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. 2020 May;26(5):581–594. doi: 10.1261/rna.073965.119

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© 2020 Aguiar et al.; Published by Cold Spring Harbor Laboratory Press for the RNA Society

This article is distributed exclusively by the RNA Society for the first 12 months after the full-issue publication date (see http://rnajournal.cshlp.org/site/misc/terms.xhtml). After 12 months, it is available under a Creative Commons License (Attribution-NonCommercial 4.0 International), as described at http://creativecommons.org/licenses/by-nc/4.0/.

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FIGURE 4. — A TE and EVE rich region in the A. aegypti genome is related to the flamenco locus. (A) Zoomed-in view of the shaded area in chromosome 2 corresponding to cluster 38 indicating EVE, gene and TE content per strand. Middle graphs show the density of transcripts and small RNAs considering single and multiple mapped reads. Bottom graph shows gap occupancy of small RNA coverage over the entire region. The dashed line represents a significance cutoff of P = 0.05 that the gap occurred by chance. Significant gaps are shown. (B) Correlation between production of long and small RNAs for each element within cluster 38. Each dot represents one element with the type (EVEs or TEs) and length indicated by colors and size of the symbol, respectively. (C,D) Size distribution (C) and base preferences (D) for EVEs and TEs within EVE cluster 38. (E) Relative frequency of distances between 3′ and 5′ ends of piRNAs derived from the same genomic strand within EVE cluster 38 in mosquitoes. (F) Nucleotide composition of the genomic neighborhood of small RNA 3′ ends. (G) Distance between 5′ ends of small RNAs in different strands for EVEs and TEs within EVE cluster 38. (H) Genomic context of promoter region of the flamenco locus and EVE cluster 38 in A. aegypti. Small RNAs between 24 and 29 nt were used for the analyses in B–F. RNA libraries from whole mosquitoes and flies were used in this analysis.