which various organisms with few available genomic resources are involved.
Nakamori
Taizo
T
Environmental Radiation Effects Research Group, National Institute of Radiological Sciences, 4-9-1 Anagawa, Inage-ku, Chiba 263-8555, Japan. taizo@fml.nirs.go.jp
Fujimori
Akira
A
Kinoshita
Keiji
K
Ban-Nai
Tadaaki
T
Kubota
Yoshihisa
Y
Yoshida
Satoshi
S
D000818:Animals; D001181:Arthropods / Q000235:genetics* / Q000528:radiation effects*; D004307:Dose-Response Relationship, Radiation; D005720:Gamma Rays; D020869:Gene Expression Profiling; D017344:Genes, Insect; D016133:Polymerase Chain Reaction; D012333:RNA, Messenger / Q000235:genetics / Q000378:metabolism; D017423:Sequence Analysis, RNA; D012987:Soil; D013312:Stress, Physiological / Q000235:genetics* / Q000528:radiation effects; D015854:Up-Regulation / Q000528:radiation effects
D012333:RNA, Messenger; D012987:Soil