Biology subjects

Smit, S.

Publications and source records attributed to Smit, S..

28 records · Page 2Linked to original sources

bioRxiv2023

Comparative transcriptomics of Hirschfeldia incana and relatives highlights differences in photosynthetic pathways

Photosynthesis is the only yield-related trait that has not yet been substantially improved by plant breeding. The limited results of previous attempts to increase yield via improvement of photosynthetic pathways suggest that more knowledge is still needed to achieve this goal. To learn more about the genetic and physiological basis of high photosynthetic light-use efficiency (LUE) at high irradiance, we study Hirschfeldia incana. Here, we compare the transcriptomic response to high light of H. incana with that of three other members of the Brassicaceae, Arabidopsis thaliana, Brassica rapa, and Brassica nigra, which have a lower photosynthetic LUE. First, we built a high-light, high-uniformity growing environment in a climate-controlled room. Plants grown in this system developed normally and showed no signs of stress during the whole growth period. Then we compared gene expression in low and high-light conditions across the four species, utilizing a panproteome to group homologous proteins efficiently. As expected, all species actively regulate genes related to the photosynthetic process. An in-depth analysis on the expression of genes involved in three key photosynthetic pathways revealed a general trend of lower gene expression in high-light conditions. However, H. incana distinguishes itself from the other species through higher expression of certain genes in these pathways, either through constitutive higher expression, as for LHCB8, ordinary differential expression, as for PSBE, or cumulative higher expression obtained by simultaneous expression of multiple gene copies, as seen for LHCA6. These differentially expressed genes in photosynthetic path-ways are interesting leads to further investigate the exact relationship between gene expression, protein abundance and turnover, and ultimately the LUE phenotype. In addition, we can also exclude thousands of genes from "explaining" the phenotype, because they do not show differential expression between both light conditions. Finally, we deliver a transcriptomic resource of plant species fully grown under, rather than briefly exposed to, a very high irradiance, supporting efforts to develop highly efficient photosynthesis in crop plants.

bioinformatics↗

bioRxiv2023

Local adaptation of Arabidopsis thaliana in a small geographic region with mild environmental clines

Natural populations of Arabidopsis thaliana provide powerful systems to study adaptation of wild plant species. Previous research has predominantly focused on global populations or accessions collected from regions with diverse climates. However, little is known about the genetics underlying adaptation in regions with mild environmental clines. We have examined a diversity panel consisting of 192 A. thaliana accessions collected from the Netherlands, a region with limited climatic variation. Despite the relatively uniform climate, we identified compelling evidence of local adaptation within this population. Notably, semidwarf accessions, due to mutation of the GIBBERELLIC ACID REQUIRING 5 (GA5) gene, occur at a relatively high frequency near the coast and these displayed enhanced tolerance to high wind velocities. Additionally, we evaluated the performance of the population under iron deficiency conditions and found that allelic variation in the FE SUPEROXIDE DISMUTASE 3 (FSD3) gene affects tolerance to low iron levels. Moreover, we explored patterns of local adaptation to environmental clines in temperature and precipitation, observing that allelic variation at LA RELATED PROTEIN 1C (LARP1c) likely affects drought tolerance. Not only is the genetic variation observed in a diversity panel of A. thaliana collected in a region with mild environmental clines comparable to that in collections sampled over larger geographic ranges, it is also sufficiently rich to elucidate the genetic and environmental factors underlying natural plant adaptation.

plant biology↗

bioRxiv2023

Genome assembly and analysis of Lactuca virosa: implications for lettuce breeding

Lettuce (Lactuca sativa L.) is a leafy vegetable crop with ongoing breeding efforts related to quality, resilience, and innovative production systems. Genetic variation of important traits in close relatives is necessary to meet lettuce breeding goals. Lactuca virosa (2x=2n=18), a wild relative assigned to the tertiary lettuce gene pool, has a much larger genome (3.7 Gbp) than Lactuca sativa (2.5 Gbp). It has been used in interspecific crosses and is a donor to modern crisphead lettuce cultivars. Here, we present a de novo reference assembly of L. virosa with high continuity and complete gene space. This assembly facilitated comparisons to the genome of L. sativa and to that of the wild species L. saligna, a representative of the secondary lettuce gene pool. To assess the diversity in gene content, we classified the genes of the three Lactuca species as core, accessory and unique. In addition, we identified three interspecific chromosomal inversions compared to L. sativa, which each may cause recombination suppression and thus hamper future introgression breeding. Using three-way comparisons in both reference-based and reference-free manners, we show that the proliferation of long-terminal repeat elements has driven the genome expansion of L. virosa. Further, we performed a genome-wide comparison of immune genes, nucleotide-binding leucine-rich repeat, and receptor-like kinases among Lactuca spp. and indicate the evolutionary patterns and mechanisms behind their expansions. These genome analyses greatly facilitate the understanding of genetic variation in L. virosa, which is beneficial for the breeding of improved lettuce varieties.

plant biology↗

bioRxiv2022

Precise overlapping neural representations between feeling and seeing touch in people with high tactile empathy

