| 1. |
- Höök, Lars, et al.
(författare)
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High-density linkage maps and chromosome level genome assemblies unveil direction and frequency of extensive structural rearrangements in wood white butterflies (Leptidea spp.)
- 2023
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Ingår i: Chromosome Research. - : Springer Science and Business Media LLC. - 0967-3849 .- 1573-6849. ; 31:1
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Tidskriftsartikel (refereegranskat)abstract
- Karyotypes are generally conserved between closely related species and large chromosome rearrangements typically have negative fitness consequences in heterozygotes, potentially driving speciation. In the order Lepidoptera, most investigated species have the ancestral karyotype and gene synteny is often conserved across deep divergence, although examples of extensive genome reshuffling have recently been demonstrated. The genus Leptidea has an unusual level of chromosome variation and rearranged sex chromosomes, but the extent of restructuring across the rest of the genome is so far unknown. To explore the genomes of the wood white (Leptidea) species complex, we generated eight genome assemblies using a combination of 10X linked reads and HiC data, and improved them using linkage maps for two populations of the common wood white (L. sinapis) with distinct karyotypes. Synteny analysis revealed an extensive amount of rearrangements, both compared to the ancestral karyotype and between the Leptidea species, where only one of the three Z chromosomes was conserved across all comparisons. Most restructuring was explained by fissions and fusions, while translocations appear relatively rare. We further detected several examples of segregating rearrangement polymorphisms supporting a highly dynamic genome evolution in this clade. Fusion breakpoints were enriched for LINEs and LTR elements, which suggests that ectopic recombination might be an important driver in the formation of new chromosomes. Our results show that chromosome count alone may conceal the extent of genome restructuring and we propose that the amount of genome evolution in Lepidoptera might still be underestimated due to lack of taxonomic sampling.
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| 2. |
- Näsvall, Karin, et al.
(författare)
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Base composition, codon usage and patterns of gene sequence evolution in butterflies.
- 2023
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Ingår i: Genome Biology and Evolution. - : Oxford University Press (OUP). - 1759-6653. ; 15:8
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Tidskriftsartikel (refereegranskat)abstract
- Coding sequence evolution is influenced by both natural selection and neutral evolutionary forces. In many species, the effects of mutation bias, codon usage and GC-biased gene conversion (gBGC) on gene sequence evolution have not been detailed. Quantification of how these forces shape substitution patterns is therefore necessary to understand the strength and direction of natural selection. Here, we used comparative genomics to investigate the association between base composition and codon usage bias on gene sequence evolution in butterflies and moths (Lepidoptera), including an in-depth analysis of underlying patterns and processes in one species, Leptidea sinapis. The data revealed significant G/C to A/T substitution bias at third codon position with some variation in the strength among different butterfly lineages. However, the substitution bias was lower than expected from previously estimated mutation rate ratios, partly due to the influence of gBGC. We found that A/T-ending codons were overrepresented in most species and there was a negative association between the magnitude of codon usage bias and GC-content in third codon positions. In contrast, the tRNA-gene population in L. sinapis showed higher GC-content at third codon positions compared to coding sequences in general and less overrepresentation of A/T-ending codons. There was an inverse relationship between synonymous substitutions and codon usage bias indicating selection on synonymous sites. We conclude that the evolutionary rate in Lepidoptera is affected by a complex interaction between underlying G/C -> A/T mutation bias and partly counteracting fixation biases, predominantly conferred by overall purifying selection, gBGC and selection on codon usage.
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| 3. |
- Näsvall, Karin, et al.
(författare)
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Nascent evolution of recombination rate differences as a consequence of chromosomal rearrangements
- 2023
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Ingår i: PLOS Genetics. - : Public Library of Science (PLoS). - 1553-7390 .- 1553-7404. ; 19:8
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Tidskriftsartikel (refereegranskat)abstract
- Reshuffling of genetic variation occurs both by independent assortment of chromosomes and by homologous recombination. Such reshuffling can generate novel allele combinations and break linkage between advantageous and deleterious variants which increases both the potential and the efficacy of natural selection. Here we used high-density linkage maps to characterize global and regional recombination rate variation in two populations of the wood white butterfly (Leptidea sinapis) that differ considerably in their karyotype as a consequence of at least 27 chromosome fissions and fusions. The recombination data were compared to estimates of genetic diversity and measures of selection to assess the relationship between chromosomal rearrangements, crossing over, maintenance of genetic diversity and adaptation. Our data show that the recombination rate is influenced by both chromosome size and number, but that the difference in the number of crossovers between karyotypes is reduced as a consequence of a higher frequency of double crossovers in larger chromosomes. As expected from effects of selection on linked sites, we observed an overall positive association between recombination rate and genetic diversity in both populations. Our results also revealed a significant effect of chromosomal rearrangements on the rate of intergenic diversity change between populations, but limited effects on polymorphisms in coding sequence. We conclude that chromosomal rearrangements can have considerable effects on the recombination landscape and consequently influence both maintenance of genetic diversity and efficiency of selection in natural populations.
