Biology subjects

Kamphuis, L. G.

Publications and source records attributed to Kamphuis, L. G..

4 recordsLinked to original sources

bioRxiv2026

Pedigree-reconciled pan-genomics reveals megabase-scale hitchhiking after a century of canola breeding

Canola breeding has been shaped by strong selection for oil quality, yet the origins of the known oil quality alleles and genomic consequences of their selection are not fully resolved. By integrating pedigree reconstruction with graph pan-genomics we trace inheritance of ancestral genomic regions across historical and contemporary germplasm. Surrounding the low erucic acid allele in BnA08.FAE1, we identify a 17.23 Mb haplotype that approached fixation in Australian canola in the early 2000s. Contradicting the prevailing model, this haplotype predates modern breeding and was likely widespread in ancestral B. napus in the early 1900s. Genomic analyses implicate centromeric recombination suppression and structural variation in its long-term persistence, which has led to megabase-scale diversity loss through hitchhiking of neighbouring alleles. The haplotype contains extensive structural variation and multiple alleles associated with polygenic disease resistance. Together, these findings reveal the long-term consequences of repeated selection on standing variation during crop improvement.

plant biology↗

bioRxiv2024

Cryptic recombination and transposition drive structural variation to shape genomic plasticity and life history traits in a host generalist fungal plant pathogen

BackgroundAn understanding of plant pathogen evolution is important for sustainable management of crop diseases. Plant pathogen populations must maintain adequate heritable phenotypic variability to survive. Polymorphisms >= 50 bp, known as structural variants (SVs), could contribute strongly to this variability by disrupting gene activities. SV acquisition is largely driven by mobile genetic elements called transposons, though a less appreciated source of SVs is erroneous meiotic double-strand break repair. The relative impacts of transposons and recombination on SV diversity and the overall contribution of SVs to phenotypic variability is elusive, especially in host generalists. ResultsWe use 25 high quality genomes to create a graphical pan-genome of the globally distributed host-generalist crop pathogen Sclerotinia sclerotiorum. Outcrossing and recombination rates in this self-fertile species have been debated. Using bisulfite sequencing, and short read data from 190 strains, we show that S. sclerotiorum has many hallmarks of eukaryotic meiosis, including recombination hot and cold spots, centromeric and genic recombination suppression, and rapid linkage disequilibrium decay. Using a new statistic that captures average pairwise structural variation, we show that recombination and transposons make distinct contributions to SV diversity. Furthermore, despite only 5 % of genes being dispensable, SVs often had a stronger impact than other variants across 14 life history traits measured in 103 distinct strains. ConclusionTransposons and recombination make distinct contributions to SV diversity in S. sclerotiorum. Despite limited gene content diversity, SVs may strongly impact phenotypic variability. This sheds light on the genomic forces shaping adaptive flexibility in host generalists.

genomics↗

bioRxiv2020

Combined degradome and replicated small RNA sequencing identifies Brassica napus small RNAs responsive to infection by a necrotrophic pathogen

BackgroundSmall RNAs are short non-coding RNAs that are key gene regulators controlling various biological processes in eukaryotes. Plants may regulate discrete sets of sRNAs in response to pathogen attack. Sclerotinia sclerotiorum is an economically important pathogen affecting hundreds of plant species, including the economically important oilseed Brassica napus. However, there are limited studies on how regulation of sRNAs occurs in the S. sclerotiorum and B. napus pathosystem. ResultsWe identified different classes of sRNAs from B. napus by high throughput sequencing of replicated mock and infected samples at 24 hours post-inoculation (HPI). Overall, 3,999 sRNA loci were highly expressed, of which 730 were significantly upregulated during infection. Degradome sequencing identified numerous likely sRNA targets that were enriched for immunity-related GO terms, including those related to jasmonic acid signalling, during infection. A total of 73 conserved miRNA families were identified in our dataset. Degradome sequencing identified 434 unique cleaved mRNA products from these miRNAs, of which 50 were unique to the infected library. A novel miR1885-triggered disease resistance gene-derived secondary sRNA locus was identified and verified with degradome sequencing. We also experimentally validated silencing of a plant immunity related ethylene response factor gene by a novel sRNA using 5-RACE. ConclusionsThe findings in this study expand the framework for understanding the molecular mechanisms of the S. sclerotiorum and B. napus pathosystem at the sRNA level.

molecular biology↗

bioRxiv2018

Selective sweeps in populations of the broad host range plant pathogenic fungus Sclerotinia sclerotiorum

The pathogenic fungus Sclerotinia sclerotiorum infects over 600 species of plant. It is present in numerous environments throughout the world and causes significant damage to many agricultural crops. Fragmentation and lack of gene flow between populations may lead to population sub-structure. Within discrete recombining populations, positive selection may lead to a selective sweep. This is characterised by an increase in frequency of a favourable allele leading to reduction in genotypic diversity in a localised genomic region due to the phenomenon of genetic hitchhiking.\n\nWe aimed to assess whether isolates of S. sclerotiorum from around the world formed genotypic clusters associated with geographical origin and to determine whether signatures of population-specific positive selection could be detected. To do this, we sequenced the genomes of 25 isolates of S. sclerotiorum collected from four different continents - Australia, Africa (north and south), Europe and North America (Canada and the northen United States) and conducted SNP based analyses of population structure and selective sweeps.\n\nAmong the 25 isolates, there was evidence for four population clusters. One of these consisted of 11 isolates from Canada, the USA and France (population 1), another consisted of five isolates from Australia and one from Morocco (population 2). A further cluster was made up of Australian isolates, and the single South African isolate appeared to be from a separate population. We found that there was evidence of distinct selective sweeps between population 1 and population 2. Many of these sweeps overlapped genes involved in transcriptional regulation, such as transcription factors. It is possible that distinct populations of S. sclerotiorum from differing global environments have undergone selective sweeps at different genomic loci. This study lays the foundation for further work into investigation of the differing selective pressures that S. sclerotiorum populations are subjected to on a global scale.

genetics↗