Molecular Inversion Probes for targeted resequencing in non-model organisms

Niedzicka, Marta; Fijarczyk, Anna; Dudek, Katarzyna; Stuglik, Michał; Babik, Wiesław

doi:10.1038/srep24051

Cited by 40 publications

(52 citation statements)

References 55 publications

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“…Fragments of 1,233 nuclear genes and one mitochondrial protein coding gene were resequenced with Molecular Inversion Probes (MIPs), following the protocol of Niedzicka, Fijarczyk, Dudek, Stuglik, and Babik (). A total of 1,485 MIPs, each targeting 112 bp of genomic sequence, were used (for details see Appendix ), in most cases a single MIP per gene.…”

Section: Methodsmentioning

confidence: 99%

Differential introgression across newt hybrid zones: Evidence from replicated transects

et al. 2019

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Genomic heterogeneity of divergence between hybridizing species may reflect heterogeneity of introgression, but also processes unrelated to hybridization. Heterogeneous introgression and its repeatability can be directly tested in natural hybrid zones by examining multiple transects. Here, we studied hybrid zones between the European newts Lissotriton montandoni and two lineages of Lissotriton vulgaris, with replicate transects within each zone. Over 1,000 nuclear genes located on a linkage map and mitochondrial DNA were investigated using geographical and genomic clines. Overall, the five transects were all similar, showing hallmarks of strong reproductive isolation: bimodal distribution of genotypes in central populations and narrow allele frequency clines. However, the extent of introgression differed between the zones, possibly as a consequence of their different ages, as suggested by the analysis of heterozygosity runs in diagnostic markers. In three transects genomic signatures of small‐scale (~2 km) zone movements were detected. We found limited overlap of cline outliers between transects, and only weak evidence of stronger differentiation of introgression between zones than between transects within zones. Introgression was heterogeneous across linkage groups, with patterns of heterogeneity similar between transects and zones. Predefined candidates for increased or reduced introgression exhibited only a subtle tendency in the expected direction, suggesting that interspecific differentiation is not a reliable indicator for the strength of introgression. These hierarchically sampled hybrid zones of apparently different ages show how introgression unfolds with time and offer an excellent opportunity to dissect the dynamics of hybridization and architecture of reproductive isolation at advanced stages of speciation.

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Section: Methodsmentioning

confidence: 99%

Differential introgression across newt hybrid zones: Evidence from replicated transects

et al. 2019

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“…Each marker was located in a single exon to allow amplification from genomic DNA. The bioinformatics pipeline used to design markers, laboratory procedures, and sequencing are described in detail in Niedzicka et al (2016). The MIP markers used to construct the linkage map fell into two groups (Supplemental Material, Table S1 in File S1):

Markers informative in the F2 cross, i.e.

…”

Section: Methodsmentioning

confidence: 99%

“…Indeed, generation P individuals were alternative homozygotes in an overwhelming majority of such SNPs. A subset of 205 group 1 markers were reported in Niedzicka et al (2016).Markers designed in genes involved in immune response reported by Fijarczyk et al (2016) and other randomly picked transcripts. Several MIPs were designed for most genes.…”

Section: Methodsmentioning

confidence: 99%

Linkage Map ofLissotritonNewts Provides Insight into the Genetic Basis of Reproductive Isolation

Niedzicka

Dudek

Fijarczyk

et al. 2017

G3 Genes|Genomes|Genetics

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Linkage maps are widely used to investigate structure, function, and evolution of genomes. In speciation research, maps facilitate the study of the genetic architecture of reproductive isolation by allowing identification of genomic regions underlying reduced fitness of hybrids. Here we present a linkage map for European newts of the Lissotriton vulgaris species complex, constructed using two families of F2 L. montandoni × L. vulgaris hybrids. The map consists of 1146 protein-coding genes on 12 linkage groups, equal to the haploid chromosome number, with a total length of 1484 cM (1.29 cM per marker). It is notably shorter than two other maps available for salamanders, but the differences in map length are consistent with cytogenetic estimates of the number of chiasmata per chromosomal arm. Thus, large salamander genomes do not necessarily translate into long linkage maps, as previously suggested. Consequently, salamanders are an excellent model to study evolutionary consequences of recombination rate variation in taxa with large genomes and a similar number of chromosomes. A complex pattern of transmission ratio distortion (TRD) was detected: TRD occurred mostly in one family, in one breeding season, and was clustered in two genomic segments. This is consistent with environment-dependent mortality of individuals carrying L. montandoni alleles in these two segments and suggests a role of TRD blocks in reproductive isolation. The reported linkage map will empower studies on the genomic architecture of divergence and interactions between the genomes of hybridizing newts.

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“…One Lm and one Lvg population sample (19 individuals each) were analyzed. Resequencing was performed with Molecular Inversion Probes (MIP, Niedzicka et al 2016, supplementary table S3, Supplementary Material online). MIPs were designed from transcripts with exon boundaries identified through BLAST searches against X. tropicalis gene models (Niedzicka et al 2016).…”

Section: Methodsmentioning

confidence: 99%

“…Resequencing was performed with Molecular Inversion Probes (MIP, Niedzicka et al 2016, supplementary table S3, Supplementary Material online). MIPs were designed from transcripts with exon boundaries identified through BLAST searches against X. tropicalis gene models (Niedzicka et al 2016). Because many vertebrate exons are short, to maximize the length of the target available for MIP design in candidate BS genes, sequence capture reads were assembled into contigs using Trinity (release v2.0.4).…”

Section: Methodsmentioning

confidence: 99%

Selective Landscapes in newt Immune Genes Inferred from Patterns of Nucleotide Variation

Fijarczyk¹,

Dudek²,

Babik³

2016

Genome Biol Evol

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Host–pathogen interactions may result in either directional selection or in pressure for the maintenance of polymorphism at the molecular level. Hence signatures of both positive and balancing selection are expected in immune genes. Because both overall selective pressure and specific targets may differ between species, large-scale population genomic studies are useful in detecting functionally important immune genes and comparing selective landscapes between taxa. Such studies are of particular interest in amphibians, a group threatened worldwide by emerging infectious diseases. Here, we present an analysis of polymorphism and divergence of 634 immune genes in two lineages of Lissotriton newts: L. montandoni and L. vulgaris graecus. Variation in newt immune genes has been shaped predominantly by widespread purifying selection and strong evolutionary constraint, implying long-term importance of these genes for functioning of the immune system. The two evolutionary lineages differ in the overall strength of purifying selection which can partially be explained by demographic history but may also signal differences in long-term pathogen pressure. The prevalent constraint notwithstanding, 23 putative targets of positive selection and 11 putative targets of balancing selection were identified. The latter were detected by composite tests involving the demographic model and further validated in independent population samples. Putative targets of balancing selection encode proteins which may interact closely with pathogens but include also regulators of immune response. The identified candidates will be useful for testing whether genes affected by balancing selection are more prone to interspecific introgression than other genes in the genome.

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Molecular Inversion Probes for targeted resequencing in non-model organisms

Cited by 40 publications

References 55 publications

Differential introgression across newt hybrid zones: Evidence from replicated transects

Differential introgression across newt hybrid zones: Evidence from replicated transects

Linkage Map ofLissotritonNewts Provides Insight into the Genetic Basis of Reproductive Isolation

Selective Landscapes in newt Immune Genes Inferred from Patterns of Nucleotide Variation

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