L'objectiu del grup és la producció de contribucions rellevants en les àrees d'expertesa dels components del grup i la seva disseminació en revistes i conferències internacionals de prestigi reconegut. És voluntat del grup que les contribucions tinguin un impacte significatiu a llarg termini. La transferència de tecnologia és considerada com una conseqüència de l'excel·lència en la recerca i s'ha de portar a terme com un mitjà per incrementar l'impacte dels resultats, obtenir recursos per al grup i explorar nous temes per a la recerca en el futur.
The availability of the genome sequence of the unisexual (male-female) Caenorhabditis nigoni offers an opportunity to compare its non-coding features with the related hermaphroditic species Caenorhabditis briggsae; to understand the evolutionary dynamics of their tandem repeat sequences (satellites), as a result of evolution from the unisexual ancestor. We take advantage of the previously developed SATFIND program to build satellite families defined by a consensus sequence. The relative number of satellites (satellites/Mb) in C. Nigoni is 24.6% larger than in C. Briggsae. Some satellites in C. Nigoni have developed from a proto-repeat present in the ancestor species and are conserved as an isolated sequence in C. Briggsae. We also identify unique satellites which occur only once and joint satellite families with a related sequence in both species. Some of these families are only found in C. Nigoni, which indicates a recent appearance; they contain conserved adjacent 50 and 30 regions, which may favor transposition. Our results show that the number, length and turnover of satellites are restricted in the hermaphrodite C. Briggsae when compared with the unisexual C. Nigoni. We hypothesize that this results from differences in unequal recombination during meiotic chromosome pairing, which limits satellite turnover in hermaphrodites.
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.
Centromere sequences in the genome are associated with the formation of kinetochores, where spindle microtubules grow in mitosis. Centromere sequences usually have long tandem repeats (satellites). In holocentric nematodes it is not clear how kinetochores are formed during mitosis; they are distributed throughout the chromosomes. For this reason it appeared of interest to study the satellites in nematodes in order to determine if they offer any clue on how kinetochores are assembled in these species. We have studied the satellites in the genome of six nematode species. We found that the presence of satellites depends on whether the nematode chromosomes are holocentric or monocentric. It turns out that holocentric nematodes are unique because they have a large number of satellites scattered throughout their genome. Their number, length and composition are different in each species: they apparently have very little evolutionary conservation. In contrast, no scattered satellites are found in the monocentric nematode Trichinella spiralis. It appears that the absence/presence of scattered satellites in the genome distinguishes monocentric from holocentric nematodes. We conclude that the presence of satellites is related to the holocentric nature of the chromosomes of most nematodes. Satellites may stabilize a higher order structure of chromatin and facilitate the formation of kinetochores. We also present a new program, SATFIND, which is suited to find satellite sequences.