Encore plus de café

diff --git a/biblio/31601616.mdwn b/biblio/31601616.mdwn
index a96cc4fe67d7bbf7a654e16c44cab5e7bfa26290..1afde776fd0abe607127501b77e9d0c56218ede3 100644 (file)
--- a/biblio/31601616.mdwn
+++ b/biblio/31601616.mdwn
@@ -8,3 +8,17 @@ 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.
 
 [[!pmid 31601616 desc="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.”

diff --git a/tags/Drosophila.mdwn b/tags/Drosophila.mdwn
index b48f6760fe4e531eae1749c0120d416a8199e4b6..9445f4848438fac6c34d85699a2080e27bedde7a 100644 (file)
--- a/tags/Drosophila.mdwn
+++ b/tags/Drosophila.mdwn
@@ -18,6 +18,9 @@ year ([[Schlötterer and coll., 1994|biblio/8015444]]).
 12 Drosophila genomes were sequenced and compared by the [[Drosophila 12
 Genomes Consortium (2007)|biblio/17994087]].
 
+Hi-C scaffolding and genome comparison between _D. virilis_ and _D. buskii_ shows
+one synteny break every 6 genes in average ([[Renschler and coll., 2019|biblio/31601616]]).
+
 See also [[Muller elements|muller_element]].
 
 [[!inline pages="tagged(Drosophila)" limit=0]]

diff --git a/tags/synteny.mdwn b/tags/synteny.mdwn
index 7877f2c53ca80523dcbef11f3686cff53f2f3b7c..296a3a30d43d7ed69d86241feb4b8c4dc79839e6 100644 (file)
--- a/tags/synteny.mdwn
+++ b/tags/synteny.mdwn
@@ -14,7 +14,8 @@ distribution follows a power law and explain it with a model that requires
 breakpoints to be in open regions (ENCODE) interacting with each other (Hi-C).
 
 [[Renschler and coll. (2019)|biblio/31601616]] found 20 synteny breakpoints
-(SB) per Mb on average. “Approximately 75% of SBs stay within the A or B
+(SB) per Mb on average (1 every 6 gene) when comparing _D. virilis_ and _D. buskii_,
+which are ~40 MY apart.  “Approximately 75% of SBs stay within the A or B
 compartment”  “Overlaps of TAD boundaries and SB breakpoints in all comparisons
 are highly significant”