BoS: a large and diverse family of short interspersed elements (SINEs) in Brassica oleracea.
Short interspersed elements (SINEs) are nonautonomous non-LTR retrotransposons that populate eukaryotic genomes. Numerous SINE families have been identified in animals, whereas only a few have been described in plants. Here we describe a new family of SINEs, named BoS, that is widespread in Brassicaceae and present at approximately 2000 copies in Brassica oleracea. In addition to sharing a modular structure and target site preference with previously described SINEs, BoS elements have several unusual features. First, the head regions of BoS RNAs can adopt a distinct hairpin-like secondary structure. Second, with 15 distinct subfamilies, BoS represents one of the most diverse SINE families described to date. Third, several of the subfamilies have a mosaic structure that has arisen through the exchange of sequences between existing subfamilies, possibly during retrotransposition. Analysis of BoS subfamilies indicate that they were active during various time periods through the evolution of Brassicaceae and that active elements may still reside in some Brassica species. As such, BoS elements may be a valuable tool as phylogenetic makers for resolving outstanding issues in the evolution of species in the Brassicaceae family.
Zhang
Xiaoyu
X
Department of Plant Biology, University of Georgia, Athens, 30602, USA.
Wessler
Susan R
SR
D020029:Base Pairing / Q000235:genetics*; D001483:Base Sequence; D001937:Brassica / Q000235:genetics*; D002874:Chromosome Mapping; D016000:Cluster Analysis; D019295:Computational Biology; D030541:Databases, Genetic; D014644:Genetic Variation; D008969:Molecular Sequence Data; D010802:Phylogeny; D012313:RNA / Q000737:chemistry*; D016415:Sequence Alignment; D020086:Short Interspersed Nucleotide Elements / Q000235:genetics*
D012313:RNA