Genome-Wide Comparative Analysis of LTR Retrotransposon Dynamics In Flax (Linum usitatissimum) and Its Related Genomes, Cassava (Manihot esculenta) and Poplar (Populus trichocarpa)

Plant genomes vary greatly in size. However, sequencing of 26 plant genomes to date, revealed similar numbers of genes among them (~35,700), occupying only a fraction of the genome (1-5%). The difference in genome size is mostly accounted for by LTR retroelements (LTR-REs; 18-84%).  LTR-REs play an important role in the evolution of genomes and regulation of genes through epigenetic mechanisms. Hence, standardized annotation of LTR-REs in any plant genome is needed for understanding their regulatory contribution and for comparative analysis. To realize this objective, a bioinformatics pipeline is being developed to annotate LTR-REs and characterize their neighbourhood. Initial results for flax (373MB; Wang et al. 2012) and related cassava (770MB; Prochnik et al. 2012) and poplar (550MB; Tuskan et al. 2006) indicated a very dynamic nature of LTR-RE evolution. The number of subfamilies varied from 2,304 (flax) to 1,068 (cassava) and 5,268 (poplar) with the average length of elements being 5,618bp, 8,223bp and 9,239bp, respectively. Average insertion time are very similar among flax (3.58 Million Years-MY), cassava (4.08 MY) and poplar (3.42 MY). Mean distance between LTR-REs and their 5’ and 3’ neighboring genes was found to be 1,874bp (flax) 1,919bp (cassava) and 2,071bp (poplar), indicating their potential to quantitatively modulate or silence the expression of these genes. Twenty other characteristics of retroelements on the genome-scale, generated using the pipeline, will be presented.

References:

Wang, Z. et al. (2012) Plant J., Doi:10.1111/j.1365-313X.2012.05093.x.

Prochnik, S.  et al. (2012) Tropical Plant Biol. 5:88-94.

Tuskan GA, et al. (2006) Science 313:1596- 1604.