From 671a4a662bc9277a4d033d08185c2e033acd7e0f Mon Sep 17 00:00:00 2001 From: Charles Date: Tue, 21 Sep 2021 12:51:32 +0900 Subject: [PATCH] =?utf8?q?Caf=C3=A9?= MIME-Version: 1.0 Content-Type: text/plain; charset=utf8 Content-Transfer-Encoding: 8bit --- biblio/34408075.mdwn | 10 ++++++++++ tags/variants.mdwn | 4 ++++ 2 files changed, 14 insertions(+) create mode 100644 biblio/34408075.mdwn diff --git a/biblio/34408075.mdwn b/biblio/34408075.mdwn new file mode 100644 index 00000000..731289c6 --- /dev/null +++ b/biblio/34408075.mdwn @@ -0,0 +1,10 @@ +[[!meta title="Genomic structural variants constrain and facilitate adaptation in natural populations of Theobroma cacao, the chocolate tree."]] +[[!tag haplotype variants]] + +Hämälä T, Wafula EK, Guiltinan MJ, Ralph PE, dePamphilis CW, Tiffin P. + +Proc Natl Acad Sci U S A. 2021 Aug 31;118(35):e2102914118. doi:10.1073/pnas.2102914118 + +Genomic structural variants constrain and facilitate adaptation in natural populations of Theobroma cacao, the chocolate tree. + +[[!pmid 34408075 desc="31 × 2 haplotype assemblies using Illumina and 10x Genomics linked reads. dN/dS (interspecies) and πN/πS (intraspecies) values in SVs are higher than expectation and vary according the type of SV and the proximity to the SV's breakpoints. Genes with allele-specific expression were over-represented at heterozygous inversions. Genetic load is higher at inversions, as expected if they suppress recombination."]] diff --git a/tags/variants.mdwn b/tags/variants.mdwn index 6eb4f28c..a4ea2c03 100644 --- a/tags/variants.mdwn +++ b/tags/variants.mdwn @@ -8,6 +8,10 @@ SVs per individual (insertios: 13,353; deletions: 9,474) [[Beyter and coll, 2021 SNP analysis in >1400 seaweed flies identified known and candidate genomic inversions ([[Mérot and coll, 2021|biblio/33963409]]). +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]]. + ### Software - _NanoSV_ ([[Cretu Stancu and coll., 2017|biblio/29109544]]) uses nanopore long -- 2.47.3