Next-generation sequencing detects repetitive elements expansion in giant genomes of annual killifish genus Austrolebias (Cyprinodontiformes, Rivulidae)
- 405 Downloads
Among Neotropical fish fauna, the South American killifish genus Austrolebias (Cyprinodontiformes: Rivulidae) constitutes an excellent model to study the genomic evolutionary processes underlying speciation events. Recently, unusually large genome size has been described in 16 species of this genus, with an average DNA content of about 5.95 ± 0.45 pg per diploid cell (mean C-value of about 2.98 pg). In the present paper we explore the possible origin of this unparallel genomic increase by means of comparative analysis of the repetitive components using NGS (454-Roche) technology in the lowest and highest Rivulidae genomes. Here, we provide the first annotated Rivulidae-repeated sequences composition and their relative repetitive fraction in both genomes. Remarkably, the genomic proportion of the moderately repetitive DNA in Austrolebias charrua genome represents approximately twice (45 %) of the repetitive components of the highly related rivulinae taxon Cynopoecilus melanotaenia (25 %). Present work provides evidence about the impact of the repeat families that could be distinctly proliferated among sublineages within Rivulidae fish group, explaining the great genome size differences encompassing the differentiation and speciation events in this family.
KeywordsGiant genomes Repetitive sequences Rivulidae
This work was partially supported by Dedicación Total_ Project (UdelaR, Uruguay) and Fondo Clemente Estable_1_2011_1_6784 (Agencia Nacional Investigación e Innovación, Uruguay) Project to G.G. We thank M. Vaio for your assistance in the RepeatExplorer processing data. G.G. and V.G. acknowledge the support of Sistema Nacional de Investigadores (ANII, Uruguay). The present paper version was improved incorporating the valuables suggestions furnished by two anonymous Reviewers.
Conflict of interest
The authors declare that they have no conflict of interest.
- Ferreira DC, Porto-Foresti F, Oliveira C, Foresti F (2011) Transposable elements as a potential source for understanding the fish genome. MGSs 1:112–117Google Scholar
- García G, Alvarez-Valin F, Gómez N (2002) Mitochondrial genes: Signals and Noise in phylogenetic reconstruction within killifish genus Cynolebias (Cyprinodontiformes, Rivulidae). Biol J Linn Soc Lond 76:49–59Google Scholar
- Gordon A, Hannon GJ (2010) FASTX-toolkit. FASTQ/A short-reads preprocessing tools. (unpublished) http://hannonlab.cshl.edu/fastx_toolkit
- Lande R (1984) The expected fixation rate of chromosomal inversions. Evolution 38:743–752Google Scholar
- Piednoël M, Aberer AJ, Schneeweiss GM, Macas J, Novak P, Gundlach H, Temsch EM, Renner S (2012) Next-generation sequencing reveals the impact of repetitive DNA across phylogenetically closely related genomes of orobanchaceae. Mol Biol Evol 29:3601–3611. doi: 10.1093/molbev/mss168 CrossRefPubMedGoogle Scholar
- Reichwald K, Lauber C, Nanda I, Kirschner J, Hartmann N, Schories S, Gausmann U, Taudien S, Schilhabel MB, Szafranski K et al (2009) High tandem repeat content in the genome of the short-lived annual fish Nothobranchius furzeri: a new vertebrate model for aging research. Genome Biol 10:R16.1–R16.17. doi: 10.1186/gb-2009-10-2-r16 CrossRefGoogle Scholar
- Schartl M, Walter RB, Shen Y, Garcia T, Catchen J, Amore A, Braasch I, Chalopin D, Volff JN, Lesch KP et al (2013) The genome of the platyfish, Xiphophorus maculatus, provides insights into evolutionary adaptation and several complex traits. Nat Genet 45:567. doi: 10.1038/ng.2604 CrossRefPubMedGoogle Scholar
- Wourms JP (1967) Annual fishes. In: Wilt FH, Wessels N (eds) Methods in developmental biology. Thomas and Crowell Company, New York, pp 123–137Google Scholar