Abstract
Whitespotted bamboo shark (Chiloscyllium plagiosum), a member of the cartilaginous fish family, has an extremely large liver and demonstrates a strong regeneration ability and immune regulation. Circular RNAs (circRNAs) is an important class of non-coding RNAs. Increasing evidences suggest that circRNAs are a kind of potential regulators. Recently, researchers have isolated and identified different circRNAs from various species, while few reports were on the circRNAs of C. plagiosum. In this study, we have identified a total of 4,558 circRNAs in the liver of C. plagiosum. This finding suggests that circRNAs are not evenly distributed in the chromosomes and follow the GT-AG rule during cyclization. Alternative back-splicing might exist in shark circRNAs as shown by the authenticity identification of predicted circRNAs. The binding strength of circRNAs (<2,000 bp) and the detected miRNAs in shark liver were simultaneously analyzed to construct an mRNA–miRNA–circRNA network for the Glutathione S-transferase P1 gene, and the circRNA authenticity was simultaneously verified. Our data provide not only novel insights into the rich existence of circRNAs in marine animals, but also a basis for characterizing functions of identified circRNAs in the liver homeostasis of C. plagiosum.
Highlights
530 million years ago, cartilaginous fishes diverged from jawed vertebrates, which are the common ancestors of teleost fish and humans
Clean reads were aligned with the C. plagiosum genome (ASM401019v1) by using bowtie2 software (Langmead and Salzberg, 2012), and circRNAs were detected and identified via find_circ software (Memczak et al, 2013)
If the 5 end of the anchor sequence is aligned to the reference sequence, the 3 end of the anchor sequence is aligned to the upstream of this position, and there is a splice site (GT-AG) between A2 and A3 of the reference sequence, this read is used as a candidate circRNA
Summary
530 million years ago, cartilaginous fishes diverged from jawed vertebrates, which are the common ancestors of teleost fish and humans. Cartilaginous fishes have complex physiological systems that include an adaptive immune system and a pressurized circulatory system. It is the first jawed vertebrate with an adaptive immune system. A member of the cartilaginous fish family, whitespotted bamboo shark (Chiloscyllium plagiosum), is mainly distributed in the Indo-West Pacific waters around several East Asian countries, such as Singapore and Indonesia. This marine animal has important research and commercial food value. The liver is an important organ with detoxification function and has a strong regeneration ability, which endows C. plagiosum with many special
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