Biology subjects

de Visser, M. C.

Publications and source records attributed to de Visser, M. C..

5 recordsLinked to original sources

bioRxiv2024

Genomic evidence suggests the balanced lethal system in Triturus newts originated in an instantaneous speciation event.

Triturus newts are afflicted by a balanced lethal system causing the spontaneous death of half of their offspring. How could such a maladaptive trait evolve? We construct genetic maps for Triturus and its sister genus Lissotriton, identifying genes involved in the balanced lethal system. Triturus chromosome 1 has diverged into two versions, which each carry a single massive deletion that is compensated for by duplication of the same region in the alternate version - indicating that the balanced lethal system arose instantaneously, in a single macromutation. Simulations show that, counterintuitively, the deleterious nature of the rearranged chromosomes protects them against competition with the ancestral arrangement via reproductive isolation. We conclude that the origin of the Triturus balanced lethal system also led to instantaneous speciation.

evolutionary biology↗

bioRxiv2024

PAV-spotter: using signal cross-correlations to identify Presence/Absence Variation in target capture data

High throughput sequencing technologies have become essential in the fields of evolutionary biology and genomics. When dealing with non-model organisms or genomic gigantism, sequencing whole genomes is still relatively costly and therefore reduced-genome representations are frequently obtained, for instance by target capture approaches. While computational tools exist that can handle target capture data and identify small-scale variants such as single nucleotide polymorphisms and micro-indels, options to identify large scale structural variants are limited. To meet this need, we introduce PAV-spotter: a tool that can identify presence/absence variation (PAV) in target capture data. PAV-spotter conducts a signal cross-correlation calculation, in which the distribution of read counts per target between samples of different a priori defined classes - e.g. male versus female, or diseased versus healthy - are compared. We apply and test our methodology by studying Triturus newts: salamanders with gigantic genomes that currently lack an annotated reference genome. Triturus newts suffer from a hereditary disease that kills half their offspring during embryogenesis. We compare the target capture data of two different types of diseased embryos, characterized by unique deletions, with those of healthy embryos. Our findings show that PAV-spotter helps to expose such structural variants, even in the face of medium to low sequencing coverage levels, low sample sizes, and background noise due to mis-mapped reads. PAV-spotter can be used to study the structural variation underlying supergene systems in the absence of whole genome assemblies. The code, including further explanation, is available through the PAV-spotter GitHub repository: https://github.com/Wielstra-Lab/PAVspotter.

bioengineering↗

bioRxiv2024

Determining zygosity with multiplex Kompetitive Allele-Specific PCR (mxKASP) genotyping

We introduce multiplex Kompetitive Allele-Specific PCR (mxKASP): a modification of classical KASP genotyping that allows zygosity to be determined in diploid organisms. Rather than targeting a SNP associated with a single marker, mxKASP targets two non-homologous markers. We show proof of concept by applying mxKASP to the balanced lethal system in Triturus newts, in which individuals are known to possess either: (1) zero copies of the 1A version of chromosome 1 and two copies of the 1B version; (2) one copy of 1A and one copy of 1B; or (3) two copies of 1A and zero copies of 1B. mxKASP is successful in amplifying both a 1A and a 1B marker in a single reaction (if present), allowing the zygosity of individuals to be inferred. We independently confirm our mxKASP results with a multiplex PCR approach. We argue that mxKASP can be applied to rapidly and economically determine zygostity in diploid organisms, for a large number of samples at once.

molecular biology↗

bioRxiv2024

Conserved gene content and unique phylogenetic history characterize the 'bloopergene' underlying Triturus' balanced lethal system

In a balanced lethal system, half the reproductive output succumbs. Triturus newts are the best-known example. Their chromosome 1 comes in two distinct versions and embryos carrying the same version twice experience developmental arrest. Those possessing two different versions survive, suggesting that each version carries something uniquely vital. With target capture we obtain over 7,000 nuclear DNA markers across the genus Triturus and all main lineages of Salamandridae (the family to which Triturus belongs) to investigate the evolutionary history of Triturus chromosome 1 versus other chromosomes. Dozens of genes are completely missing from either one or the other version of chromosome 1 in Triturus. Furthermore, the unique gene content of 1A versus 1B is remarkably similar across Triturus species, suggesting that the balanced lethal system evolved before Triturus radiated. The tree topology of chromosome 1 differs from the rest of the genome, presumably due to pervasive, ancient hybridization between Triturus ancestor and other newt lineages. Our findings accentuate the complex nature of Triturus chromosome 1 - the bloopergene driving the evolutionarily enigmatic balanced lethal system.

evolutionary biology↗

bioRxiv2024

NewtCap: an efficient target capture approach to boost genomic studies in Salamandridae (True Salamanders and Newts)

Salamanders have large and complex genomes, hampering whole genome sequencing. However, reduced representation sequencing provides a feasible alternative to obtain genome-wide data. We present NewtCap: a sequence capture bait set that targets c.7k coding regions across the genomes of all true salamanders and newts (the family Salamandridae, also known as salamandrids). We test the efficacy of NewtCap, originally designed for the Eurasian Triturus newts, in 30 species, belonging to 17 different genera, that cover all main Salamandridae lineages. We also test NewtCap in two other salamander families. We discover that NewtCap performs well across all Salamandridae lineages (but not in the salamander families Ambystomatidae and Hynobiidae). As expected, the amount of genetic divergence from the genus Triturus correlates negatively to capture efficacy and mapping success. However, this does not impede our downstream analyses. We showcase the potential of NewtCap in the contexts of; 1) phylogenomics, by reconstructing the phylogeny of Salamandridae, 2) phylogeography, by sequencing the four closely related species comprising the genus Taricha, 3) hybrid zone analysis, by genotyping two Lissotriton species and different classes of interspecific hybrids, and 4) conservation genetics, by comparing Triturus ivanbureschi samples from several wild populations and one captive-bred population. Overall, NewtCap has the potential to boost straightforward, reproducible, and affordable genomic studies, tackling both fundamental and applied research questions across salamandrids.

genomics↗