title: Homology-based annotation of non-coding RNAs in the genomes of Schistosoma mansoni and Schistosoma japonicum.
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.
  
  
  CONCLUSIONS
  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.
authors.affiliation: Bioinformatics Group, Department of Computer Science and Interdisciplinary Center for Bioinformatics, University of Leipzig, Härtelstrasse 16-18, D-04107 Leipzig, Germany. cclaudia@bioinf.uni-leipzig.de
authors.forename: Claudia S
authors.initials: CS
authors.lastname: Copeland
authors.forename: Manja
authors.initials: M
authors.lastname: Marz
authors.forename: Dominic
authors.initials: D
authors.lastname: Rose
authors.forename: Jana
authors.initials: J
authors.lastname: Hertel
authors.forename: Paul J
authors.initials: PJ
authors.lastname: Brindley
authors.forename: Clara Bermudez
authors.initials: CB
authors.lastname: Santana
authors.forename: Stephanie
authors.initials: S
authors.lastname: Kehr
authors.forename: Camille Stephan-Otto
authors.initials: CS
authors.lastname: Attolini
authors.forename: Peter F
authors.initials: PF
authors.lastname: Stadler
mesh_terms: D000818:Animals; D001483:Base Sequence; D017124:Conserved Sequence; D049751:Genome, Helminth; D035683:MicroRNAs / Q000235:genetics; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D018510:RNA, Helminth / Q000235:genetics*; D012335:RNA, Ribosomal / Q000235:genetics; D020537:RNA, Small Nucleolar / Q000235:genetics; D020038:RNA, Spliced Leader / Q000235:genetics; D012343:RNA, Transfer / Q000235:genetics; D022661:RNA, Untranslated / Q000235:genetics*; D012549:Schistosoma japonicum / Q000235:genetics*; D012550:Schistosoma mansoni / Q000235:genetics*; D016415:Sequence Alignment; D017423:Sequence Analysis, RNA; D012689:Sequence Homology, Nucleic Acid
chemical_list: D035683:MicroRNAs; D018510:RNA, Helminth; D012335:RNA, Ribosomal; D020537:RNA, Small Nucleolar; D020038:RNA, Spliced Leader; D022661:RNA, Untranslated; D012343:RNA, Transfer