Figure 4. ALVE6 is the primary piRNA-producing locus for viral piRNAs.
(A) Cumulative distributions for all piRNAs (Blue) and for uniquely mapping piRNAs (Red) on the 1633 piRNA loci in White Leghorn. (B) An example of conserved piRNA-producing loci, Cluster33, in chicken. Normalized RNA-seq reads of piRNA precursors, piRNAs in White Leghorn, and piRNAs in Red Jungle Fowl. Blue represents Watson-strand piRNAs; Red represents Crick-strand piRNAs. (C) Box plots showing abundance of piRNA precursors in 12 chicken tissues. (D) Venn diagram showing piRNA clusters defined in Red Jungle Fowl (White) and White Leghorn (Black). (E) Normalized RNA-seq reads of piRNA precursors in White Leghorn, White Leghorn piRNAs, unique mapping piRNAs, and Red Jungle Fowl small RNA reads (>23 nt).
Figure 4—figure supplement 1. Divergent transcription of piRNA clusters.
(A) Scatter plots of Watson-strand piRNA abundance versus Crick-strand piRNA abundance (left); scatter plots of Watson-strand piRNA precursor abundance versus Crick-strand piRNA precursor abundance (right). Each filled circle represents a conserved piRNA cluster and each open circle represent a divergent piRNA cluster. (B) Length distributions of testis small RNAs from conserved piRNA clusters (left) and divergent piRNA clusters (right). (C) Sequence logo showing the nucleotide composition of piRNA species from conserved piRNA clusters (left) and from divergent piRNA clusters (right).
Figure 4—figure supplement 2. ALVE6 existed in chicken genome prior domestication.
(A) From top to bottom, the genomic location of Cluster719, White Leghorn genomic re-sequencing signals mapping to Crick strand and Watson strand, Ref-Seq track showing depletion of annotated gene, RepeatMasker track showing the annotated ALVE region, the position of primers used for genomic PCRs, and genomic PCR sequences. Separation of genomic PCR products is shown on the agarose gel, and the primers used for genomic PCRs are labeled in each lane. The sequences of these PCR products were blasted against Red Jungle Fowl with complete alignment. A red tick-mark represents a base substitution; an orange tick-mark represents an insertion. (B) Sequence logo showing the nucleotide composition of ALVE piRNA species from ALVE6 locus (top) and from new ALVE insertions (bottom).