Journal ArticleDOI
Genomic structural variants constrain and facilitate adaptation in natural populations of Theobroma cacao, the chocolate tree.
Tuomas Hämälä,Eric K. Wafula,Mark J. Guiltinan,Paula E. Ralph,Claude W. dePamphilis,Peter Tiffin +5 more
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TLDR
It is found that most SVs are deleterious and thus constrain adaptation in natural populations of Theobroma cacao, and empirical support is provided for a theoretical prediction that SVs, particularly inversions, increase genetic load through the accumulation of deleteriously nucleotide variants as a result of suppressed recombination.Abstract:
Genomic structural variants (SVs) can play important roles in adaptation and speciation. Yet the overall fitness effects of SVs are poorly understood, partly because accurate population-level identification of SVs requires multiple high-quality genome assemblies. Here, we use 31 chromosome-scale, haplotype-resolved genome assemblies of Theobroma cacao—an outcrossing, long-lived tree species that is the source of chocolate—to investigate the fitness consequences of SVs in natural populations. Among the 31 accessions, we find over 160,000 SVs, which together cover eight times more of the genome than single-nucleotide polymorphisms and short indels (125 versus 15 Mb). Our results indicate that a vast majority of these SVs are deleterious: they segregate at low frequencies and are depleted from functional regions of the genome. We show that SVs influence gene expression, which likely impairs gene function and contributes to the detrimental effects of SVs. We also provide empirical support for a theoretical prediction that SVs, particularly inversions, increase genetic load through the accumulation of deleterious nucleotide variants as a result of suppressed recombination. Despite the overall detrimental effects, we identify individual SVs bearing signatures of local adaptation, several of which are associated with genes differentially expressed between populations. Genes involved in pathogen resistance are strongly enriched among these candidates, highlighting the contribution of SVs to this important local adaptation trait. Beyond revealing empirical evidence for the evolutionary importance of SVs, these 31 de novo assemblies provide a valuable resource for genetic and breeding studies in T. cacao.read more
Citations
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Identification of a Functional Transposon Insertion in the Maize Domestication Gene tb1
TL;DR: This paper showed that a transposable element (Hopscotch) inserted in a regulatory region of the maize domestication gene, teosinte branched1 (tb1), acts as an enhancer of gene expression and partially explains the increased apical dominance in maize compared to its progenitor.
Journal ArticleDOI
Sheltering of deleterious mutations explains the stepwise extension of recombination suppression on sex chromosomes and other supergenes
TL;DR: It is shown here, by mathematical modeling and stochastic simulation, that recombination suppression on sex chromosomes and around supergenes can expand under a wide range of parameter values simply because it shelters recessive deleterious mutations, which are ubiquitous in genomes.
Journal ArticleDOI
Genome assembly, structural variants, and genetic differentiation between Lake Whitefish young species pairs (Coregonus sp.) with long and short reads
Claire Mérot,Kristina Severine Rudskjær Stenløkk,Clare J. Venney,Martin Laporte,Michel Moser,Eric Normandeau,Mariann Arnyasi,Matthew Peter Kent,Clément Rougeux,Jullien M. Flynn,Sigbjørn Lien,Louis Bernatchez +11 more
TL;DR: Investigating genomic patterns of differentiation between sympatric species pairs belonging to the Lake Whitefish species complex suggests that SVs may play an important role in speciation and that, by combining second and third generation sequencing, the authors now have the ability to integrate SVs into speciation genomics.
Journal ArticleDOI
OUP accepted manuscript
TL;DR: The first chromosome-level genome assembly of Vatica mangachapoi was presented by combining data from PacBio long read sequencing with Hi-C proximity ligation and Illumina short-read sequencing as discussed by the authors .
Journal ArticleDOI
Chromosome-scale assembly with a phased sex-determining region resolves features of early Z and W chromosome differentiation in a wild octoploid strawberry
Caroline M S Cauret,Sebastian M. E. Mortimer,Marcelina C Roberti,Tia-Lynn Ashman,Aaron Liston +4 more
TL;DR: Limited genetic differentiation of the sex chromosomes coupled with structural variation may indicate an early stage of W degeneration, as differences in the pattern of repeats apparently precede sex chromosome differentiation, thus potentially contributing to recombination cessation as opposed to being a consequence of it.
References
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Book
Molecular Evolutionary Genetics
TL;DR: Recent developments of statistical methods in molecular phylogenetics are reviewed and it is shown that the mathematical foundations of these methods are not well established, but computer simulations and empirical data indicate that currently used methods produce reasonably good phylogenetic trees when a sufficiently large number of nucleotides or amino acids are used.
Journal ArticleDOI
A direct approach to false discovery rates
TL;DR: The calculation of the q‐value is discussed, the pFDR analogue of the p‐value, which eliminates the need to set the error rate beforehand as is traditionally done, and can yield an increase of over eight times in power compared with the Benjamini–Hochberg FDR method.
Journal ArticleDOI
Estimation of levels of gene flow from DNA sequence data.
TL;DR: It is found that in general when there is no recombination, the cladistic method performed better than FST while the reverse was true for rates of recombination similar to those found in eukaryotic nuclear genes, although FST performed better for all recombination rates for very low levels of migration.
Journal ArticleDOI
The distribution of fitness effects of new mutations
TL;DR: The distribution of fitness effects (DFE) of new mutations is a fundamental entity in genetics that has implications ranging from the genetic basis of complex disease to the stability of the molecular clock.
Journal ArticleDOI
Chromosomal rearrangements and speciation.
TL;DR: It is argued that rearrangements reduce gene flow more by suppressing recombination and extending the effects of linked isolation genes than by reducing fitness.
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