Homology-based annotation of non-coding RNAs in the genomes of Schistosoma mansoni and Schistosoma japonicum Journal Article

   

Authors:	Copeland, C. C.; Marz, M.; Rose, D.; Hertel, J.; Brindley, P. J.; Santana, C. B.; Kehr, S.; Attolini, C. S.; Stadler, P. F.
Article 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. 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. © 2009 Copeland et al; licensee BioMed Central Ltd.
Keywords:	controlled study; gene sequence; promoter region; sequence analysis; genetics; nonhuman; molecular genetics; protein motif; animal; animals; microrna; genetic variability; gene expression regulation; transcription regulation; conserved sequence; molecular sequence data; sequence alignment; eukaryota; gene identification; nucleotide sequence; base sequence; genome; conformation; nucleic acid conformation; bacterial genome; codon; eukaryotic cell; protein secondary structure; protein structure; rna structure; schistosoma japonicum; schistosoma mansoni; sequence homology; spliceosome; lophotrochozoa; planaria; platyhelminthes; schmidtea mediterranea; trematoda; vermes; helminth rna; ribosome rna; small nucleolar rna; spliced leader rna; transfer rna; untranslated rna; genome, helminth; micrornas; rna, helminth; rna, ribosomal; rna, small nucleolar; rna, spliced leader; rna, transfer; rna, untranslated; sequence analysis, rna; sequence homology, nucleic acid
Journal Title:	BMC Genomics
Volume:	10
ISSN:	1471-2164
Publisher:	Biomed Central Ltd
Date Published:	2009-10-08
Start Page:	464
Language:	English
DOI:	10.1186/1471-2164-10-464
PUBMED:	19814823
PROVIDER:	scopus
PMCID:	PMC2770079
DOI/URL:	http://www.scopus.com/inward/record.url?eid=2-s2.0-70449717378&partnerID=40&md5=1180d3478aa1e2a7abe73949841d0c0d
Notes:	--- - "Cited By (since 1996): 5" - "Export Date: 30 November 2010" - "Art. No.: 1471" - "CODEN: BGMEE" - "Source: Scopus"

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