From c215707bc2263790f18d3d3125235f2d9401251e Mon Sep 17 00:00:00 2001 From: Charles Date: Mon, 2 Aug 2021 15:03:17 +0900 Subject: [PATCH] =?utf8?q?Encore=20plus=20de=20caf=C3=A9?= MIME-Version: 1.0 Content-Type: text/plain; charset=utf8 Content-Transfer-Encoding: 8bit --- biblio/31601616.mdwn | 14 ++++++++++++++ tags/Drosophila.mdwn | 3 +++ tags/synteny.mdwn | 3 ++- 3 files changed, 19 insertions(+), 1 deletion(-) diff --git a/biblio/31601616.mdwn b/biblio/31601616.mdwn index a96cc4fe..1afde776 100644 --- 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 b48f6760..9445f484 100644 --- 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 7877f2c5..296a3a30 100644 --- 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” -- 2.47.3