Niklaus Zemp

Last Name

Zemp

First Name

Niklaus

ORCID

0000-0002-0991-5130

Organisational unit

02868 - Genetic Diversity Centre / Genetic Diversity Centre

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Publications 1 - 10 of 31

Monitoring genetic diversity: A genomics-based pilot study for Switzerland
Fischer, Martin C.; Reutimann, Oliver; Tschan, Jasmine Noëlle; et al. (2023)
Identification of Internal Reference Genes for Gene Expression Normalization between the Two Sexes in Dioecious White Campion
Zemp, Niklaus; Minder, Aria; Widmer, Alex (2014)
PLoS ONE
Quantitative real time (qRT)-PCR is a precise and efficient method for studying gene expression changes between two states of interest, and is frequently used for validating interesting gene expression patterns in candidate genes initially identified in genome-wide expression analyses, such as RNA-seq experiments. For an adequate normalisation of qRT-PCR data, it is essential to have reference genes available whose expression intensities are constant among the different states of interest. In this study we present and validate a catalogue of traditional and newly identified reference genes that were selected from RNA-seq data from multiple individuals from the dioecious plant Silene latifolia with the aim of studying gene expression differences between the two sexes in both reproductive and vegetative tissues. The catalogue contains more than 15 reference genes with both stable expression intensities and a range of expression intensities in flower buds and leaf tissues. These reference genes were used to normalize expression differences between reproductive and vegetative tissues in eight candidate genes with sex-biased expression. Our results suggest a trend towards a reduced sex-bias in sex-linked gene expression in vegetative tissues. In this study, we report on the systematic identification and validation of internal reference genes for adequate normalization of qRT-PCR-based analyses of gene expression differences between the two sexes in S. latifolia. We also show how RNA-seq data can be used efficiently to identify suitable reference genes in a wide diversity of species.
Species ecology explains the spatial components of genetic diversity in tropical reef fishes
Azzurra Donati, Giulia Francesca; Zemp, Niklaus; Manel, Stéphanie; et al. (2021)
Proceedings of the Royal Society B: Biological Sciences
Generating genomic data for 19 tropical reef fish species of the Western Indian Ocean, we investigate how species ecology influences genetic diversity patterns from local to regional scales. We distinguish between the alpha, beta and gamma components of genetic diversity, which we subsequently link to six ecological traits. We find that the alpha and gamma components of genetic diversity are strongly correlated so that species with a high total regional genetic diversity display systematically high local diversity. The alpha and gamma diversity components are negatively associated with species abundance recorded using underwater visual surveys and positively associated with body size. Pelagic larval duration is found to be negatively related to genetic beta diversity supporting its role as a dispersal trait in marine fishes. Deviation from the neutral theory of molecular evolution motivates further effort to understand the processes shaping genetic diversity and ultimately the diversification of the exceptional diversity of tropical reef fishes.
Has adaptation occurred in males and females since separate sexes evolved in the plant Silene latifolia
Zemp, Niklaus; Widmer, Alex; Charlesworth, Deborah (2018)
Proceedings of the Royal Society B: Biological Sciences
Comparative analysis of a plant pseudoautosomal region (PAR) in Silene latifolia with the corresponding S-vulgaris autosome
Blavet, Nicolas; Blavet, Hana; Čegan, Radim; et al. (2012)
BMC Genomics
