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FISH mapping of microsatellite loci from Drosophila
subobscura and its comparison to related species
Josiane Santos & Lluis Serra & Elisabet Solé &
Marta Pascual
Received: 9 October 2009 /Revised: 6 January 2010 /Accepted: 8 January 2010 /Published online: 3 March 2010
# Springer Science+Business Media B.V. 2010
Abstract Microsatellites are highly polymorphic
markers that are distributed through all the genome
being more abundant in non-coding regions. Whether
they are neutral or under selection, these markers if
localized can be used as co-dominant molecular markers
to explore the dynamics of the evolutionary processes.
Their cytological localization can allow identifying
genes under selection, inferring recombination from a
genomic point of view, or screening for the genomic
reorganizations occurring during the evolution of a
lineage, among others. In this paper, we report for the
first time the localization of microsatellite loci by
fluorescent in situ hybridization on Drosophila polytene
chromosomes. In Drosophila subobscura, 72 dinucleo-
tide microsatellite loci were localized by fluorescent in
situ hybridization yielding unique hybridization signals.
In the sex chromosome, microsatellite distribution was
not uniform and its density was higher than in
autosomes. We identified homologous segments to the
sequence flanking the microsatellite loci by browsing
the genome sequence of Drosophila pseudoobscura
and Drosophila melanogaster. Their localization sup-
ports the conservation of Muller’s chromosomal ele-
ments among Drosophila species and the existence of
multiple intrachromosomal rearrangements within each
evolutionary lineage. Finally, the lack of microsatellite
repeats in the homologous D. melanogaster sequences
suggests convergent evolution for high microsatellite
density in the distal part of the X chromosome.
Keywords cytogeneticmap . Drosophila . fluorescentin
situ hybridization . genome rearrangement .
microsatellite loci . repetitive DNA . genome comparison
Abbreviations
DAPI 4'-6-Diamidino-2-phenylindole
dsub ID names of the clones
FISH fluorescent in-situ hybridization
HP1 Heterochromatin Protein 1
NTP nucleotides triphosphate
PCR polymerase chain reaction
rDNA ribosomal DNA
SSC Sodium Chloride-Sodium Citrate buffer
SSR simple sequence repeats
UCSC University of California Santa Cruz
Introduction
Microsatellites are highly polymorphic markers consti-
tuted by simple sequence tandem repeats (SSR) of one
to six nucleotides per unit (Bachtrog et al. 1999). They
are ubiquitous among eukaryotes and have been
described from a great variety of taxa (Wilder et al.
2002), being generally considered neutral unless linked
to loci under strong selection. Although SSRs typically
Chromosome Research (2010) 18:213–226
DOI 10.1007/s10577-010-9112-4
Responsible Editor: Pat Heslop-Harrison.
J. Santos :L. Serra :E. Solé :M. Pascual (*)
Departament de Genètica, Facultat de Biologia,
Universitat de Barcelona,
08028 Barcelona, Spain
e-mail: martapascual@ub.edu
J. Santos
CBA, Departamento de Biologia, Faculdade de Ciências,
Universidade de Lisboa,
1749-016 Lisbon, Portugal

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Santos et al 2010 Chr Res

  • 1. FISH mapping of microsatellite loci from Drosophila subobscura and its comparison to related species Josiane Santos & Lluis Serra & Elisabet Solé & Marta Pascual Received: 9 October 2009 /Revised: 6 January 2010 /Accepted: 8 January 2010 /Published online: 3 March 2010 # Springer Science+Business Media B.V. 2010 Abstract Microsatellites are highly polymorphic markers that are distributed through all the genome being more abundant in non-coding regions. Whether they are neutral or under selection, these markers if localized can be used as co-dominant molecular markers to explore the dynamics of the evolutionary processes. Their cytological localization can allow identifying genes under selection, inferring recombination from a genomic point of view, or screening for the genomic reorganizations occurring during the evolution of a lineage, among others. In this paper, we report for the first time the localization of microsatellite loci by fluorescent in situ hybridization on Drosophila polytene chromosomes. In Drosophila subobscura, 72 dinucleo- tide microsatellite loci were localized by fluorescent in situ hybridization yielding unique hybridization signals. In the sex chromosome, microsatellite distribution was not uniform and its density was higher than in autosomes. We identified homologous segments to the sequence flanking the microsatellite loci by browsing the genome sequence of Drosophila pseudoobscura and Drosophila melanogaster. Their localization sup- ports the conservation of Muller’s chromosomal ele- ments among Drosophila species and the existence of multiple intrachromosomal rearrangements within each evolutionary lineage. Finally, the lack of microsatellite repeats in the homologous D. melanogaster sequences suggests convergent evolution for high microsatellite density in the distal part of the X chromosome. Keywords cytogeneticmap . Drosophila . fluorescentin situ hybridization . genome rearrangement . microsatellite loci . repetitive DNA . genome comparison Abbreviations DAPI 4'-6-Diamidino-2-phenylindole dsub ID names of the clones FISH fluorescent in-situ hybridization HP1 Heterochromatin Protein 1 NTP nucleotides triphosphate PCR polymerase chain reaction rDNA ribosomal DNA SSC Sodium Chloride-Sodium Citrate buffer SSR simple sequence repeats UCSC University of California Santa Cruz Introduction Microsatellites are highly polymorphic markers consti- tuted by simple sequence tandem repeats (SSR) of one to six nucleotides per unit (Bachtrog et al. 1999). They are ubiquitous among eukaryotes and have been described from a great variety of taxa (Wilder et al. 2002), being generally considered neutral unless linked to loci under strong selection. Although SSRs typically Chromosome Research (2010) 18:213–226 DOI 10.1007/s10577-010-9112-4 Responsible Editor: Pat Heslop-Harrison. J. Santos :L. Serra :E. Solé :M. Pascual (*) Departament de Genètica, Facultat de Biologia, Universitat de Barcelona, 08028 Barcelona, Spain e-mail: martapascual@ub.edu J. Santos CBA, Departamento de Biologia, Faculdade de Ciências, Universidade de Lisboa, 1749-016 Lisbon, Portugal