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. 2006 Oct 23:7:269.
doi: 10.1186/1471-2164-7-269.

Analyses of carnivore microsatellites and their intimate association with tRNA-derived SINEs

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Analyses of carnivore microsatellites and their intimate association with tRNA-derived SINEs

Francesc López-Giráldez et al. BMC Genomics. .

Abstract

Background: The popularity of microsatellites has greatly increased in the last decade on account of their many applications. However, little is currently understood about the factors that influence their genesis and distribution among and within species genomes. In this work, we analyzed carnivore microsatellite clones from GenBank to study their association with interspersed repeats and elucidate the role of the latter in microsatellite genesis and distribution.

Results: We constructed a comprehensive carnivore microsatellite database comprising 1236 clones from GenBank. Thirty-three species of 11 out of 12 carnivore families were represented, although two distantly related species, the domestic dog and cat, were clearly overrepresented. Of these clones, 330 contained tRNALys-derived SINEs and 357 contained other interspersed repeats. Our rough estimates of tRNA SINE copies per haploid genome were much higher than published ones. Our results also revealed a distinct juxtaposition of AG and A-rich repeats and tRNALys-derived SINEs suggesting their coevolution. Both microsatellites arose repeatedly in two regions of the interspersed repeat. Moreover, microsatellites associated with tRNALys-derived SINEs showed the highest complexity and less potential instability.

Conclusion: Our results suggest that tRNALys-derived SINEs are a significant source for microsatellite generation in carnivores, especially for AG and A-rich repeat motifs. These observations indicate two modes of microsatellite generation: the expansion and variation of pre-existing tandem repeats and the conversion of sequences with high cryptic simplicity into a repeat array; mechanisms which are not specific to tRNALys-derived SINEs. Microsatellite and interspersed repeat coevolution could also explain different distribution of repeat types among and within species genomes.Finally, due to their higher complexity and lower potential informative content of microsatellites associated with tRNALys-derived SINEs, we recommend avoiding their use as genetic markers.

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Figures

Figure 1
Figure 1
Typical structure of a carnivore tRNA SINE. Typical structure of a carnivore tRNA SINE with two promoter elements for RNA polymerase III (A-box and B-box), a polypyrimidine region and an A-rich tail with polymerase III termination signal (underlined). Direct repeats (DR) that result from the insertion process lie at both termini of the interspersed repeat. Restriction site for Sau3AI enzyme is indicated.
Figure 2
Figure 2
Relative abundance of repeat motifs within tRNA SINE regions. Relative abundance of repeat motifs within tRNA SINE regions: poly-Y (N = 161), A-rich tail (N = 134), and other parts (N = 227). Differences in specific motif abundance were tested using Fisher's exact tests comparing specific region/motif with the combined values of the other two regions. Repeat motif with frequencies which have a significant departure compared to Bonferroni-corrected alpha for 18 comparisons (P-value < .0028) are indicated with an asterisk (*). Thirty-five MSs were excluded because they were associated with SINEs which did not have a typical structure.
Figure 3
Figure 3
Frequency distribution of repeat array length. Relative frequency of repeat array length (number of repeats) for the most abundant motif classes – a) dimers and b) tetramers – in: the whole database, non-masked clones, poly-Y region and A-rich tail.

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