Renschler G, Richard G, Valsecchi CIK, Toscano S, Arrigoni L, Ramírez F, Akhtar A.

Genes Dev. 2019 Oct 10. doi: 10.1101/gad.328971.119

Hi-C guided assemblies reveal conserved regulatory topologies on X and autosomes despite extensive genome shuffling.

Found 20 synteny breakpoints (SB) per Mb on average. “Approximately 75% of SBs stay within the A or B compartment” “Overlaps of TAD boundaries and SB breakpoints in all comparisons are highly significant”

“Hi-C data of D. melanogaster, D. virilis, and D. busckii embryos”

“D. virilis and D. busckii [...] cover ∼40 million years of evolution and multiple subgenera (Russo et al. 2013).”

“conserved sequences mostly reside on the same chromosomal arms”

“we defined synteny blocks (SBs), which are chains of conserved collinear regions that are used to identify and compare homologous regions between different species. On average, we find 20 synteny breakpoints per megabase (3726 and 3252 breakpoints in the D. melanogaster vs. D. virilis comparison, respectively, and 3340 and 2776 breakpoints in the D. melanogaster vs. D. busckii comparison, respectively), corresponding to about one breakpoint every six genes.”

“Approximately 75% of SBs stay within the A or B compartment and 25% switch between compartments. In general, about double the number of SBs lie within the A compartment than the B compartment.”

“many SB breakpoints overlap with TAD boundaries”

“To identify synteny blocks (SBs) we use LASTZ (Harris 2007) with the following parameters: “–gfextend –nochain –gapped,” which identifies local alignment blocks. We then chained blocks that are within 10-kb distance, have the same orientation, and contain at least four LASTZ-defined blocks. Chained results that were <4 kb or completely overlapped a bigger synteny block were removed.”