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Unlike PIWI-interacting RNA (piRNA) in other species that mostly target transposable elements (TEs), >80% of piRNAs in adult mammalian testes lack obvious targets. However, mammalian piRNA sequences and piRNA-producing loci evolve more rapidly than the rest of the genome for unknown reasons. Here, through comparative studies of chickens, ducks, mice, and humans, as well as long-read nanopore sequencing on diverse chicken breeds, we find that piRNA loci across amniotes experience: (1) a high local mutation rate of structural variations (SVs, mutations ≥ 50 bp in size); (2) positive selection to suppress young and actively mobilizing TEs commencing at the pachytene stage of meiosis during germ cell development; and (3) negative selection to purge deleterious SV hotspots. Our results indicate that genetic instability at pachytene piRNA loci, while producing certain pathogenic SVs, also protects genome integrity against TE mobilization by driving the formation of rapid-evolving piRNA sequences., (© 2023. The Author(s).)

Bird whole-genome alignments. a Alignment of chicken to zebra finch [Rhie et al., 2021], Anna's hummingbird [Rhie et al., 2021], superb fairywren [Penalba et al., 2020], and the ancestral emu genome [Liu J et al., 2021]. b Alignment of the chicken genome to species that have undergone significant chromosome rearrangement: saker falcon, California condor [Robinson et al., 2021], and golden eagle [Mead et al., 2021]. The Bird 10,000 Genomes (B10K) Project [Zhang et al., 2015] has generated insightful results and the future bird T2T genome and pan-genome will undoubtedly reveal more genes. The chicken genome aligns very well with the emu genome, which is considered to represent the ancestral bird genome [Liu J et al., 2021]. Chicken as a Model for Bird Genome Alignments (Prepared by P.D. Waters, J.A.M. Graves, and H.R. Patel) Chicken has long been a model for bird genomes [International Chicken Genome Sequencing Consortium, 2004], but it is only in recent years that a chromosome-level assembly has been available that includes the gene-dense microchromosomes. The GC content of most of these "missing" genes is more than 60%, and few genes even have over 80% (the median GC content of the chicken genome is 42.22% and the median GC content of the duck genome is 41.99%) [Hron et al., 2015; Bornelov et al., 2017; Botero-Castro et al., 2017; Yin et al., 2019b]. [Extracted from the article]