From: Charles Date: Fri, 16 Jul 2021 04:17:58 +0000 (+0900) Subject: Café X-Git-Url: https://source.charles.plessy.org/?a=commitdiff_plain;h=23af596a306015669c36da8eb6d93dd5b63543a1;p=source.git Café --- diff --git a/biblio/33963409.mdwn b/biblio/33963409.mdwn new file mode 100644 index 00000000..219e4217 --- /dev/null +++ b/biblio/33963409.mdwn @@ -0,0 +1,12 @@ +[[!meta title="Locally adaptive inversions modulate genetic variation at different geographic scales in a seaweed fly"]] +[[!tag variants genome]] + +Mérot C, Berdan E, Cayuela H, Djambazian H, Ferchaud AL, Laporte M, Normandeau E, Ragoussis J, Wellenreuther M, Bernatchez L. + +Mol Biol Evol. 2021 May 7:msab143. doi:10.1093/molbev/msab143 + +Locally adaptive inversions modulate genetic variation at different geographic scales in a seaweed fly. + +[[!pmid 33963409 desc="Chromosomal assembly of Coelopa frigida. SNP analysis and PCA revealed known and candidate genomic inversions."]] + +“We sampled the seaweed fly _Coelopa frigida_ along a bioclimatic gradient stretching across 10° of latitude, a salinity gradient and a range of heterogeneous, patchy habitats. We generated a chromosome-level genome assembly to analyse 1,446 low-coverage whole genomes collected along those gradients.“ “Analyses of more than 1,400 whole genomes of _C. frigida_ flies revealed four large chromosomal inversions affecting a large fraction of the genome (36.1Mb, 15%), and three low recombining genomic regions.” “Among the 124,701 candidate SNPs identified by the GWAS, more than 99.8% were located in Cf-Inv(1)” “At a finer geographic scale, outlier SNPs associated with wrackbed abiotic characteristics (depth, temperature and salinity) were strongly enriched in the inverted region Cf-Inv(1) with an odds ratio of 5, including outliers with very strong support” diff --git a/tags/variants.mdwn b/tags/variants.mdwn index 864be2d8..6eb4f28c 100644 --- a/tags/variants.mdwn +++ b/tags/variants.mdwn @@ -5,6 +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]]. +SNP analysis in >1400 seaweed flies identified known and candidate genomic inversions +([[Mérot and coll, 2021|biblio/33963409]]). + ### Software - _NanoSV_ ([[Cretu Stancu and coll., 2017|biblio/29109544]]) uses nanopore long