Data from: High evolutionary turnover of satellite families in Caenorhabditis

Background: The high density of tandem repeat sequences (satellites) in
nematode genomes and the availability of genome sequences from several
species in the group offer a unique opportunity to better understand the
evolutionary dynamics and the functional role of these sequences. We take
advantage of the previously developed SATFIND program to study the
satellites in four Caenorhabditis species and investigate these questions.
Methods: The identification and comparison of satellites is carried out in
three steps. First we find all the satellites present in each species with
the SATFIND program. Each satellite is defined by its length, number of
repeats, and repeat sequence. Only satellites with at least ten repeats
are considered. In the second step we build satellite families with a
newly developed alignment program. Satellite families are defined by a
consensus sequence and the number of satellites in the family. Finally we
compare the consensus sequence of satellite families in different species.
Results: We give a catalog of individual satellites in each species. We
have also identified satellite families with a related sequence and
compare them in different species. We analyze the turnover of satellites:
they increased in size through duplications of fragments of 100-300 bases.
It appears that in many cases they have undergone an explosive expansion.
In C. elegans we have identified a subset of large satellites that have
strong affinity for the centromere protein CENP-A. We have also compared
our results with those obtained from other species, including one nematode
and three mammals. Conclusions: Most satellite families found in
Caenorhabditis are species-specific; in particular those with long
repeats. A subset of these satellites may facilitate the formation of
kinetochores in mitosis. Other satellite families in C. elegans are either
related to Helitron transposons or to meiotic pairing centers.