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Comparative Study
. 2018 Feb 13;19(1):141.
doi: 10.1186/s12864-018-4516-1.

Comparative Genome Analysis of 52 Fish Species Suggests Differential Associations of Repetitive Elements With Their Living Aquatic Environments

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Free PMC article
Comparative Study

Comparative Genome Analysis of 52 Fish Species Suggests Differential Associations of Repetitive Elements With Their Living Aquatic Environments

Zihao Yuan et al. BMC Genomics. .
Free PMC article

Abstract

Background: Repetitive elements make up significant proportions of genomes. However, their roles in evolution remain largely unknown. To provide insights into the roles of repetitive elements in fish genomes, we conducted a comparative analysis of repetitive elements of 52 fish species in 22 orders in relation to their living aquatic environments.

Results: The proportions of repetitive elements in various genomes were found to be positively correlated with genome sizes, with a few exceptions. More importantly, there appeared to be specific enrichment between some repetitive element categories with species habitat. Specifically, class II transposons appear to be more abundant in freshwater bony fish than in marine bony fish when phylogenetic relationship is not considered. In contrast, marine bony fish harbor more tandem repeats than freshwater species. In addition, class I transposons appear to be more abundant in primitive species such as cartilaginous fish and lamprey than in bony fish.

Conclusions: The enriched association of specific categories of repetitive elements with fish habitats suggests the importance of repetitive elements in genome evolution and their potential roles in fish adaptation to their living environments. However, due to the restriction of the limited sequenced species, further analysis needs to be done to alleviate the phylogenetic biases.

Keywords: Evolution; Fish; Habitat; Microsatellite; Repeat; Transposon.

Conflict of interest statement

Ethics approval and consent to participate

This study is a retrospective analysis of the public available data and therefore no ethics approval was needed. The Genome sequences are downloaded and cited from Genbank, https://www.ncbi.nlm.nih.gov/genbank/; EMBL Nucleotide Sequence Database (ENA), http://www.ebi.ac.uk/ena/ as outlined in the additional file (Additional file 1: Table S1).

Consent for publication

Not applicable.

Competing interests

The authors declare that they have no competing interests exist.

Publisher’s Note

Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Figures

Fig. 1
Fig. 1
Correlation between genome sizes and contents of repetitive elements. Genome sizes against the percentages of repetitive elements to the whole genome are plotted for 52 species of species for which genome sequences are available. The major orders are plotted in different colors and shapes: Yellow circle: Tetraodontiformes; Orange circle: Perciformes circle; Green circle: Scorpaeniformes; Brown circle: Cypriniformes; Red circle: Cyclostomata; Purple circle: Cyprinodontiformes; Blue triangle: Chondrichthyes; Blue circle: Other species
Fig. 2
Fig. 2
Classification and distribution of 128 repetitive elements in 52 species. The total number of each category of repeats to the all repeats are displayed in columns while different species are displayed in rows. The pink shade represents the freshwater living bony fish, the blue represents the marine living bony fish and yellow represents the diadromous species
Fig. 3
Fig. 3
Divergence distribution analysis of DNA/TcMar-Tc1 transposons in the representative fish genomes. The Cyprinodontiformes, Labroidei species (red) and marine bony fish (blue) are displayed. The y-axis represents the percentage of the genome comprised of repeat classes (%) and the x-axis represents the substitution rate from consensus sequences (%). Please note that not all y-axis scales are the same, particularly in marine species which are 10 times smaller

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