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BMC Genomics. 2009; 10: 464.
Published online Oct 8, 2009. doi:  10.1186/1471-2164-10-464
PMCID: PMC2770079
Homology-based annotation of non-coding RNAs in the genomes of Schistosoma mansoni and Schistosoma japonicum
Claudia S Copeland,1,2 Manja Marz,1 Dominic Rose,1 Jana Hertel,1 Paul J Brindley,2 Clara Bermudez Santana,1,8 Stephanie Kehr,1 Camille Stephan-Otto Attolini,3 and Peter F Stadlercorresponding author1,4,5,6,7
1Bioinformatics Group, Department of Computer Science and Interdisciplinary Center for Bioinformatics, University of Leipzig, Härtelstraße 16-18, D-04107 Leipzig, Germany
2Department of Microbiology, Immunology & Tropical Medicine, George Washington University Medical Center, 2300 I Street, NW, Washington, DC 20037, USA
3Memorial Sloan-Kettering Cancer Center, Computational Biology Department, 1275 York Avenue, Box # 460, New York, NY 10065, USA
4Max Planck Institute for Mathematics in the Sciences, Inselstrasse 22, D-04103 Leipzig, Germany
5Fraunhofer Institute for Cell Therapy and Immunology, Perlickstraße 1, D-04103 Leipzig, Germany
6Santa Fe Institute, 1399 Hyde Park Rd, Santa Fe, NM 87501, USA
7Institute for Theoretical Chemistry, University of Vienna, Währingerstraße 17, A-1090 Wien, Austria
8Department of Biology, National University of Colombia, Carrera 45 No. 26-85, Bogotá, D.C., Colombia
corresponding authorCorresponding author.
Claudia S Copeland: cclaudia/at/bioinf.uni-leipzig.de; Manja Marz: manja/at/bioinf.uni-leipzig.de; Dominic Rose: dominic/at/bioinf.uni-leipzig.de; Jana Hertel: jana/at/bioinf.uni-leipzig.de; Paul J Brindley: mtmpjb/at/gwumc.edu; Clara Bermudez Santana: clara/at/bioinf.uni-leipzig.de; Stephanie Kehr: steffi/at/bioinf.uni-leipzig.de; Camille Stephan-Otto Attolini: camille/at/bioinf.uni-leipzig.de; Peter F Stadler: studla/at/bioinf.uni-leipzig.de
Received May 27, 2009; Accepted October 8, 2009.
Abstract
Background
Schistosomes are trematode parasites of the phylum Platyhelminthes. They are considered the most important of the human helminth parasites in terms of morbidity and mortality. Draft genome sequences are now available for Schistosoma mansoni and Schistosoma japonicum. Non-coding RNA (ncRNA) plays a crucial role in gene expression regulation, cellular function and defense, homeostasis, and pathogenesis. The genome-wide annotation of ncRNAs is a non-trivial task unless well-annotated genomes of closely related species are already available.
Results
A homology search for structured ncRNA in the genome of S. mansoni resulted in 23 types of ncRNAs with conserved primary and secondary structure. Among these, we identified rRNA, snRNA, SL RNA, SRP, tRNAs and RNase P, and also possibly MRP and 7SK RNAs. In addition, we confirmed five miRNAs that have recently been reported in S. japonicum and found two additional homologs of known miRNAs. The tRNA complement of S. mansoni is comparable to that of the free-living planarian Schmidtea mediterranea, although for some amino acids differences of more than a factor of two are observed: Leu, Ser, and His are overrepresented, while Cys, Meth, and Ile are underrepresented in S. mansoni. On the other hand, the number of tRNAs in the genome of S. japonicum is reduced by more than a factor of four. Both schistosomes have a complete set of minor spliceosomal snRNAs. Several ncRNAs that are expected to exist in the S. mansoni genome were not found, among them the telomerase RNA, vault RNAs, and Y RNAs.
Conclusion
The ncRNA sequences and structures presented here represent the most complete dataset of ncRNA from any lophotrochozoan reported so far. This data set provides an important reference for further analysis of the genomes of schistosomes and indeed eukaryotic genomes at large.
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