| 1. |
- Dawson, Deborah A., et al.
(författare)
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Gene order and recombination rate in homologous chromosome regions of the chicken and a passerine bird
- 2007
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Ingår i: Molecular biology and evolution. - : Oxford University Press (OUP). - 0737-4038 .- 1537-1719. ; 24:7, s. 1537-1552
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Tidskriftsartikel (refereegranskat)abstract
- Genome structure has been found to be highly conserved between distantly related birds and recent data for a limited part of the genome suggest that this is true also for the gene order (synteny) within chromosomes. Here, we confirm that synteny is maintained for large chromosomal regions in chicken and a passerine bird, the great reed warbler Acrocephalus arundinaceus, with few rearrangements, but in contrast show that the recombination-based linkage map distances differ substantially between these species. We assigned a chromosomal location based on sequence similarity to the chicken genome sequence to a set of inicrosatellite loci mapped in a pedigree of great reed warblers. We detected homologous loci on 14 different chromosomes corresponding to chicken chromosomes Gga1-5, 7-9, 13, 19, 20, 24, 25, and Z. It is known that 2 passerine macrochromosomes correspond to the chicken chromosome Gga1. Homology of 2 different great reed warbler linkage groups (LG13 and LG5) to Gga1 allowed us to locate the split to a position between 20.8 and 84.8 Mb on Gga1. Data from the 5 chromosomal regions (on Gga1, 2, 3, 5, and Z) with 3 or more homologous loci showed that synteny was conserved with the exception of 2 large previously unreported inversions on Gga1/LG5 and Gga2/LG3, respectively. Recombination data from the 9 chromosomal regions in which we identified 2 or more homologous loci (accounting for the inversions) showed that the linkage map distances in great reed warblers were only 6.3% and 13.3% of those in chickens for males and females, respectively. This is likely to reflect the true interspecific difference in recombination rate because our markers were not located in potentially low-recombining regions: several linkage groups covered a substantial part of their corresponding chicken chromosomes and were not restricted to centromeres. We conclude that recombination rates may differ strongly between bird species with highly conserved genome structure and synteny and that the chicken linkage map may not be suitable, in terms of genetic distances, as a model for all bird species.
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| 2. |
- Menzel, Mandy, et al.
(författare)
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Inbreeding Affects Gene Expression Differently in Two Self-Incompatible Arabidopsis lyrata Populations with Similar Levels of Inbreeding Depression
- 2015
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Ingår i: Molecular biology and evolution. - : Oxford University Press (OUP). - 0737-4038 .- 1537-1719. ; 32:8, s. 2036-2047
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Tidskriftsartikel (refereegranskat)abstract
- Knowledge of which genes and pathways are affected by inbreeding may help understanding the genetic basis of inbreeding depression, the potential for purging (selection against deleterious recessive alleles), and the transition from outcrossing to selfing. Arabidopsis lyrata is a predominantly self-incompatible perennial plant, closely related to the selfing model species A. thaliana. To examine how inbreeding affects gene expression, we compared the transcriptome of experimentally selfed and outcrossed A. lyrata originating from two Scandinavian populations that express similar inbreeding depression for fitness ((partial derivative approximate to 0.80). The number of genes significantly differentially expressed between selfed and outcrossed individuals were 2.5 times higher in the Norwegian population (approximate to 500 genes) than in the Swedish population (approximate to 200 genes). In both populations, a majority of genes were upregulated on selfing (approximate to 80%). Functional annotation analysis of the differentially expressed genes showed that selfed offspring were characterized by 1) upregulation of stress-related genes in both populations and 2) upregulation of photosynthesis-related genes in Sweden but downregulation in Norway. Moreover, we found that reproduction-and pollination-related genes were affected by inbreeding only in Norway. We conclude that inbreeding causes both general and population-specific effects. The observed common effects suggest that inbreeding generally upregulates rather than downregulates gene expression and affects genes associated with stress response and general metabolic activity. Population differences in the number of affected genes and in effects on the expression of photosynthesis-related genes show that the genetic basis of inbreeding depression can differ between populations with very similar levels of inbreeding depression.
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| 3. |
- Pala, Irene, et al.
(författare)
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Patterns of molecular evolution of an avian neo-sex chromosome.
