Differences in non-LTR retrotransposons within C. elegans and C. briggsae genomes.
An exhaustive study of the Sam/Frodo family of non-LTR retrotransposons in the Caenorhabditis elegans and Caenorhabditis briggsae genomes demonstrated that C. briggsae contains 60 Sam/Frodo elements including a new subfamily designated Merry, while at least 1000 elements are present in C. elegans. In contrast to C. elegans, C. briggsae does not contain any other non-LTR retrotransposons. The Sam/Frodo/Merry sequences in C. briggsae are shorter and less complete than the Sam/Frodo sequences in C. elegans probably because they all lack a functional first open reading frame (ORF1) and because the genome only encodes one functional reverse transcriptase gene of a non-LTR retrotransposon. Evidence of purifying selection for a functional reverse transcriptase sequence in master/leader elements was found in both nematodes in spite of low copy numbers in C. briggsae. Sam elements in C. elegans are the most abundant Sam/Frodo/Merry family members. They contain the only functional ORF1 copies and, unlike Frodo and Merry members, have a higher GC content than the genomic regions in which they reside. This may indicate a higher transcription rate within this subfamily.
Zagrobelny
Mika
M
Department of Evolutionary Biology, Zoological Institute, University of Copenhagen, Copenhagen, Denmark. miz@kvl.dk
Jeffares
Daniel C
DC
Arctander
Peter
P
D000818:Animals; D001482:Base Composition; D002107:Caenorhabditis / Q000235:genetics*; D017173:Caenorhabditis elegans / Q000235:genetics*; D019295:Computational Biology / Q000379:methods; D030561:Databases, Nucleic Acid; D016678:Genome; D016366:Open Reading Frames / Q000235:genetics; D010802:Phylogeny; D018626:Retroelements / Q000235:genetics*; D013045:Species Specificity
D018626:Retroelements