Background The sex chromosomes of Silene latifolia are heteromorphic as in mammals, with females being homogametic (XX) and males heterogametic (XY). While recombination occurs along the entire X chromosome in females, recombination between the X and Y chromosomes in males is restricted to the pseudoautosomal region (PAR). In the few mammals so far studied, PARs are often characterized by elevated recombination and mutation rates and high GC content compared with the rest of the genome. However, PARs have not been studied in plants until now. In this paper we report the construction of a BAC library for S. latifolia and the first analysis of a > 100 kb fragment of a S. latifolia PAR that we compare to the homologous autosomal region in the closely related gynodioecious species S. vulgaris. Results Six new sex-linked genes were identified in the S. latifolia PAR, together with numerous transposable elements. The same genes were found on the S. vulgaris autosomal segment, with no enlargement of the predicted coding sequences in S. latifolia. Intergenic regions were on average 1.6 times longer in S. latifolia than in S. vulgaris, mainly as a consequence of the insertion of transposable elements. The GC content did not differ significantly between the PAR region in S. latifolia and the corresponding autosomal region in S. vulgaris. Conclusions Our results demonstrate the usefulness of the BAC library developed here for the analysis of plant sex chromosomes and indicate that the PAR in the evolutionarily young S. latifolia sex chromosomes has diverged from the corresponding autosomal region in the gynodioecious S. vulgaris mainly with respect to the insertion of transposable elements. Gene order between the PAR and autosomal region investigated is conserved, and the PAR does not have the high GC content observed in evolutionarily much older mammalian sex chromosomes.
Evolution of Sex-Biased Gene Expression During Transitions to Separate Sexes in the Silene Genus
Prentout, Djivan; Muyle, Aline; Zemp, Niklaus; et al. (2025)
Molecular Biology and Evolution
Sexual dimorphism is widespread among species with separate sexes, and its extent is thought to be governed by the differential expression of thousands of genes between males and females known as sex-biased genes (SBGs). SBGs have been studied in numerous species, but rarely through comparative approaches, which limits our understanding of their evolution, especially during multiple, independent transitions to separate sexes. We sequenced the transcriptomes of nine dioecious species (with separate males and females), two gynodioecious species (with separate females and hermaphrodites), and two hermaphrodite species from the Silene genus. Our dataset encompasses three independent transitions to dioecy, ranging from less than 1 million years ago (Mya) to about 11 Mya. We found that the number of both female- and male-biased genes positively correlates with the age of separate sexes, with species with older sex separation exhibiting the most numerous sex-biased genes. More specifically, male-biased expression tends to emerge early, as soon as females coexist with hermaphrodites (gynodioecy). Numbers of female-biased genes are rare at first, and their numbers only increase after a transition to separate males and females (dioecy). Additionally, we found that both positive selection and genetic drift contribute to the evolution of SBGs. Overall, this study provides new insights into the mechanisms underlying sex-biased gene evolution during transitions to separate sexes.
Minimally destructive hDNA extraction method for retrospective genetics of pinned historical Lepidoptera specimens
Rayo, Enrique; Ulrich, Gabriel F.; Zemp, Niklaus; et al. (2024)
Scientific Reports
The millions of specimens stored in entomological collections provide a unique opportunity to study historical insect diversity. Current technologies allow to sequence entire genomes of historical specimens and estimate past genetic diversity of present-day endangered species, advancing our understanding of anthropogenic impact on genetic diversity and enabling the implementation of conservation strategies. A limiting challenge is the extraction of historical DNA (hDNA) of adequate quality for sequencing platforms. We tested four hDNA extraction protocols on five body parts of pinned false heath fritillary butterflies, Melitaea diamina, aiming to minimise specimen damage, preserve their scientific value to the collections, and maximise DNA quality and yield for whole-genome re-sequencing. We developed a very effective approach that successfully recovers hDNA appropriate for short-read sequencing from a single leg of pinned specimens using silica-based DNA extraction columns and an extraction buffer that includes SDS, Tris, Proteinase K, EDTA, NaCl, PTB, and DTT. We observed substantial variation in the ratio of nuclear to mitochondrial DNA in extractions from different tissues, indicating that optimal tissue choice depends on project aims and anticipated downstream analyses. We found that sufficient DNA for whole genome re-sequencing can reliably be extracted from a single leg, opening the possibility to monitor changes in genetic diversity maintaining the scientific value of specimens while supporting current and future conservation strategies.
