Rhum raisin

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+[[!meta title="How repeats rearrange chromosomes: The molecular basis of chromosomal inversions in deer mice."]]
+[[!tag mouse variants]]
+
+Gozashti L, Harringmeyer OS, Hoekstra HE.
+
+Cell Rep. 2025 May 27;44(5):115644. doi:10.1016/j.celrep.2025.115644
+
+How repeats rearrange chromosomes: The molecular basis of chromosomal inversions in deer mice.
+
+[[!pmid 40327505 desc="Centromeres based on repeat analysis and methylation calls of PacBio HiFi data.  “at least 14 [inversions] are likely pericentric [...] based on our predicted centromere locations”  “[we] found examples of independently derived inversions sharing the same breakpoint (within 10 kb)”. “We found no evidence for the overrepresentation of LINE or SINE retrotransposons at the breakpoints of megabase-scale inversions [... where we observed ...] a 4-fold increase in SD occupancy with respect to random expectations.”  “We also observed a strong enrichment of PMSat at the breakpoints of large inversions”. “the inversion breakpoints often coincide with contig boundaries from the initial hifi-asm contig-level assemblies”. “highly similar LINE copies [occupy] >1% of the deer mouse genome”.  “9 [large] inversions had PMSat arrays at both breakpoints in at least one of the ancestral or derived haplotypes”"]]

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@@ -91,6 +91,10 @@ on sister chromatids in G2 phase.
 recombination between X and Y chromosomes was low despite the absence of
 large-scale inversions.
 
+In deer mice, [[Gozashti, Harringmeyer and Hoekstra, 2025|biblio/40327505]]
+propose that megabase-scale inversions are caused by structural duplications,
+some of which being centromere-like repeats (possible ancient centromeres).
+
 ## Indels
 
 Indel-seq ([[Min and coll., 2023|biblio/37402370]]) shows insertions at