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Evolutionary History of Teleost Intron-Containing and Intron-Less

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Evolutionary History of Teleost Intron-Containing and Intron-Less www.nature.com/scientificreports OPEN Evolutionary history of teleost intron-containing and intron-less rhodopsin genes Received: 15 February 2019 Chihiro Fujiyabu1, Keita Sato 2, Ni Made Laksmi Utari2,3, Hideyo Ohuchi2, Accepted: 9 July 2019 Yoshinori Shichida1,4,5 & Takahiro Yamashita1,5 Published: xx xx xxxx Recent progress in whole genome sequencing has revealed that animals have various kinds of opsin genes for photoreception. Among them, most opsin genes have introns in their coding regions. However, it has been known for a long time that teleost retinas express intron-less rhodopsin genes, which are presumed to have been formed by retroduplication from an ancestral intron-containing rhodopsin gene. In addition, teleosts have an intron-containing rhodopsin gene (exo-rhodopsin) exclusively for pineal photoreception. In this study, to unravel the evolutionary origin of the two teleost rhodopsin genes, we analyzed the rhodopsin genes of non-teleost fshes in the Actinopterygii. The phylogenetic analysis of full-length sequences of bichir, sturgeon and gar rhodopsins revealed that retroduplication of the rhodopsin gene occurred after branching of the bichir lineage. In addition, analysis of the tissue distribution and the molecular properties of bichir, sturgeon and gar rhodopsins showed that the abundant and exclusive expression of intron-containing rhodopsin in the pineal gland and the short lifetime of its meta II intermediate, which leads to optimization for pineal photoreception, were achieved after branching of the gar lineage. Based on these results, we propose a stepwise evolutionary model of teleost intron-containing and intron-less rhodopsin genes. Opsins are photoreceptive molecules that universally underlie the molecular basis of visual and non-visual pho- toreception in animals1–3. Opsins have common structural elements, including seven α-helical transmembrane domains and a chromophore, retinal. Vertebrate rhodopsin is the best-studied opsin that functions as a visual photoreceptor in the retina. Rhodopsin binds 11-cis-retinal in the dark, and the photoisomerization of the retinal to the all-trans form induces the formation of the meta II intermediate, the active state of rhodopsin, to bind to a G protein, transducin (Gt). Tus, opsins are defned as G protein-coupled receptors (GPCRs) specialized for photoreception. Recent identifcation and characterization of opsin genes revealed that opsins can be classifed into several groups based on their amino acid sequences. Tis classifcation corresponds well to the diferences of the molecular properties of opsins, such as the photoreaction property and the coupling G protein subtypes. In addition, the phylogenetic classifcation is strengthened in part by the diferences of the exon/intron structures (the number of exons and the boundary positions of exons and introns) of opsin genes4. Among the nine human opsin genes, the genes encoding rhodopsin, cone visual pigments and Opn3 are phylogenetically closely related to each other and share the basic exon/intron structures (Fig. S1A). Rhodopsin and blue cone pigment genes have fve exons separated by four introns in their coding regions. Red and green cone pigment genes contain an additional intron, and the Opn3 gene lacks one intron. By contrast, the Opn4 and Opn5 genes belong to diferent opsin groups than vertebrate rhodopsin and have their respective characteristic exon/intron structures: ten exons for the Opn4 gene and seven exons for the Opn5 gene5,6. Te presence of introns in the human opsin genes is in contrast with the fact that the amino acid sequences of many vertebrate rhodopsin-like GPCRs are encoded by intron-less single-exon genes7,8. Among the opsin genes that have been characterized in various animals, several opsin genes are single-exon genes. For example, it is well known that the coding regions of teleost rhodopsin genes Rh1 and Rh1-2 contain 1Faculty of Science, Kyoto University, Kyoto, 606-8502, Japan. 2Department of Cytology and Histology, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama, 700-8558, Japan. 3Department of Ophthalmology, Faculty of Medicine, Udayana University, Bali, Indonesia. 4Research Organization for Science and Technology, Ritsumeikan University, Shiga, 525-8577, Japan. 