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Genes 2018, 9(2), 96; doi:10.3390/genes9020096

Vertebrate Genome Evolution in the Light of Fish Cytogenomics and rDNAomics

Faculty of Science, Department of Biology, University of Hradec Králové, 500 03 Hradec Králové, Czech Republic
Department of Biological and Environmental Sciences, Samford University, Birmingham, AL 35229, USA
Author to whom correspondence should be addressed.
Received: 30 November 2017 / Revised: 25 January 2018 / Accepted: 29 January 2018 / Published: 14 February 2018
(This article belongs to the Special Issue Chromosomal Evolution)
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To understand the cytogenomic evolution of vertebrates, we must first unravel the complex genomes of fishes, which were the first vertebrates to evolve and were ancestors to all other vertebrates. We must not forget the immense time span during which the fish genomes had to evolve. Fish cytogenomics is endowed with unique features which offer irreplaceable insights into the evolution of the vertebrate genome. Due to the general DNA base compositional homogeneity of fish genomes, fish cytogenomics is largely based on mapping DNA repeats that still represent serious obstacles in genome sequencing and assembling, even in model species. Localization of repeats on chromosomes of hundreds of fish species and populations originating from diversified environments have revealed the biological importance of this genomic fraction. Ribosomal genes (rDNA) belong to the most informative repeats and in fish, they are subject to a more relaxed regulation than in higher vertebrates. This can result in formation of a literal ‘rDNAome’ consisting of more than 20,000 copies with their high proportion employed in extra-coding functions. Because rDNA has high rates of transcription and recombination, it contributes to genome diversification and can form reproductive barrier. Our overall knowledge of fish cytogenomics grows rapidly by a continuously increasing number of fish genomes sequenced and by use of novel sequencing methods improving genome assembly. The recently revealed exceptional compositional heterogeneity in an ancient fish lineage (gars) sheds new light on the compositional genome evolution in vertebrates generally. We highlight the power of synergy of cytogenetics and genomics in fish cytogenomics, its potential to understand the complexity of genome evolution in vertebrates, which is also linked to clinical applications and the chromosomal backgrounds of speciation. We also summarize the current knowledge on fish cytogenomics and outline its main future avenues. View Full-Text
Keywords: fish cytogenomics; repetitive sequences; rDNAome; genome evolution; AT/GC compositional evolution; quantitative cytogenomics. fish cytogenomics; repetitive sequences; rDNAome; genome evolution; AT/GC compositional evolution; quantitative cytogenomics.

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This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. (CC BY 4.0).

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Symonová, R.; Howell, W.M. Vertebrate Genome Evolution in the Light of Fish Cytogenomics and rDNAomics. Genes 2018, 9, 96.

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