Biology subjects

Brysting, A. K.

Publications and source records attributed to Brysting, A. K..

6 recordsLinked to original sources

bioRxiv2024

DNA metabarcoding diet analysis in ruminants is quantitative and integrates feeding over several weeks

Dietary DNA metabarcoding is an established method, especially useful for resolving the diverse diets of large mammalian herbivores (LMH). However, despite longstanding research interest on the topic, we still lack unequivocal evidence on the potential of DNA metabarcoding to reflect proportions of ingested dietary plants in LMH. One major aspect to consider is the time window during which ingested diet remains detectable in faecal samples. This parameter is currently unknown for LMH, thus potentially hindering the scope of ecological conclusions. Another unknown factor is quantitative performance, i.e. the extent to which the amount of ingested biomass can be assessed based on sequence read abundances. We assessed DNA metabarcoding quantitative performance and DNA half-life detectability for plants with different digestibilities in a controlled feeding experiment with three female Eurasian tundra reindeer (Rangifer tarandus tarandus). Reindeer were fed birch twigs (Betula pubescens) and increasing biomass of lichen (mainly Cladonia stellaris). Relative read abundance positively correlated with ingested lichen biomass, suggesting potential for deriving dietary proportions in free-ranging reindeer on natural pastures. Dietary DNA was consistently detected within a few hours upon ingestion, with a mean half-life detectability of 30 and 14 hours for birch and lichen, respectively. However, dietary DNA remained detectable in faeces for at least 26 days post-feeding, indicating that a single faecal sample can provide an unsuspectedly integrative estimate of diet in ruminants. Together, our findings provide novel empirical validation of DNA metabarcoding as a tool for diet analysis in LMH.

ecology↗

bioRxiv2024

Low parental conflict, no endosperm hybrid barriers, and maternal bias in genomic imprinting in selfing Draba species

In flowering plants, a distinct post-zygotic hybridization barrier between closely related species can arise during seed maturation, resulting in embryo lethality due to abnormal endosperm development. The endosperm initially works as a nutrient sink, acquiring nutrients from adjacent tissues, but later undergoes cellularization, switching to serve as a nutrient source. In hybrid seeds, this cellularization switch can be hampered if the endosperm genomic ratio is imbalanced. Disruption in the genomic ratio can be caused when species of different ploidy are crossed, but also by crosses between species with identical ploidy, if the effective ploidy differs. One factor proposed to influence effective ploidy is the epigenetic phenomenon genomic imprinting, the parent-of-origin specific expression of alleles inherited either maternally or paternally. It has been proposed that outbreeding species exhibit higher effective ploidy compared to selfing species, as a consequence of parental conflict in resource allocation to the developing progenies. This suggests a low anticipation of endosperm-based post-zygotic hybridization barriers between selfing species of similar ploidy. Here, we show that in crosses between the diploid selfing arctic species Draba fladnizensis, D. nivalis and D. subcapitata, the endosperm-based post-zygotic hybridization barrier is absent, supporting low parental conflict. To investigate parent-of-origin allele specific expression, we conducted a genomic imprinting study in D. nivalis and compared to previous studies in other Brassicaceae species. We report a high number of maternally expressed genes (MEGs) and concomitantly low numbers of paternally expressed genes (PEGs). Our results suggest rapid evolution of MEGs and loss of PEGs in a mating system with low parental conflict, proposing that selfing arctic species may exhibit a generally stronger maternal expression bias as an adaptive mechanism to efficiently cope with an extreme environment.

plant biology↗

bioRxiv2023

Structural evidence for MADS-box type I family expansion seen in new assemblies of A. arenosa and A. lyrata

Arabidopsis thaliana diverged from A. arenosa and A. lyrata at least 6 million years ago and are identified by genome-wide polymorphisms or morphological traits. The species are to a high degree reproductively isolated, but hybridization barriers are incomplete. A special type of hybridization barrier is based in the triploid endosperm of the seed, where embryo lethality is caused by endosperm failure to support the developing embryo. The MADS-box type I family of transcription factors are specifically expressed in the endosperm and has been proposed to play a role in endosperm-based hybridization barriers. The gene family is well known for a high evolutionary duplication rate, as well as being regulated by genomic imprinting. Here we address MADS-box type I gene family evolution and the role of type I genes in the context of hybridization. Using two de-novo assembled and annotated chromosome-level genomes of A. arenosa and A. lyrata ssp. petraea we analyzed the MADS-box type I gene family in Arabidopsis to predict orthologs, copy number and structural genomic variation related to the type I loci. Our findings were compared to gene expression profiles sampled before and after the transition to endosperm cellularization in order to investigate the involvement of MADS-box type I loci in endosperm-based hybridization barriers. We observed substantial differences in type-I expression between A. arenosa and A. lyrata ssp. petraea in the endosperm, suggesting a genetic cause for the endosperm-based hybridization barrier in A. arenosa and A. lyrata ssp. petraea hybrid seeds.

