Fig. 3: Identification of a non-syntenic flam-like locus in D. ficusphila. | Nature Communications

Fig. 3: Identification of a non-syntenic flam-like locus in D. ficusphila.

From: Unistrand piRNA clusters are an evolutionarily conserved mechanism to suppress endogenous retroviruses across the Drosophila genus

Fig. 3: Identification of a non-syntenic flam-like locus in D. ficusphila.The alternative text for this image may have been generated using AI.

a Genome-wide detection of flam-like loci in D. ficusphila using a sliding window approach. Predicted LTR content (blue, plus strand; red, minus strand) and total repeat content (grey) is shown across the whole genome (100 kb bins). Arrows indicate the flam-syntenic region, and the de novo identified flamlike1 region. b Genome browser tracks showing D. ficusphila (GCF_018152265 genome) flam-syntenic region (black bar) with transposon annotations by RepeatMasker (RM) and EDTA, and gene annotation by NCBI. Uniquely mapping piRNA (cpm) and total RNA levels (ln(cpm+1)) are presented (green/orange, unique mappers; grey, multi-mappers). Mappability is displayed at the bottom. The pie chart to the right indicates LTR content per strand in the cluster region. c Relative piRNA size distribution of piRNAs mapping sense (light brown) and antisense (dark brown) to D. ficusphila flam-syntenic region. d Ping-pong signature for piRNA pairs mapping onto the flam-syntenic region. e Same as in (b), but for D. ficusphila flamlike1 region (blue bar). f Relative piRNA size distribution of sense (light brown) and antisense (dark brown) piRNAs mapping to D. ficusphila flamlike1 region. g Phasing signature (3’ end to 5’ end distance) for piRNAs mapping onto flamlike1. h Zoom-in on genic region indicating presence of a piRNA cluster in the flam-syntenic region in D. ficusphila. i Macrosynteny plot indicating gene synteny between D. melanogaster and D. ficusphila highlighting flam (red) and flamlike1 (blue). j Zoom-in on genic region indicating the absence of a piRNA cluster in flamlike1-syntenic region in D. melanogaster. Source data are available in the source data file.

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