From: Charles Plessy Date: Tue, 7 Feb 2023 05:03:29 +0000 (+0900) Subject: Reorganise avec du café X-Git-Url: https://source.charles.plessy.org/?a=commitdiff_plain;h=31a082aa67cc165731be6b9c9f20ed62024f343f;p=source%2F.git Reorganise avec du café --- diff --git a/tags/variants.mdwn b/tags/variants.mdwn index dc41893b..65fbf91b 100644 --- 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