Ratio of solo-LTR [Long terminal repeat] to complete elements

Range Picea abies ~1:9: Arabidopsis thaliana 1:1: rice 0.6:1: barley 16:1 unitless
Organism Plants
Reference Nystedt B et al., The Norway spruce genome sequence and conifer genome evolution. Nature. 2013 May 30 497(7451):579-84. doi: 10.1038/nature12211 p.581 right column top paragraphPubMed ID23698360
Primary Source [33] Devos, K. M., Brown, J. K. M. & Bennetzen, J. L. Genome size reduction through illegitimate recombination counteracts genome expansion in Arabidopsis. Genome Res. 12, 1075–1079 (2002) DOI: 10.1101/gr.132102 [34] Vitte, C. & Panaud, O. Formation of solo-LTRs through unequal homologous recombination counterbalances amplifications of LTR retrotransposons in rice Oryza sativa L. Mol. Biol. Evol. 20, 528–540 (2003) DOI: 10.1093/molbev/msg055 [35] Vicient, C. M. et al. Retrotransposon BARE-1 and its role in genome evolution in the genus Hordeum. Plant Cell 11, 1769–1784 (1999)PubMed ID12097344, 12654934, 10488242
Comments P.581 right column top paragraph: "[Investigators] clustered LTRs of complete elements to identify transposable element families (ref 32). More than 86% of the elements remained as singletons, indicating that LTR-RTs [Long terminal repeat-retrotransposons] are quite divergent and that there are several low-abundance families. [They] searched three LTR-RT families for signatures of unequal intra-element recombination events in scaffolds >50 kb and 20 complete fosmids (primary source 33). For families ALISEI, 3K05 and 4D08_5 [they] identified 21, 22 and 39 complete elements, and four, five and no solo LTRs, respectively (Supplementary Information 3.10). Although this data set is limited, the analysis suggested that LTR-RT-related sequences might be removed less frequently by unequal recombination than in other plant genomes. The ratio of solo-LTRs to complete elements in P. abies is ~1:9, whereas in A. thaliana, rice and barley it is 1:1 (primary source 33), 0.6:1 (primary source 34) and 16:1 (for the abundant BARE 1 element, primary source 35), respectively. Taken together, these findings indicated that the extant set of transposable elements in P. abies accumulated slowly over tens or hundreds of millions years, mainly by the insertion of LTR-RT elements with limited transposable element removal."
Entered by Uri M
ID 113651