5Department of Biophysics, Graduate School of Science, Kyoto University, Kyoto, 606-8502, Japan. Correspondence and requests for materials should be addressed to T.Y. (email: [email protected]) SCIENTIFIC REPORTS | (2019) 9:10653 | https://doi.org/10.1038/s41598-019-47028-4 1 www.nature.com/scientificreports/ www.nature.com/scientificreports no introns9,10 (Fig. S1B). Te conservation of the exon/intron structures of rhodopsin genes isolated from cyclos- tomes, cartilaginous fshes and tetrapods suggests the possibility that the teleost intron-less rhodopsin genes emerged by retroduplication near the base of the Actinopterygii11,12. A previous analysis of rhodopsin genes in non-teleost fshes revealed partial sequences of these rhodopsin genes and provided an evolutionary model for the appearance of teleost intron-less rhodopsin genes13. Afer that analysis, paralogs of rhodopsin genes were identifed in teleosts and were named exo-rhodopsin14. Te exo-rhodopsin gene (Exorho) also shares the fve exon/four intron structure and functions exclusively in the teleost pineal gland. Tus, the analysis of both intron-containing and intron-less rhodopsin genes of non-teleost fshes in the Actinopterygii is crucial to reveal the evolutionary origin of the teleost intron-containing and intron-less rhodopsin genes. In this study, we char- acterized the full-length coding sequences of intron-containing and intron-less rhodopsin genes from major lineages of non-teleost fshes in the Actinopterygii and analyzed their phylogenetic relationship. In addition, we determined their expression patterns in the retina and pineal gland, and the molecular properties of the proteins they encode. Based on these results, we propose the evolutionary history of rhodopsin in the Actinopterygii, including when retroduplication of the rhodopsin gene occurred and when diferent expression patterns of teleost intron-containing and intron-less rhodopsins emerged. Results and Discussion Isolation of full-length cDNAs of bichir and sturgeon rhodopsin. Among non-teleost fshes in the Actinopterygii, spotted gar is the only species whose genomic data are available in the public database. Te spot- ted gar genome contains two rhodopsin genes, an intron-containing gene (Rh1-1 (Exorho)) and an intron-less gene (Rh1-2) (Fig. S1B)15. First, we searched for full-length rhodopsin cDNAs from gray bichir (Polypterus sene- galus) and reedfsh (Erpetoichthys calabaricus) in the Polypteriformes and Siberian sturgeon (Acipenser baerii) in the Acipenseriformes. We successfully obtained one full-length rhodopsin cDNA from the eyes of each species and showed the amino acid sequences they encoded in Fig. S2. Next, we examined whether or not these rhodop- sin genes have introns (Fig. 1). To perform genomic PCR of gray bichir, reedfsh and Siberian sturgeon rhodopsin, we designed three pairs of primers based on their mRNA sequences. First pair (Fw1/Rv1) targets the putative exons 1 and 2, and second pair (Fw2/Rv2) targets the putative exon 1 (Fig. 1A). Tus, if the rhodopsin gene has no introns, a band of around 200 bp can be amplifed by the genomic PCR using primer pairs Fw1/Rv1 and Fw2/ Rv2. If the rhodopsin gene has introns whose positions are the same as those of tetrapod Rh1 and teleost Exorh, a band of around 200 bp can be amplifed by the genomic PCR using primer pair Fw2/Rv2 but not using primer pair Fw1/Rv1. In addition, third pair (Fw3/Rv3) was designed to amplify the full-length ORF of the rhodopsin gene by RT-PCR on eye total RNA (Fig. 1A). Te genomic PCR on gray bichir and reedfsh rhodopsin showed amplifcation of a DNA fragment around 200 bp only when using primer pair Fw2/Rv2 (Fig. 1B,C), which indi- cated that the gray bichir and reedfsh rhodopsin genes contain introns. In contrast, the genomic PCR on Siberian sturgeon rhodopsin amplifed a band of around 200 bp using primer pairs Fw1/Rv1 and Fw2/Rv2 and a band of around 1,060 bp corresponding to the full-length ORF using primer pair Fw3/Rv3 (Fig. 1D). Tis showed that the Siberian sturgeon rhodopsin gene has no introns. Next, we performed phylogenetic analysis of rhodopsin genes isolated from various species in the Actinopterygii (Fig. 2). Te most likely phylogenetic tree revealed that the rhodopsin genes (Rh1) from the Polypteriformes (gray bichir and reedfsh) are branched from the common ancestor of teleost rhodopsin and exo-rhodopsin, whereas the rhodopsin gene (Rh1-2) of Siberian sturgeon in the Acipenseriformes is clustered with teleost rhodopsin genes. Taking account of the evolution of the Actinopterygii (Fig. S1B), these find- ings suggest that a common ancestral rhodopsin gene (intron-containing gene) in the Actinopterygii was frst branched into the intron-containing gene (Rh1) in the Polypteriformes and the ancestor of intron-containing (Rh1-1 (Exorh)) and intron-less (Rh1 and Rh1-2) genes by speciation and was subsequently diversifed into intron-containing and intron-less genes by retroduplication. Terefore, we speculate that the intron-less rhodop- sin genes emerged afer the divergence of the Polypteriformes and other Actinopterygii. In this diversifcation model, the intron-containing rhodopsin gene (Rh1-1) should be present in the stur- geon lineage.
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