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| 4. |
- Näsvall, Karin, 1974-
(författare)
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Rates and patterns of genome evolution in Lepidoptera
- 2023
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- The evolutionary consequences of genome restructuring and chromosomal rearrangements can be significant, but the underlying mechanisms are poorly understood. This thesis explores the relationships between genome restructuring, recombination, and maintenance of genetic diversity in different butterfly species. I also investigate the genetic underpinnings of different types of adaptations in two butterfly species with distinct life-history characteristics and adaptations. In Chapter I, whole genome alignments and linkage maps were used to characterize inter- and intra-specific chromosomal rearrangements in wood white butterflies (Leptidea spp.), revealing extensive reorganization of the chromosomes predominantly driven by fusions and fissions. Several fusion-fission polymorphisms were found segregating within populations, confirming the dynamic and ongoing process of karyotype evolution. In Chapter II, I used the linkage map information to show that chromosomal rearrangements have had considerable effects on the recombination landscape and maintenance of genetic diversity. Chapter III presents a detailed annotation of the genome of a long-distance migrant, the painted lady butterfly (Vanessa cardui). The annotation was used to identify expanded gene families, providing insight into the genetic underpinnings of this unique life-history. Here, I also developed linkage maps confirming a well-preserved karyotype in this species and showed that chromosome size is a major determinant of the recombination landscape. In Chapter IV, I explored the relationship between nucleotide composition, codon usage, and substitution rates across multiple Lepidoptera species, in an attempt to disentangle the relative effects of natural selection and neutral evolutionary forces on gene sequence evolution. The final two chapters focus on understanding the genetic basis of key adaptive traits in butterflies. Specifically, in Chapter V, I investigated potential local adaption in Leptidea sinapis by studying how host plant switch is associated with oviposition rates, larval growth and development, gene expression, and microbiome composition in populations experiencing different environmental conditions. In Chapter VI, I assessed the differential activation of regulatory elements in V. cardui females in response to host plant availability, which together with the gene family analysis in Chapter III, resulted in a set of candidate genes potentially associated with a migratory lifestyle. In conclusion, I have explored the complex interplay between proximate mechanisms and evolutionary forces shaping the genome structure and levels of genetic variation. I also investigated the genetic and regulatory underpinnings of adaptive traits in different butterfly species. In addition, I provided resources including chromosome-level genome assemblies, recombination maps, and annotations that will contribute to our understanding of evolutionary processes in general.
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| 5. |
- Palahi i Torres, Aleix, et al.
(författare)
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The fine-scale recombination rate variation and associations with genomic features in a butterfly
- 2023
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Ingår i: Genome Research. - : Cold Spring Harbor Laboratory. - 1088-9051 .- 1549-5469. ; 33:5, s. 810-823
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Tidskriftsartikel (refereegranskat)abstract
- Recombination is a key molecular mechanism that has profound implications on both micro- and macroevolutionary processes. However, the determinants of recombination rate variation in holocentric organisms are poorly understood, in particular in Lepidoptera (moths and butterflies). The wood white butterfly (Leptidea sinapis) shows considerable intraspecific variation in chromosome numbers and is a suitable system for studying regional recombination rate variation and its potential molecular underpinnings. Here, we developed a large whole-genome resequencing data set from a population of wood whites to obtain high-resolution recombination maps using linkage disequilibrium information. The analyses revealed that larger chromosomes had a bimodal recombination landscape, potentially caused by interference between simultaneous chiasmata. The recombination rate was significantly lower in subtelomeric regions, with exceptions associated with segregating chromosome rearrangements, showing that fissions and fusions can have considerable effects on the recombination landscape. There was no association between the inferred recombination rate and base composition, supporting a limited influence of GC-biased gene conversion in butterflies. We found significant but variable associations between the recombination rate and the density of different classes of transposable elements, most notably a significant enrichment of short interspersed nucleotide elements in genomic regions with higher recombination rate. Finally, the analyses unveiled significant enrichment of genes involved in farnesyltranstransferase activity in recombination coldspots, potentially indicating that expression of transferases can inhibit formation of chiasmata during meiotic division. Our results provide novel information about recombination rate variation in holocentric organisms and have particular implications for forthcoming research in population genetics, molecular/genome evolution, and speciation.
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| 6. |
- Ringblom, Christian, et al.
(författare)
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No reduction in parastomal hernia rate 3 years after stoma construction with prophylactic mesh : Three-year follow-up results from stomamesh-a multicenter double-blind randomized controlled trial
- 2023
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Ingår i: Annals of Surgery. - : Wolters Kluwer. - 0003-4932 .- 1528-1140. ; 277:1, s. 38-42
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Tidskriftsartikel (refereegranskat)abstract
- OBJECTIVE: The primary objective was to compare rates of parastomal hernia (PSH) 3 years after stoma construction with prophylactic mesh or no mesh. A secondary objective was to compare complications requiring reintervention within 3 years.BACKGROUND: Recent studies have shown that a prophylactic mesh does not reduce the rate of PSH contrary to older studies. Long-term data on efficacy and safety is however scarce.METHODS: A randomized controlled double-blind multicenter trial. Patients planned for permanent end colostomy were randomized to either prophylactic mesh in the retromuscular position around the stoma site or no mesh. They were evaluated for PSH clinically and with computed tomography (CT) 3 years after stoma construction. Medical records of all patients included were also reviewed at 3 years to detect any abdominal or abdominal wall surgery during that period.RESULTS: A total of 232 patients were randomized. At 3 years, 154 patients were available for clinical evaluation and 137 underwent a CT scan. No significant difference in PSH rates was seen between the treatment allocation arms (clinical: P=0.829 and CT: P=0.761, respectively), nor was there a significant difference in the number of reinterventions, but 2 patients had their mesh removed at emergency surgery.CONCLUSIONS: Prophylactic mesh does not reduce the rate of PSH and cannot be recommended for routine use.
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