Evolutionary dynamics of two satellite DNA families in rock lizards of the genus Iberolacerta (Squamata, Lacertidae): different histories but common traits

Abstract

Satellite DNAs compose a large portion of all higher eukaryotic genomes. The turnover of these highly repetitive sequences is an important element in genome organization and evolution. However, information about the structure and dynamics of reptilian satellite DNA is still scarce. Two satellite DNA families, HindIII and TaqI, have been previously characterized in four species of the genus Iberolacerta. These families showed different chromosomal locations, abundances, and evolutionary rates. Here, we extend the study of both satellite DNAs (satDNAs) to the remaining Iberolacerta species, with the aim to investigate the patterns of variability and factors influencing the evolution of these repetitive sequences. Our results revealed disparate patterns but also common traits in the evolutionary histories of these satellite families: (i) each satellite DNA is made up of a library of monomer variants or subfamilies shared by related species; (ii) species-specific profiles of satellite repeats are shaped by expansions and/or contractions of different variants from the library; (iii) different turnover rates, even among closely related species, result in great differences in overall sequence homogeneity and in concerted or non-concerted evolution patterns, which may not reflect the phylogenetic relationships among taxa. Contrasting turnover rates are possibly related to genomic constraints such as karyotype architecture and the interspersed organization of diverging repeat variants in satellite arrays. Moreover, rapid changes in copy number, especially in the centromeric HindIII satDNA, may have been associated with chromosomal rearrangements and even contributed to speciation within Iberolacerta.

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Abbreviations

Cy3:

Cyanine 3

dNTP:

Deoxyribonucleotide triphosphate

FCA:

Factorial correspondence analysis

FISH:

Fluorescence in situ hybridization

FITC:

Fluorescein iso-thyocianate

Mya:

Million years ago

π :

Nucleotide diversity

satDNA:

Satellite DNA

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Acknowledgments

This work was supported by grants REN2003-02931/GLO (Ministerio de Ciencia y Tecnología, Spain), PGIDIT03RFO10301PR and PGIDIT06RFO10301PR (Xunta de Galicia, Spain) awarded to Horacio Naveira, GRC2014/050 awarded to Ana González, and by grant PRIN2009/20093HYH97 (Ministry of Education, University and Research, Italy) awarded to Vincenzo Caputo Barucchi. Verónica Rojo has been supported by a “FPU” fellowship from Ministerio de Educación, Cultura y Deporte (Spain).

Ethical standards

Permissions for field work and experimental procedures were issued by the competent authorities: Xunta de Galicia (for I. monticola and I. galani), Junta de Castilla y León (for I. cyreni and I. martinezricai), Gobierno de Aragón (for I. bonnali), and Italian Environment Ministry (for I. horvathi). All institutional and national guidelines for the care and use of laboratory animals were followed.

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Correspondence to Horacio Naveira.

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Responsible Editors: Maria Assunta Biscotti, Pat Heslop-Harrison and Ettore Olmo.

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Supplementary Fig. 1
figure6figure6

Sequence alignment of consensus sequences of the different HindIII (a) and TaqI (b) sequence groups. The first line shows the general consensus for all the sequences of each satDNA. Diagnostic positions for each group are indicated by colored shading. (GIF 743 kb)

(GIF 1039 kb)

High Resolution Image (TIFF 30589 kb)

High Resolution Image (TIFF 40349 kb)

Supplementary Table 1

(DOC 16 kb)

Supplementary Table 2

(DOC 74 kb)

Supplementary Table 3

(DOC 46 kb)

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Rojo, V., Martínez-Lage, A., Giovannotti, M. et al. Evolutionary dynamics of two satellite DNA families in rock lizards of the genus Iberolacerta (Squamata, Lacertidae): different histories but common traits. Chromosome Res 23, 441–461 (2015). https://doi.org/10.1007/s10577-015-9489-1

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Keywords

  • Concerted evolution
  • FISH
  • Iberolacerta
  • Library model
  • Satellite DNA
  • Squamate reptiles