Identification of transposable elements fused in the exonic region of the olive flounder genome

• Published in: Genes & genomics Vol. 40; no. 7; pp. 707 - 713
• Main Authors: Nam, Gyu-Hwi, Gim, Jeong-An, Mishra, Anshuman, Ahn, Kung, Kim, Suhkmann, Kim, Do-Hyung, Cha, Hee-Jae, Choi, Yung Hyun, Park, Chan-Il, Kim, Heui-Soo
• Format: Journal Article
• Language: English
• Published: Seoul The Genetics Society of Korea 01.07.2018; Springer Nature B.V; 한국유전학회
• Subjects: Aldehydes; Animal Genetics and Genomics; Biomedical and Life Sciences; Deoxyribonucleic acid; DNA; Fish; Gene expression; Genomes; Human Genetics; Life Sciences; Microbial Genetics and Genomics; Paralichthys olivaceus; Plant Genetics and Genomics; Research Article; Transposons; 생물학; Transcriptome analysis; Bioinformatics; Transposable elements; TE-fused genes; Paralichthys olivaceus
• ISSN: 1976-9571; 2092-9293
• DOI: 10.1007/s13258-018-0676-2

Transposable elements (TEs) are mobile genetic sequences that comprise a large portion of vertebrate genomes. The olive flounder ( Paralichthys olivaceus ) is a valuable marine resource in East Asia. The scope of most genomic studies on the olive flounder is limited to its immunology as their focus is the prevention of mass mortality of this species. Thus, for a broader understanding of the species, its genomic information is consistently in demand. Transcripts sequences were acquired from transcriptome analysis using gill tissues of 12 olive flounders. Distribution of TEs inserted in exonic region of the olive flounder genome was analyzed using RepeatMasker ( http://www.repeatmasker.org/ ). We found 1140 TEs in the exonic region of the genome and long interspersed nuclear elements (LINEs) and long terminal repeats (LTRs) insertions occurred with forward orientation preferences. Transposons belonging to the hAt, Gypsy, and LINE 1 (L1) subfamilies were the most abundant DNA transposons, LTRs, and long interspersed elements (LINEs), respectively. Finally, we carried out a gene ontology analysis to determine the function of TE-fused genes. These results provide some genomic information about TEs that is useful for future research on changes in properties and functions of genes by TEs in the olive flounder genome.