Reorganise avec du café

diff --git a/tags/variants.mdwn b/tags/variants.mdwn
index dc41893b0bc1d846c8ce21059845aa70ddb9ca49..65fbf91b7649dca7c483fd48c347efb9ae29893a 100644 (file)
--- a/tags/variants.mdwn
+++ b/tags/variants.mdwn
@@ -5,7 +5,9 @@ _in progress_
 Long read sequencing data from 3,622 Icelanders identified a median of 22,636
 SVs per individual (insertios: 13,353; deletions: 9,474) [[Beyter and coll, 2021|biblio/33972781]].
 
-### Inversions
+## Inversions
+
+### Within-population
 
 SNP analysis in >1400 seaweed flies identified known and candidate genomic inversions
 ([[Mérot and coll, 2021|biblio/33963409]]).
@@ -14,6 +16,15 @@ SV analysis of 31 diploid assemblies of _Theobroma cacao_ showed relaxed
 selection and increased genetic load in inversions and other types of variants
 [[Hämälä and coll., 2021|biblio/34408075]].
 
+[[Stefansson and coll, 2005||biblio/15654335]] found an inversion in the human
+genome and calculated that it appeared ~3 million years ago, before the
+speciation of _Homo sapiens_.  Low-copy repeated sequences were found in the
+vicinity.  [[Donelly and coll., 2010|biblio/20116045]] gave a radically lower
+time estimate of 13,600 to 108,400 years, but an ancient origin was again
+supported by [[Steinberg and coll in 2012|biblio/22751100]].
+
+### Between-species
+
 ~1100 small-scale inversions are estimated to have happened between _S.
 cerevisiae_ and _C. albicans_ ([[Seoighe and coll., 2000|biblio/11087826]]).  The authors propose that
 “successive multigene inversions” have “distrupted” the “precise arrangement”
@@ -36,16 +47,6 @@ isochromatid or chromatid, and that this, rather than ectopic exchange between
 inverted repetitive sequences, is the prevalent mechanism for the generation of
 inversions in the melanogaster species group”. 
 
-[[Stefansson and coll, 2005||biblio/15654335]] found an inversion in the human
-genome and calculated that it appeared ~3 million years ago, before the
-speciation of _Homo sapiens_.  Low-copy repeated sequences were found in the
-vicinity.  [[Donelly and coll., 2010|biblio/20116045]] gave a radically lower
-time estimate of 13,600 to 108,400 years, but an ancient origin was again
-supported by [[Steinberg and coll in 2012|biblio/22751100]].
-
-Ectopic recombination of a Galileo element may have caused a recent large-scale
-inversion in _D. buzzati_ ([[Delprat and coll, 2009|biblio/19936241]]).
-
 Flanking an inversion in _D. buzzati_ between two _Galileo_ elements, the
 exchange of Target-Site Duplication sequences was observed by Cáceres and
 coll., [[(1999|biblio/10411506]]). 
@@ -53,7 +54,16 @@ coll., [[(1999|biblio/10411506]]).
 [[Kent and coll., 2003|biblio/14500911]] reported 2 inversions per Mbp in
 human/mouse comparisons, median length 814. 
 
-### Software
+### Mechanism
+
+_Staggered breaks_ ([[Ranz and coll., 2007|bilbio/17550304]]) caused
+by inverted duplications.  The duplicated sequnces may be coding genes or
+pseudogenes, not just transposable elements.
+
+Ectopic recombination of a Galileo element may have caused a recent large-scale
+inversion in _D. buzzati_ ([[Delprat and coll, 2009|biblio/19936241]]).
+
+## Software
 
  - _NanoSV_ ([[Cretu Stancu and coll., 2017|biblio/29109544]]) uses nanopore long
    reads aligned to a reference genome with last-split