Café

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+[[!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."]]

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@@ -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