plant biology↗

bioRxiv2023

Genetic and environmental manipulation of Arabidopsis hybridization barriers uncover antagonistic functions in endosperm cellularization

Speciation by reproductive isolation can occur by hybridization barriers acting in the endosperm of the developing seed. The nuclear endosperm is a nutrient sink, accumulating sugars from surrounding tissues, and undergoes coordinated cellularization, switching to serve as a nutrient source for the developing embryo. Tight regulation of cellularization is therefore vital for seed and embryonic development. Here we show that hybrid seeds from crosses between Arabidopsis thaliana as maternal contributor and A. arenosa or A. lyrata as pollen donors result in an endosperm based post-zygotic hybridization barrier that gives rise to a reduced seed germination rate. Hybrid seeds display opposite endosperm cellularization phenotypes, with late cellularization in crosses with A. arenosa and early cellularization in crosses with A. lyrata. Stage specific endosperm reporters display temporally ectopic expression in developing hybrid endosperm, in accordance with the early and late cellularization phenotypes, confirming a disturbance of the source-sink endosperm phase change. We demonstrate that the hybrid barrier is under the influence of abiotic factors, and show that a temperature gradient leads to diametrically opposed cellularization phenotype responses in hybrid endosperm with A. arenosa or A. lyrata as pollen donors. Furthermore, different A. thaliana accession genotypes also enhance or diminish seed viability in the two hybrid cross-types, emphasizing that both genetic and environmental cues control the hybridization barrier. We have identified an A. thaliana MADS-BOX type I family single locus that is required for diametrically opposed cellularization phenotype responses in hybrid endosperm. Loss of AGAMOUS-LIKE 35 significantly affects the germination rate of hybrid seeds in opposite directions when transmitted through the A. thaliana endosperm, and is suggested to be a locus that promotes cellularization as part of an endosperm based mechanism involved in post-zygotic hybrid barriers. The role of temperature in hybrid speciation and the identification of distinct loci in control of hybrid failure have great potential to aid the introduction of advantageous traits in breeding research and to support models to predict hybrid admixture in a changing global climate.

developmental biology↗

bioRxiv2021

What can the cold-induced transcriptomes of Arctic Brassicaceae tell us about the evolution of cold tolerance?

O_LILittle is known about the evolution of cold tolerance in polar plant species and how they differ from their temperate relatives. To gain insight into their biology and the evolution of cold tolerance, we compared the molecular basis of cold response in three Arctic Brassicaceae species. C_LIO_LIWe conducted a comparative time series experiment to examine transcriptional responses to low temperature. RNA was sampled at 22 {degrees}C, and after 3h, 6h, and 24h at 2 {degrees}C. We then identified sets of genes that were differentially expressed in response to cold and compared them between species, as well as to published data from the temperate Arabidopsis thaliana. C_LIO_LIMost differentially expressed genes were species-specific, but a significant portion of the cold response was also shared among species. Among thousands of differentially expressed genes, [~]200 were shared among the three Arctic species and A. thaliana, while [~]100 were exclusively shared among the three Arctic species. C_LIO_LIOur results show that cold response differs markedly between Arctic Brassicaceae species, but likely builds on a conserved basis found across the family. They also confirm that highly polygenic traits such as cold tolerance may show little repeatability in their patterns of adaptation. C_LI

evolutionary biology↗

bioRxiv2017

What’s in the box? Authentication of Echinacea herbal products using DNA metabarcoding and HPTLC

BackgroundDifferences in regulatory policies between countries as well as a lack of appropriate standardized methods for authentication and quality control of herbal products lead to concerns over quality and safety. Echinacea products are among the top selling herbal products in Europe and the United States with indications for broad range of ailments.\n\nPurposeThis study approached the need for a novel analytical strategy in authentication of herbal products.\n\nMethodsA combination of high performance thin layer chromatography (HPTLC) and DNA metabarcoding was employed. Fifty-three Echinacea herbal products marketed across Europe were tested to evaluate the accuracy of these methods in plant identification and their potential in detecting substitutes, adulterants and other unreported plant constituents.\n\nResultsHPTLC provides a high resolution in detecting Echinacea phytochemical target compounds, but does not offer information on the other species within the product. Alternatively, we showed that the limitation of HPTLC to detect non-targeted species can be overcome through the complementary use of DNA metabarcoding. Using DNA metabarcoding, Echinacea species were detected in 34 out of the 38 retained products (89 %), but with a lack of discriminatory resolution at the species level due to the low level of molecular divergence within the Echinacea genus. All herbal products showed considerable discrepancies between ingredients listed on the label and the ones detected using DNA metabarcoding registering an overall ingredient fidelity of 43 %.\n\nConclusionThe results confirm that DNA metabarcoding can be used to test for the presence of Echinacea and simultaneously to detect other species present in even highly processed and multi-ingredient herbal products.\n\nAbbreviations

plant biology↗