GenDiv - Monitoring der genetischen Vielfalt in der Schweiz
Fischer, Martin C.; Reutimann, Oliver; Ulrich, Gabriel F.; et al. (2023)
Quantitative trait locus analysis of parasitoid counteradaptation to symbiont-conferred resistance
Ulrich, Gabriel F.; Zemp, Niklaus; Vorburger, Christoph; et al. (2021)
Heredity
Insect hosts and parasitoids are engaged in an intense struggle of antagonistic coevolution. Infection with heritable bacterial endosymbionts can substantially increase the resistance of aphids to parasitoid wasps, which exerts selection on parasitoids to overcome this symbiont-conferred protection (counteradaptation). Experimental evolution in the laboratory has produced counteradapted populations of the parasitoid wasp Lysiphlebus fabarum. These populations can parasitize black bean aphids (Aphis fabae) protected by the bacterial endosymbiont Hamiltonella defensa, which confers high resistance against L. fabarum. We used two experimentally evolved parasitoid populations to study the genetic architecture of the counteradaptation to symbiont-conferred resistance by QTL analysis. With simple crossing experiments, we showed that the counteradaptation is a recessive trait depending on the maternal genotype. Based on these results, we designed a customized crossing scheme to genotype a mapping population phenotyped for the ability to parasitize Hamiltonella-protected aphids. Using 1835 SNP markers obtained by ddRAD sequencing, we constructed a high-density linkage map consisting of six linkage groups (LGs) with an overall length of 828.3 cM and an average marker spacing of 0.45 cM. We identified a single QTL associated with the counteradaptation to Hamiltonella in L. fabarum on linkage group 2. Out of 120 genes located in this QTL, several genes encoding putative venoms may represent candidates for counteradaptation, as parasitoid wasps inject venoms into their hosts during oviposition.
Isolation and Comparative Genomic Analysis of Reuterin-Producing Lactobacillus reuteri From the Chicken Gastrointestinal Tract
Greppi, Anna; Asare, Paul T.; Schwab, Clarissa; et al. (2020)
Frontiers in Microbiology
Lactobacillus reuteri is a natural inhabitant of selected animal and human gastrointestinal tract (GIT). Certain strains have the capacity to transform glycerol to 3-hydroxypropionaldehyde (3-HPA), further excreted to form reuterin, a potent antimicrobial system. Reuterin-producing strains may be applied as a natural antimicrobial in feed to prevent pathogen colonization of animals, such as in chicken, and replace added antimicrobials. To date, only seven L. reuteri strains isolated from chicken have been characterized which limits phylogenetic studies and host-microbes interactions characterization. This study aimed to isolate L. reuteri strains from chicken GIT and to characterize their reuterin production and antimicrobial resistance (AMR) profiles using phenotypic and genetic methods. Seventy strains were isolated from faces, crops and ceca of six chicken from poultry farms and samples from slaughterhouse. Twenty-five strains were selected for further characterization. Draft genomes were generated for the new 25 isolates and integrated into a phylogenetic tree of 40 strains from different hosts. Phylogenetic analysis based on gene content as well as on core genomes showed grouping of the selected 25 L. reuteri chicken isolates within the poultry/human lineage VI. Strains harboring pdu-cob-cbi-hem genes (23/25) produced between 156 mM ± 11 and 330 mM ± 14 3-HPA, from 600 mM of glycerol, in the conditions of the test. All 25 chicken strains were sensitive to cefotaxime (MIC between 0.016 and 1 μg/mL) and penicillin (MIC between 0.02 and 4 μg/mL). Akin to the reference strains DSM20016 and SD2112, the novel isolates were resistant to penicillin, possibly associated with identified point mutations in ponA, pbpX, pbpF and pbpB. All strains resistant to erythromycin (4/27) carried the ermB gene, and it was only present in chicken strains. All strains resistant to tetracycline (5/27) harbored tetW gene. This study confirms the evolutionary history of poultry/human lineage VI and identifies pdu-cob-cbi-hem as a frequent trait but not always present in this lineage. L. reuteri chicken strains producing high 3-HPA yield may have potential to prevent enteropathogen colonization of chicken.

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Niklaus Zemp

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