Figure 1. Active ERVs in White Leghorn testis.

(A) A254 absorbance profile of 10% to 50% sucrose density gradients of testis lysates from adult rooster. From top to bottom, plots show the relative abundance of 18S rRNA, β-ACTIN mRNA, CILI mRNA, CIWI mRNA, chicken Malat1 lncRNA, CR1B, CR1F, EAV-HP, and ALVE quantified by RT-qPCR. Data were normalized to a spike-in control RNA. (B) Scatter plots of transcript abundance versus ribosome density. Each black dot represents an mRNA expressed in testis. Each filled red circle represents an ERV family, and each open red circle represents any other TE family, including DNA transposons and CR1 superfamily; rpkm, reads per kilobase of transcript per million mapped reads; fpkm, fragments per kilobase of transcript per million mapped reads. (C) Normalized reads of White Leghorn RPFs (Top), White Leghorn piRNAs (Middle), and Red Jungle Fowl small RNA reads (>23 nt) (Bottom). Blue represents sense mapping reads; Red represents anti-sense mapping reads. The gene organization of ALVE is also shown. Gag, group-specific antigen; Pol, polymerase; Env, envelope protein; ppm, parts per million. (D) Circos plot representing the locations, from periphery to center, of cytological position (black lines represent centromeres), piRNA clusters in White Leghorn (Black lines represent conserved piRNA clusters; White lines represent divergent piRNA clusters), putative new insertions discovered by TEMP (tiles) using genomic resequencing of White Leghorn, and 2 × 2 contingency table for Fisher’s exact test to assess the significance of the coincidence of transcription and translation of each TE family. The table data correspond to the number of TE families in each category and, in parentheses, the number of TE families in each category with recent transpositions.

DOI: http://dx.doi.org/10.7554/eLife.24695.003

Figure 1—figure supplement 1. Tissue distribution of ERVs and piRNA pathway genes.

(A) Box plots show the abundance of ERV families in different chicken tissues measured by RNA-seq data. (B) Expression of A-MYB, CILI, and CIWI in each tissue measured by RNA-seq data.

DOI: http://dx.doi.org/10.7554/eLife.24695.004

Figure 1—figure supplement 2. PIWI proteins are conserved between mammals and birds.

Phylogenetic tree of PIWI proteins, including four human PIWI proteins, three mouse PIWI proteins, and two chicken PIWI proteins.

DOI: http://dx.doi.org/10.7554/eLife.24695.005

Figure 1—figure supplement 3. Ribosome profiling in adult rooster testes.

(A) Schematic of ribosome profiling library construction. (B) Length distributions of RPFs mapped to mRNA CDS (black) and ALVE (purple). (C) Metagene plots of RNA-seq (top) and RPF (bottom) at 5´ leader, CDS, and 3´ trailer of mRNAs. The x-axis shows the median length of these regions, and the y-axis represents the mean of normalized abundance. (D) Discrete Fourier transformation of the distance spectrum of 5´ ends of RPFs across mRNA CDSs (black) and ALVE (purple).

DOI: http://dx.doi.org/10.7554/eLife.24695.006

Figure 1—figure supplement 4. A recent ALVE insertion in the SOX5 gene detected by genome-resequencing of White Leghorn.

From top to bottom, the genomic location of the insertion, the genome resequencing signals mapping to Crick strand and Watson strand, Ref-Seq track showing the first intron of SOX5, RepeatMasker track showing no other TEs in these regions, and example reads that map to the first intron of SOX5 genes are shown (the rest of reads that map to ALVE do not align to the reference genome). The 6 bp targeted site duplication is labeled on the example reads.

DOI: http://dx.doi.org/10.7554/eLife.24695.007