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Article

Gene Characterization of Nocturnin Paralogues in Goldfish: Full Coding Sequences, Structure, Phylogeny and Tissue Expression

by
Diego Madera
,
Aitana Alonso-Gómez
,
María Jesús Delgado
,
Ana Isabel Valenciano
and
Ángel Luis Alonso-Gómez
*
Departamento de Genética, Fisiología y Microbiología, Universidad Complutense de Madrid, 28040 Madrid, Spain
*
Author to whom correspondence should be addressed.
Int. J. Mol. Sci. 2024, 25(1), 54; https://doi.org/10.3390/ijms25010054
Submission received: 30 October 2023 / Revised: 5 December 2023 / Accepted: 14 December 2023 / Published: 19 December 2023
(This article belongs to the Section Molecular Biology)
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Abstract

The aim of this work is the full characterization of all the nocturnin (noc) paralogues expressed in a teleost, the goldfish. An in silico analysis of the evolutive origin of noc in Osteichthyes is performed, including the splicing variants and new paralogues appearing after teleostean 3R genomic duplication and the cyprinine 4Rc. After sequencing the full-length mRNA of goldfish, we obtained two isoforms for noc-a (noc-aa and noc-ab) with two splice variants (I and II), and only one for noc-b (noc-bb) with two transcripts (II and III). Using the splicing variant II, the prediction of the secondary and tertiary structures renders a well-conserved 3D distribution of four α-helices and nine β-sheets in the three noc isoforms. A synteny analysis based on the localization of noc genes in the patrilineal or matrilineal subgenomes and a phylogenetic tree of protein sequences were accomplished to stablish a classification and a long-lasting nomenclature of noc in goldfish, and valid to be extrapolated to allotetraploid Cyprininae. Finally, both goldfish and zebrafish showed a broad tissue expression of all the noc paralogues. Moreover, the enriched expression of specific paralogues in some tissues argues in favour of neo- or subfunctionalization.
Keywords: nocturnin nomenclature; Carassius auratus; zebrafish; molecular cloning; gene evolution; synteny analysis; synteny quantification; phylogenetic tree; protein structure; tissue distribution nocturnin nomenclature; Carassius auratus; zebrafish; molecular cloning; gene evolution; synteny analysis; synteny quantification; phylogenetic tree; protein structure; tissue distribution

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MDPI and ACS Style

Madera, D.; Alonso-Gómez, A.; Delgado, M.J.; Valenciano, A.I.; Alonso-Gómez, Á.L. Gene Characterization of Nocturnin Paralogues in Goldfish: Full Coding Sequences, Structure, Phylogeny and Tissue Expression. Int. J. Mol. Sci. 2024, 25, 54. https://doi.org/10.3390/ijms25010054

AMA Style

Madera D, Alonso-Gómez A, Delgado MJ, Valenciano AI, Alonso-Gómez ÁL. Gene Characterization of Nocturnin Paralogues in Goldfish: Full Coding Sequences, Structure, Phylogeny and Tissue Expression. International Journal of Molecular Sciences. 2024; 25(1):54. https://doi.org/10.3390/ijms25010054

Chicago/Turabian Style

Madera, Diego, Aitana Alonso-Gómez, María Jesús Delgado, Ana Isabel Valenciano, and Ángel Luis Alonso-Gómez. 2024. "Gene Characterization of Nocturnin Paralogues in Goldfish: Full Coding Sequences, Structure, Phylogeny and Tissue Expression" International Journal of Molecular Sciences 25, no. 1: 54. https://doi.org/10.3390/ijms25010054

APA Style

Madera, D., Alonso-Gómez, A., Delgado, M. J., Valenciano, A. I., & Alonso-Gómez, Á. L. (2024). Gene Characterization of Nocturnin Paralogues in Goldfish: Full Coding Sequences, Structure, Phylogeny and Tissue Expression. International Journal of Molecular Sciences, 25(1), 54. https://doi.org/10.3390/ijms25010054

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