The SIDER2 elements, interspersed repeated sequences that populate the Leishmania genomes, constitute subfamilies showing chromosomal proximity relationship

<p>Abstract</p> <p>Background</p> <p>Protozoan parasites of the genus <it>Leishmania </it>are causative agents of a diverse spectrum of human diseases collectively known as leishmaniasis. These eukaryotic pathogens that diverged early from the main eukaryotic lineage possess a number of unusual genomic, molecular and biochemical features. The completion of the genome projects for three <it>Leishmania </it>species has generated invaluable information enabling a direct analysis of genome structure and organization.</p> <p>Results</p> <p>By using DNA macroarrays, made with <it>Leishmania infantum </it>genomic clones and hybridized with total DNA from the parasite, we identified a clone containing a repeated sequence. An analysis of the recently completed genome sequence of <it>L. infantum</it>, using this repeated sequence as bait, led to the identification of a new class of repeated elements that are interspersed along the different <it>L. infantum </it>chromosomes. These elements turned out to be homologues of SIDER2 sequences, which were recently identified in the <it>Leishmania major </it>genome; thus, we adopted this nomenclature for the <it>Leishmania </it>elements described herein. Since SIDER2 elements are very heterogeneous in sequence, their precise identification is rather laborious. We have characterized 54 LiSIDER2 elements in chromosome 32 and 27 ones in chromosome 20. The mean size for these elements is 550 bp and their sequence is G+C rich (mean value of 66.5%). On the basis of sequence similarity, these elements can be grouped in subfamilies that show a remarkable relationship of proximity, i.e. SIDER2s of a given subfamily locate close in a chromosomal region without intercalating elements. For comparative purposes, we have identified the SIDER2 elements existing in <it>L. major </it>and <it>Leishmania braziliensis </it>chromosomes 32. While SIDER2 elements are highly conserved both in number and location between <it>L. infantum </it>and <it>L. major</it>, no such conservation exists when comparing with SIDER2s in <it>L. braziliensis </it>chromosome 32.</p> <p>Conclusion</p> <p>SIDER2 elements constitute a relevant piece in the <it>Leishmania </it>genome organization. Sequence characteristics, genomic distribution and evolutionarily conservation of SIDER2s are suggestive of relevant functions for these elements in <it>Leishmania</it>. Apart from a proved involvement in post-trancriptional mechanisms of gene regulation, SIDER2 elements could be involved in DNA amplification processes and, perhaps, in chromosome segregation as centromeric sequences.</p