Heterochromatin genomics: dynamics and evolution of repetitive sequences in arthropods and molluscs.

Notwithstanding the advances in genome-wide, high throughput technologies, the comprehension of genome function/evolution especially in gene-depleted portions highly enriched in repetitive sequences remains poor and  limited even if these domains have been recently shown to play genomic fundamental roles ranging from chromatin structure to genome expression. Repetitive sequences dynamics may have a driving role in genome evolution and its impact on species divergence deserves attention.

At present we are investigating the dynamics and evolution of satellite DNA, non-LTR retrotransposons and SINEs  in both non canonical and bisexually reproducing mating systems. Main recent results and ongoing projects are below reported.

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Satellite DNA

 a) The satDNA family BIV160 appears the most ancient satDNA so far described: being present in the three main bivalve clades (Protobranchia, Pteriomorphia, Heterochonchia), its origin must be dated to 540 MYA. The pattern of sequence variation observed allows to explain the dichotomy between monomers homogeneity and variant richness often observed in genomes (PLOHL M, PETROVIC V, LUCHETTI A, RICCI A, SATOVIC E , PASSAMONTI M AND MANTOVANI B  2009 Long-term conservation vs high sequence divergence: the case of an extraordinarily old satellite DNA in bivalve mollusks. Heredity, in press). SatDNA studies focused on Venerupis decussata and V. philippinarum are at present one of the topics of the collaboration with prof. Miroslav Plohl (Ruder Boskovic Institute, Zagreb, Croatia) and his coworkers.

b) A review of the most recent data on satellite DNAs  showed that  these repetitive elements once considered an inert by-product of genome dynamics in heterochromatic regions do have functional significance and their evolution is linked to both stochastic events and selective pressures (PLOHL M., LUCHETTI A., MEŠTROVIĆ N. AND MANTOVANI B. 2008 Satellite DNAs between selfishness and functionality: structure, genomics and evolution of tandem repeats in centromeric (hetero)chromatin. Gene, 409: 72–82).

Mobile elements - Non LTR retrotransposons: R2

Many efforts have been recently dedicated to the analysis of R2 retrotransposons in Triops cancriformis and Reticulitermes / Kalotermes termites. Specific papers have been sent for publication and are under consideration.

Studies have started in Bacillus rossius and B. grandii. In termites and stick insects  we are also performing progeny analyses.

Mobile elements - SINEs

A lot of work has been recently dedicated to understand if and how highly inbred genomes, such those of termites, can manage SINE proliferation. The SINE Talua  isolated from Reticulitermes lucifugus (Rhinotermitidae) is the only mobile element described so far in termites (LUCHETTI A,  MANTOVANI B 2009 Talua SINE biology in the genome of the Reticulitermes subterranean termites (Isoptera, Rhinotermitidae). J Mol Evol (2009) 69:589–600). The Muller’s ratchet theory expectations for inbred genomes are not here retrieved.

Other three SINE families isolated from the Reticulitermes genome are under study, while a Bacillus genomic library for SINE isolation is under construction.