- 2012
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Ingår i: Molecular biology and evolution. - : Oxford University Press (OUP). - 0737-4038 .- 1537-1719. ; 29:12, s. 3741-3754
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Tidskriftsartikel (refereegranskat)abstract
- Newer parts of sex chromosomes, neo-sex chromosomes, offer unique possibilities for studying gene degeneration and sequence evolution in response to loss of recombination and population size decrease. We have recently described a neo-sex chromosome system in Sylvioidea passerines that has resulted from a fusion between the first half (10 Mb) of chromosome 4a and the ancestral sex chromosomes. In the present study, we report the results of molecular analyses of neo-Z and neo-W gametologues and intronic parts of neo-Z and autosomal genes on the second half of chromosome 4a in three species within different Sylvioidea lineages (Acrocephalidea, Timaliidae and Alaudidae). In line with hypotheses of neo-sex chromosome evolution, we observe (i) lower genetic diversity of neo-Z genes comparatively to autosomal genes, (ii) moderate synonymous and weak non-synonymous sequence divergence between neo-Z and the neo-W gametologues and (iii) lower GC content on neo-W than on neo-Z gametologues. Phylogenetic reconstruction of eight neo-Z and neo-W gametologues suggests that recombination continued after the split of Alaudidae from the rest of the Sylvioidea lineages (i.e. after approximately 42.2 MYA) and with some exceptions also after the split of Acrocephalidea and Timaliidae (i.e. after approximately 39.4 36 MYA). The Sylvioidea neo-sex chromosome shares classical evolutionary features with the ancestral sex chromosomes, but as expected from its more recent origin shows weaker divergence between gametologues.
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| 4. |
- Sigeman, Hanna, et al.
(författare)
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Avian Neo-Sex Chromosomes Reveal Dynamics of Recombination Suppression and W Degeneration
- 2021
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Ingår i: Molecular biology and evolution. - : Oxford University Press. - 0737-4038 .- 1537-1719. ; 38:12, s. 5275-5291
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Tidskriftsartikel (refereegranskat)abstract
- How the avian sex chromosomes first evolved from autosomes remains elusive as 100 million years (My) of divergence and degeneration obscure their evolutionary history. The Sylvioidea group of songbirds is interesting for understanding avian sex chromosome evolution because a chromosome fusion event similar to 24 Ma formed "neo-sex chromosomes" consisting of an added (new) and an ancestral (old) part. Here, we report the complete female genome (ZW) of one Sylvioidea species, the great reed warbler (Acrocephalus arundinaceus). Our long-read assembly shows that the added region has been translocated to both Z and W, and whereas the added-Z has retained its gene order the added-W part has been heavily rearranged. Phylogenetic analyses show that recombination between the homologous added-Z and -W regions continued after the fusion event, and that recombination suppression across this region took several million years to be completed. Moreover, recombination suppression was initiated across multiple positions over the added-Z, which is not consistent with a simple linear progression starting from the fusion point. As expected following recombination suppression, the added-W show signs of degeneration including repeat accumulation and gene loss. Finally, we present evidence for nonrandom maintenance of slowly evolving and dosage-sensitive genes on both ancestral- and added-W, a process causing correlated evolution among orthologous genes across broad taxonomic groups, regardless of sex linkage.
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| 5. |
- Videvall, Elin, et al.
(författare)
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Strong Maternal Effects on Gene Expression in Arabidopsis lyrata Hybrids
- 2016
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Ingår i: Molecular biology and evolution. - : Oxford University Press (OUP). - 0737-4038 .- 1537-1719. ; 33:4, s. 984-994
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Tidskriftsartikel (refereegranskat)abstract
- Hybridization between populations or species can have pronounced fitness consequences. Yet little is known about how hybridization affects gene regulation. Three main models have been put forward to explain gene expression patterns in hybrids: additive, dominance, or parental effects. Here, we use high throughput RNA-sequencing to examine the extent to which hybrid gene expression follows predictions by each of the three models. We performed a reciprocal crossing experiment between two differentiated populations of the perennial herb Arabidopsis lyrata and sequenced RNA in rosette leaves of 12-week-old plants grown in greenhouse conditions. The two parental populations had highly differentiated gene expression patterns. In hybrids, a majority of genes showed intermediate expression relative to that of their parental populations (i.e., additive effects), but expression was frequently more similar to the maternal than to their paternal population (i.e., maternal effects). Allele-specific expression analyses showed that in the vast majority of cases, genes with pronounced maternal effect expressed both the maternal and the paternal allele. Maternal effects on hybrid gene expression have rarely been documented previously and our study suggests it could be more common than previously assumed. Whether the maternal effect on gene expression persists to later life-stages, and whether the variation in gene expression is manifested in other aspects of the phenotype, remain to be elucidated. Our findings are relevant for understanding the consequences of outbreeding and hybridization and open up several questions for future studies.
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