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Genome-wide identification and transcriptome-based expression analysis of sox gene family in the Japanese flounder Paralichthys olivaceus

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Abstract

Sox genes are transcription factors that ubiquitously exist in animal species, and share a conserved high mobility group (HMG) box. They play important biological roles in diverse developmental processes, such as sex determination and differentiation, chondrogenesis, neurogenesis, and early embryonic development. In this study, we identified 25 sox genes from genome and transcriptome of Japanese flounder Paralichthys olivaceus. These sox genes could be mainly classified into seven subfamilies (B1, B2, C, D, E, F, and K), and each subfamily exhibited a relatively conserved gene structure. Besides, subfamilies A and G were found exclusively in human and mouse, and sox 32 in subfamily K only existed in teleosts. Compared with other mammals, some sox genes in teleosts had two duplicates. The loss, duplication, and divergence of sox genes during evolution provided an evidence for whole-genome duplication that occurred in the radiation of teleosts. The expression of Japanese flounder sox genes was also analyzed by FPKM value. Our results showed that certain sox genes exhibited obviously tissue-specific and spatio-temproal expression. Especially, gonal-basied expression analysis uncovered that sox7 and sox2 were ovary-biased, and sox8b was testis-biased. Moreover, sox10a was expressed specifically in ovary, and sox8a in testis. Therefore this study provide a solid foundation for future functional and evolutionary analysis of sox genes in Japanese flounder.

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  1. Key Laboratory of Marine Genetics and Breeding, Ministry of Education, College of Marine Life Sciences, Ocean University of China, Qingdao, 266000, China

    Haiyang Yu  (俞海洋), Xinxin Du  (杜昕昕), Xiaojing Li  (李晓静), Jiangbo Qu  (曲江波), He Zhu  (朱鹤), Quanqi Zhang  (张全启) & Xubo Wang  (王旭波)

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  1. Haiyang Yu  (俞海洋)
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  2. Xinxin Du  (杜昕昕)
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Correspondence to Xubo Wang  (王旭波).

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Supported by the National Natural Science Foundation of China (No. 31672646) and the Fundamental Research Funds for the Central Universities (No. 201762016)

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Yu, H., Du, X., Li, X. et al. Genome-wide identification and transcriptome-based expression analysis of sox gene family in the Japanese flounder Paralichthys olivaceus. J. Ocean. Limnol. 36, 1731–1745 (2018). https://doi.org/10.1007/s00343-018-7216-4

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