Bioinformatic analysis of female-specific, repetitive sequences
Exceptional within the phylum Plathelminthes is the genus Schistosoma, which covers species exhibiting sexual dimorphism at the adult stage. It has long been of great interest to detect female-specific sequences and to analyze their function1-3. Genetically, the sexes differ e.g. in their karyotype, females have one W and one Z chromosome, males in contrast have two Z chromosomes. Large parts of the Z and W chromosomes are identical. However, there is a large heterochromatic area on the W chromosome, which does not appear on the Z chromosome, and which has been considered as female-specific. In previous studies, repetitive sequences in S. mansoni were detected in the heterochromatic region of the W chromosome and declared as female-specific W elements1-3. However, later studies revealed that these W elements can also occur in males. This led to the assumption of illegitimate recombination processes4,5. Furthermore, the possibility was discussed that these sequences are transcribed6, have a mobile, transposon-like character7 and are involved in the evolution of sex chromosomes8.
In this project, we intend to further investigate the phenomenon of mobile W elements. Therefore, W elements will be bioinformatically analyzed in the context of genome and transcriptome analyses9-12. The aim is to characterize W elements with respect to their group memberships, their activities in different stages of the life cycle of S. mansoni (Fig. 1) and additionally on a structural basis (Fig. 2) in order to get clues about their mobile behavior and their possible function.
Fig. 1: Exemplary presentation of examined RNA-Seq data sets in the Genome Browser (IGV)13,14 to analyze transcript profiles of W-elements. The bars indicate transcripts of one W-element, which occurs in the respective RNA-Seq data set. The repetitive character of this W-element can be recognized by the repeated bar pattern. There are significant differences between the different samples with regard to transcript occurrence. In ovaries of unpaired females (sO1), a high level of transcripts of this W-element was detected, significantly more than in ovaries of paired females (bO1). In testes of unpaired males (sT1), transcripts were found in contrast to testes of paired males (bT1). In cercariae, transcript amounts in both sexes were almost identical (Mcer1, Fcer1; M=male, F=female, cer=cercariae).
Fig. 2: Dotplot diagram (left) and enlarged areas (center, right) to investigate W-elements in S. mansoni. In this analysis, a sequence is compared to itself in order to identify specific patterns within the sequence. Outside the main diagonal, repetitive units appear as lines. In this example, a 403 bp long sequence occuring 101 times on the W chromosome was detected. The graphic was generated using the program Gepard V. 1.4015.
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