title: RNA seq- and DEG-based comparison of developmental toxicity in fish embryos of two species exposed to Iranian heavy crude oil.
abstract: To determine and compare the toxic effects of Iranian heavy crude oil (IHCO) on the embryonic development of two fish species, we examined transcriptome profiles using RNA-seq. The assembled contigs were 66,070 unigenes in olive flounder embryos and 76,498 unigenes in spotted seabass embryos. In the differential gene expression (DEG) profiles, olive flounder embryos showed different up- and down-regulated patterns than spotted seabass embryos in response to fresh IHCO (FIHCO) and weathered IHCO (WIHCO). In this work, we categorized DEG profiles into six pathways: ribosome, oxidative phosphorylation, Parkinson's disease, Alzheimer's disease, Huntington's disease, and cardiac muscle contraction, validating the expression patterns of 13 DEGs using real-time quantitative RT-PCR. The expression of the CYP1A, CYP1B1, and CYP1C1 genes in spotted seabass embryos was higher than in olive flounder embryos, whereas genes related to cell processing, development, and the immune system showed the opposite trend. Orthologous gene cluster analysis showed that olive flounder embryos were sensitive (fold change of genes with cutoff P<0.05) to both FIHCO and WIHCO, but spotted seabass embryos exhibited higher sensitivity to WIHCO than FIHCO, indicating that species-specific differences are likely to be reflected in population levels after oil spills. Overall, our study provides new insight on the different embryonic susceptibilities of two marine fish species to FIHCO and WIHCO and a better understanding of the underlying molecular mechanisms via RNA-seq and DEGs.
authors.affiliation: Oil & POPs Research Group, Korea Institute of Ocean Science & Technology, Geoje 53201, Republic of Korea; Department of Marine Environmental Science, Korea University of Science and Technology, Daejeon 34113, Republic of Korea. Electronic address: jungjh@kiost.ac.kr.
authors.forename: Jee-Hyun
authors.initials: JH
authors.lastname: Jung
authors.affiliation: Theragen Etex Bio Institute Inc., Suwon 16229, Republic of Korea.
authors.forename: Junsu
authors.initials: J
authors.lastname: Ko
authors.affiliation: Oil & POPs Research Group, Korea Institute of Ocean Science & Technology, Geoje 53201, Republic of Korea.
authors.forename: Eun-Hee
authors.initials: EH
authors.lastname: Lee
authors.affiliation: Oil & POPs Research Group, Korea Institute of Ocean Science & Technology, Geoje 53201, Republic of Korea.
authors.forename: Kwang-Min
authors.initials: KM
authors.lastname: Choi
authors.affiliation: Oil & POPs Research Group, Korea Institute of Ocean Science & Technology, Geoje 53201, Republic of Korea; Department of Marine Environmental Science, Korea University of Science and Technology, Daejeon 34113, Republic of Korea.
authors.forename: Moonkoo
authors.initials: M
authors.lastname: Kim
authors.affiliation: Oil & POPs Research Group, Korea Institute of Ocean Science & Technology, Geoje 53201, Republic of Korea; Department of Marine Environmental Science, Korea University of Science and Technology, Daejeon 34113, Republic of Korea.
authors.forename: Un Hyuk
authors.initials: UH
authors.lastname: Yim
authors.affiliation: Department of Biological Science, College of Science, Sungkyunkwan University, Suwon 16419, Republic of Korea.
authors.forename: Jae-Seong
authors.initials: JS
authors.lastname: Lee
authors.affiliation: Oil & POPs Research Group, Korea Institute of Ocean Science & Technology, Geoje 53201, Republic of Korea; Department of Marine Environmental Science, Korea University of Science and Technology, Daejeon 34113, Republic of Korea.
authors.forename: Won Joon
authors.initials: WJ
authors.lastname: Shim
mesh_terms: D000818:Animals; D017756:Aquaculture; D001492:Bass / Q000196:embryology* / Q000378:metabolism; D016000:Cluster Analysis; D019295:Computational Biology; D000072461:Cytochrome P450 Family 1 / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D004351:Drug Resistance; D029941:Fish Proteins / Q000819:agonists / Q000037:antagonists & inhibitors / Q000235:genetics / Q000378:metabolism; D005432:Flounder / Q000196:embryology* / Q000378:metabolism; D020869:Gene Expression Profiling; D018507:Gene Expression Regulation, Developmental / Q000187:drug effects*; D063990:Gene Ontology; D009024:Morphogenesis / Q000187:drug effects*; D010578:Petroleum / Q000633:toxicity*; D059392:Petroleum Pollution / Q000009:adverse effects; D012333:RNA, Messenger / Q000378:metabolism; D011897:Random Allocation; D056910:Republic of Korea; D013045:Species Specificity; D064793:Teratogenesis / Q000187:drug effects*; D018675:Toxicity Tests; D014874:Water Pollutants, Chemical / Q000633:toxicity*
chemical_list: D029941:Fish Proteins; D010578:Petroleum; D012333:RNA, Messenger; D014874:Water Pollutants, Chemical; D000072461:Cytochrome P450 Family 1
keywords: DEGs; Fish embryos; Iranian heavy crude oil; RNA-sequencing; Toxicity