Short Interspersed Elements (SINEs) in plant genomes

Transposable elements (TEs) were discovered in all/every until studding organisms, including animal, fungi and Protozoa species. They are abundant component of plant genomes also. They undergo constant amplification and proliferate throughout genome. Transposable elements are usually classified in two major groups. The class I - retrotransposons, elements that use an RNA intermediate and reverse transcriptase and the class II, DNA transposons that use a DNA intermediate and transposase. First class of TEs includes long terminal repeat (LTR) and non-LTR retrotransposons. Non-LTR retrotransposons are further divided into two major superfamilies - long interspersed nuclear elements (LINE) and short interspersed nuclear elements (SINE). SINE are short nonautonomous retroelements without discernible open reading frames (ORF) and do not encode any proteins. Presumably LINE elements might be a source of the enzymatic machinery required for retroposition of SINEs (some of tRNA-derived SINEs have sequence similarity in their 3'-end regions to the partner LINE found in the same genome). All SINEs share key characteristics, including an internal polymerase III promoter (made of A and B boxes) in their 5' tRNA-related region, a tRNA-unrelated region of variable length, a short stretch of T or A at their 3'-end. In contrast to animal all of known plant SINEs originate from tRNA. They are also much less abundant in plant genomes than in animal, they reach 104 copies per haploid genome (in comparison to 104-106 copies in animal genomes). First plant SINE p-SINE1 were identified in intron region of Waxy gene in Oryza sativa genome. Subsequent SINEs elements were found in genomes of another Gramineae family members (Zea mays, Aegilops umbellulata, Triticum aestivum). They have been identified also in dicots species genomes including Brassicaceae (Arabidopsis thaliana, Brassica napus, Brassica oleracea), Solanaceae (Nicotiana tabacum, Capsicum annuum, Lycopersicon esculentum), Fabaceae (Medicago truncatula, Lotus japonicus, Glycine max). Plant SINEs are mainly dispersed randomly in genomes although they are rarely present in heterochromatic, pericentromeric regions, and have a preference for gene-rich regions. Great number and variety of these elements caused that they were grouped into families. High polymorphism of SINEs makes possible to isolate subfamilies within families. This feature makes SINEs very convenient as markers, they can be use in classification cultivars, species and in filogenetic studies.