@article{Copeland:Marz:Rose:Homol_annot_non:2009,
author = {Copeland, Claudia S. and Marz, Manja and Rose, Dominic and 
          Hertel, Jana and Brindley, Paul J. and Santana, Clara 
          Bermudez and Kehr, Stephanie and Attolini, Camille 
          Stephan-Otto and Stadler, Peter F.},
title = {Homology-based annotation of non-coding {RNAs} in the 
         genomes of {Schistosoma} mansoni and {Schistosoma} japonicum},
journal = {BMC Genomics},
year = {2009},
doi = {10.1186/1471-2164-10-464},
volume = {10},
user = {dominic},
pmid = {19814823},
pages = {464},
number = {},
issn = {1471-2164},
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.}
}