| 1. |
- Cortazar-Chinarro, Maria, et al.
(författare)
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Antimicrobial peptide and sequence variation along a latitudinal gradient in two anurans
- 2020
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Ingår i: BMC Genetics. - : BMC. - 1471-2156. ; 21:1
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Tidskriftsartikel (refereegranskat)abstract
- Background While there is evidence of both purifying and balancing selection in immune defense genes, large-scale genetic diversity in antimicrobial peptides (AMPs), an important part of the innate immune system released from dermal glands in the skin, has remained uninvestigated. Here we describe genetic diversity at three AMP loci (Temporin, Brevinin and Palustrin) in two ranid frogs (Rana arvalis and R. temporaria) along a 2000 km latitudinal gradient. We amplified and sequenced part of the Acidic Propiece domain and the hypervariable Mature Peptide domain ( 150-200 bp) in the three genes using Illumina Miseq and expected to find decreased AMP genetic variation towards the northern distribution limit of the species similarly to studies on MHC genetic patterns. Results We found multiple loci for each AMP and relatively high gene diversity, but no clear pattern of geographic genetic structure along the latitudinal gradient. We found evidence of trans-specific polymorphism in the two species, indicating a common evolutionary origin of the alleles. Temporin and Brevinin did not form monophyletic clades suggesting that they belong to the same gene family. By implementing codon evolution models we found evidence of strong positive selection acting on the Mature Peptide. We also found evidence of diversifying selection as indicated by divergent allele frequencies among populations and high Theta k values. Conclusion Our results suggest that AMPs are an important source of adaptive diversity, minimizing the chance of microorganisms developing resistance to individual peptides.
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| 2. |
- Jansson, E., et al.
(författare)
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Genome wide analysis reveals genetic divergence between Goldsinny wrasse populations
- 2020
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Ingår i: Bmc Genetics. - : Springer Science and Business Media LLC. - 1471-2156. ; 21:1
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Tidskriftsartikel (refereegranskat)abstract
- Background: Marine fish populations are often characterized by high levels of gene flow and correspondingly low genetic divergence. This presents a challenge to define management units. Goldsinny wrasse (Ctenolabrus rupestris) is a heavily exploited species due to its importance as a cleaner-fish in commercial salmonid aquaculture. However, at the present, the population genetic structure of this species is still largely unresolved. Here, full-genome sequencing was used to produce the first genomic reference for this species, to study population-genomic divergence among four geographically distinct populations, and, to identify informative SNP markers for future studies. Results: After construction of a de novo assembly, the genome was estimated to be highly polymorphic and of similar to 600Mbp in size. 33,235 SNPs were thereafter selected to assess genomic diversity and differentiation among four populations collected from Scandinavia, Scotland, and Spain. GlobalF(ST)among these populations was 0.015-0.092. Approximately 4% of the investigated loci were identified as putative global outliers, and similar to 1% within Scandinavia. SNPs showing large divergence (F-ST > 0.15) were picked as candidate diagnostic markers for population assignment. One hundred seventy-three of the most diagnostic SNPs between the two Scandinavian populations were validated by genotyping 47 individuals from each end of the species' Scandinavian distribution range. Sixty-nine of these SNPs were significantly (p < 0.05) differentiated (meanF(ST_173_loci) = 0.065, F-ST_69_loci = 0.140). Using these validated SNPs, individuals were assigned with high probability (>= 94%) to their populations of origin. Conclusions: Goldsinny wrasse displays a highly polymorphic genome, and substantial population genomic structure. Diversifying selection likely affects population structuring globally and within Scandinavia. The diagnostic loci identified now provide a promising and cost-efficient tool to investigate goldsinny wrasse populations further.
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| 3. |
- Rochus, Christina, et al.
(författare)
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Population structure of five native sheep breeds of Sweden estimated with high density SNP genotypes
- 2020
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Ingår i: BMC Genetics. - : Springer Science and Business Media LLC. - 1471-2156. ; 21
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Tidskriftsartikel (refereegranskat)abstract
- Background Native Swedish sheep breeds are part of the North European short-tailed sheep group; characterized in part by their genetic uniqueness. Our objective was to study the population structure of native Swedish sheep. Five breeds were genotyped using the 600 K SNP array. Dalapals and Klovsjo sheep are from the middle of Sweden; Gotland and Gute sheep from Gotland, an island in the Baltic Sea; and Fjallnas sheep from northern Sweden. We studied population structure by: principal component analysis (PCA), cluster-based analysis of admixture, and an estimated population tree. Results The analyses of the five Swedish breeds revealed that these breeds are five distinct breeds, while Gute and Gotland are more closely related to each other as seen in all analyses. All breeds had long branch lengths in the population tree indicating they've been subjected to drift. We repeated our analyses using 39 K SNP and including 50 K SNP genotypes from other European and southwestern Asian breeds from the Sheep HapMap project and 600 K SNP genotypes from a dataset of French sheep. Results arranged breeds into five groups: south-west Asia, south-west Europe, central Europe, north Europe and north European short-tailed sheep. Within this last group, Norwegian and Icelandic breeds, Finn and Romanov sheep, Scottish breeds, and Gute and Gotland sheep were more closely related while the remaining Swedish breeds and Ouessant sheep were distinct from all breeds and had longer branches in the population tree. Conclusions We showed population structure of five Swedish breeds and their structure within European and southwestern Asian breeds. Swedish breeds are unique, distinct breeds that have been subjected to drift but group with other north European short-tailed sheep.
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