Methods for accurate quantification of LTR-retrotransposon copy number using short-read sequence data: a case study in Sorghum

• Published in: Molecular genetics and genomics : MGG Vol. 291; no. 5; pp. 1871 - 1883
• Main Authors: Ramachandran, Dhanushya, Hawkins, Jennifer S.
• Format: Journal Article
• Language: English
• Published: Berlin/Heidelberg Springer Berlin Heidelberg 01-10-2016; Springer Nature B.V
• Subjects: Animal Genetics and Genomics; Biochemistry; Biomedical and Life Sciences; Case studies; Computer Simulation; Datasets; Estimates; Gene Dosage; Genetic Variation; Genome Size; Genome, Plant; Genomes; Genomics; Human Genetics; Life Sciences; Methods; Microbial Genetics and Genomics; Original Article; Plant Genetics and Genomics; Plant Leaves - genetics; Retroelements - genetics; Sequence Analysis, DNA - methods; Sorghum; Sorghum - genetics; Sorghum bicolor; LTR-retrotransposons; Genome evolution; Transposable elements; Sorghum
• ISSN: 1617-4615; 1617-4623
• DOI: 10.1007/s00438-016-1225-9

Transposable elements (TEs) are ubiquitous in eukaryotic genomes and their mobility impacts genome structure and function in myriad ways. Because of their abundance, activity, and repetitive nature, the characterization and analysis of TEs remain challenging, particularly from short-read sequencing projects. To overcome this difficulty, we have developed a method that estimates TE copy number from short-read sequences. To test the accuracy of our method, we first performed an in silico analysis of the reference
Sorghum bicolor
genome, using both reference-based and de novo approaches. The resulting TE copy number estimates were strikingly similar to the annotated numbers. We then tested our method on real short-read data by estimating TE copy numbers in several accessions of
S. bicolor
and its close relative
S. propinquum
. Both methods effectively identify and rank similar TE families from highest to lowest abundance. We found that de novo characterization was effective at capturing qualitative variation, but underestimated the abundance of some TE families, specifically families of more ancient origin. Also, interspecific reference-based mapping of
S. propinquum
reads to the
S. bicolor
database failed to fully describe TE content in
S. propinquum
, indicative of recent TE activity leading to changes in the respective repetitive landscapes over very short evolutionary timescales. We conclude that reference-based analyses are best suited for within-species comparisons, while de novo approaches are more reliable for evolutionarily distant comparisons.