Extended Data Fig. 6: Correlation between expression of transposable element families and copy number in the genome.

a, Expression was estimated for each transposable element family using poly (A)-enriched RNA-seq data from gonad, brain and liver. For all tissues and transposable element classes, a positive correlation is observed between expression level and copy number. When a transposable element family is highly expressed, this family tend to have more copies. However, some families are distant from the correlation line, with a high expression and low copy number or vice versa. The expression levels of transposable element families are globally correlated in the three tissues. b, Composition of different classes of repetitive elements in genic regions. Gene and repetitive element annotations were obtained from published reference genomes (see ‘Repeats and transposable elements annotation’ in Methods). The percentage of different classes of repetitive elements in genic region (including UTRs, exons and introns) were calculated as percentage of the number of bp covered by the repetitive element, normalized by the size of the genes. Genes are grouped by length. As the size of genes varies across species, we grouped them by quartile division per species. The genic LTR percentage (orange) increases in longer genes in lungfish, axolotl and caecilian (vertical lines show the minimum and maximum of the percentage of transposable elements in genes). The box plot shows the median, and the 25% and the 75% quartiles; whiskers show 1.5× the interquartile range. Outliers extend beyond 1.5× interquartile ranges from either hinge. c, Percentage of the genic regions that are occupied by different classes of transposable elements. Top and middle, LINE CR1 and LINE L2 (which are classified in the same clade of LINE and are closely related) compose about 5.1% and 2.9% of the lungfish genome, respectively. Bottom, on average, introns (blue) contain a higher number of LTRs and DIRS (about 20 to 30%) than exons (red). d, Percentage of LTR families in genic regions (including UTRs). The LTRs and DIRS are enriched in genic regions in lungfish and axolotl.