Length and GC content variability of introns among teleostean genomes in the light of the metabolic rate hypothesis

A comparative analysis of five teleostean genomes, namely zebrafish, medaka, three-spine stickleback, fugu and pufferfish was performed with the aim to highlight the nature of the forces driving both length and base composition of introns (i.e., bpi and GCi). An inter-genome approach using orthologo...

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Bibliographic Details
Published in:PloS one 2014-08, Vol.9 (8), p.e103889-e103889
Main Authors: Chaurasia, Ankita, Tarallo, Andrea, Bernà, Luisa, Yagi, Mitsuharu, Agnisola, Claudio, D'Onofrio, Giuseppe
Format: Article
Language:English
Subjects:
Animals
Base Composition
Base Sequence
Biology and Life Sciences
Comparative analysis
Correlation analysis
Danio rerio
Deoxyribonucleic acid
DNA
DNA methylation
Drosophila
Earth Sciences
Energy Metabolism - genetics
Evolution
Fishes - genetics
Fishes - metabolism
Gasterosteus aculeatus
Gene expression
Gene sequencing
Genetic Variation
Genome
Genomes
Genomics
Hypotheses
Insects
Inteins - genetics
Introns
Masking
Metabolic rate
Metabolism
Oryzias - genetics
Oryzias - metabolism
Oryzias latipes
Oxygen Consumption - genetics
Physiology
Sigma factor
Smegmamorpha - genetics
Smegmamorpha - metabolism
Takifugu - genetics
Takifugu - metabolism
Takifugu rubripes
Temperature
Tetraodontiformes - genetics
Tetraodontiformes - metabolism
Vertebrates
Zebrafish
Zebrafish - genetics
Zebrafish - metabolism
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Summary:A comparative analysis of five teleostean genomes, namely zebrafish, medaka, three-spine stickleback, fugu and pufferfish was performed with the aim to highlight the nature of the forces driving both length and base composition of introns (i.e., bpi and GCi). An inter-genome approach using orthologous intronic sequences was carried out, analyzing independently both variables in pairwise comparisons. An average length shortening of introns was observed at increasing average GCi values. The result was not affected by masking transposable and repetitive elements harbored in the intronic sequences. The routine metabolic rate (mass specific temperature-corrected using the Boltzmann's factor) was measured for each species. A significant correlation held between average differences of metabolic rate, length and GC content, while environmental temperature of fish habitat was not correlated with bpi and GCi. Analyzing the concomitant effect of both variables, i.e., bpi and GCi, at increasing genomic GC content, a decrease of bpi and an increase of GCi was observed for the significant majority of the intronic sequences (from ∼ 40% to ∼ 90%, in each pairwise comparison). The opposite event, concomitant increase of bpi and decrease of GCi, was counter selected (from
ISSN:1932-6203
1932-6203
DOI:10.1371/journal.pone.0103889