Simulation theories propose that vicarious touch arises when seeing someone else being touched triggers corresponding representations of being touched. Prior electroencephalography (EEG) findings show that seeing touch modulates both early and late somatosensory responses (measured with or without direct tactile stimulation). Functional Magnetic Resonance Imaging (fMRI) studies have shown that seeing touch increases somatosensory cortical activation. These findings have been taken to suggest that when we see someone being touched, we simulate that touch in our sensory systems. The somatosensory overlap when seeing and feeling touch differs between individuals, potentially underpinning variation in vicarious touch experiences. Increases in amplitude (EEG) or cerebral blood flow response (fMRI), however, are limited in that they cannot test for the information contained in the neural signal: seeing touch may not activate the same information as feeling touch. Here, we use time-resolved multivariate pattern analysis on whole-brain EEG data from people with and without vicarious touch experiences to test whether seen touch evokes overlapping neural representations with the first-hand experience of touch. Participants felt touch to the fingers (tactile trials) or watched carefully matched videos of touch to another persons fingers (visual trials). In both groups, EEG was sufficiently sensitive to allow decoding of touch location (little finger vs. thumb) on tactile trials. However, only in individuals who reported feeling touch when watching videos of touch could a classifier trained on tactile trials distinguish touch location on visual trials. This demonstrates that, for people who experience vicarious touch, there is overlap in the information about touch location held in the neural patterns when seeing and feeling touch. The timecourse of this overlap implies that seeing touch evokes similar representations to later stages of tactile processing. Therefore, while simulation may underlie vicarious tactile sensations, our findings suggest this involves an abstracted representation of directly felt touch.

neuroscience↗

bioRxiv2022

The genome sequence of Hirschfeldia incana, a species with high photosynthetic light-use efficiency

Photosynthesis is a biophysical and biochemical process that plays a key role in sustaining plant and human life, being the first step in the production of energy-rich molecules and oxygen in the biosphere. Improving the photosynthetic capacity of agricultural crops is highly desirable to increase their yields. While the core mechanisms of photosynthesis are highly conserved, certainly in higher plants, plants that can maintain a high photosynthetic light-use efficiency at high irradiance are exceptional and may be useful to understand and improve high irradiance photosynthesis of crops. One such exceptional species is Hirschfeldia incana, a member of the well-studied Brassicaceae family that is easy to grow under standard laboratory conditions, providing an excellent resource for studying the genetic and physiological basis of this trait. Here, we present a reference assembly of H. incana and affirm its high photosynthetic efficiency relative to the Brassicaceae species Brassica rapa, Brassica nigra, and Arabidopsis thaliana. We estimate that it diverged from B. rapa and B. nigra 10-11 million years ago and that its genome has diversified from that of the latter two species through large chromosomal rearrangements, species-specific transposon activity, and differential retention of duplicated genes. Genes present at copy numbers different from B. rapa and B. nigra include those involved in photosynthesis and/or abiotic stress, which may mediate the high photosynthetic efficiency of H. incana. We expect the reference assembly of H. incana to be a valuable genomic resource for identifying ways to enhance photosynthetic rates in crop species.

bioinformatics↗

bioRxiv2020

The development of a novel diagnostic PCR for Madurella mycetomatis using a comparative genome approach

Eumycetoma is a neglected tropical disease characterized by large tumorous lesions. It is most commonly caused by the fungus Madurella mycetomatis which accounts for more than 70% of cases in central Africa. Currently, identification of the causative agent can only be reliably performed by a species-specific PCR. However, we recently demonstrated that our M. mycetomatis specific PCR can cross-react with Madurella pseudomycetomatis. We therefore used a comparative genome approach to develop a new M. mycetomatis specific PCR for species identification. For this we compared the published M. mycetomatis genome to genomes of other organisms in BLASTCLUST to identify unique M. mycetomatis predicted protein coding sequences. Based on 16 of these unique sequences, PCR primers were developed. The specificity of these primers was further evaluated in other eumycetoma causing agents including the Madurella sibling species. Out of the 16 tested sequences, only one was unique for M. mycetomatis and this should be used as a novel diagnostic marker for M. mycetomatis.

microbiology↗

bioRxiv2019

Pangenomic read mapping

In modern genomics, mapping reads to a single reference genome is common practice. However, a reference genome does not necessarily accurately represent a population or species and as a result a substantial percentage of reads often cannot be mapped. A number of graph-based variation-aware mapping methods have recently been proposed to remedy this. Here, we propose an alternative multi-reference approach, which aligns reads to large collections of genomes simultaneously. Our approach, an extension to our pangenomics suite PanTools (https://git.wur.nl/bioinformatics/pantools), is as accurate as state-of the-art tools but more efficient on large numbers of genomes. We successfully applied PanTools to map genomic and metagenomic reads to large collections of viral, archaeal, bacterial, fungal and plant genomes.

bioinformatics↗

bioRxiv2019

Hecaton: reliably detecting copy number variation in plant genomes using short read sequencing data

Copy number variation (CNV) is thought to actively contribute to adaptive evolution of plant species. While many computational algorithms are available to detect copy number variation from whole genome sequencing datasets, the typical complexity of plant data likely introduces false positive calls.\n\nTo enable reliable and comprehensive detection of CNV in plant genomes, we developed Hecaton, a novel computational workflow tailored to plants, that integrates calls from multiple state-of-the-art algorithms through a machine-learning approach. In this paper, we demonstrate that Hecaton outperforms current methods when applied to short read sequencing data of A. thaliana, rice, maize, and tomato. Moreover, it correctly detects dispersed duplications, a type of CNV commonly found in plant species, in contrast to several state-of-the-art tools that erroneously represent this type of CNV as overlapping deletions and tandem duplications. Finally, Hecaton scales well in terms of memory usage and running time when applied to short read datasets of domesticated and wild tomato accessions. Hecaton provides a robust method to detect CNV in plants. We expect it to be of immediate interest to both applied and fundamental research on the relationship between genotype and phenotype in plants.

bioinformatics↗

bioRxiv2019

Visual body form and orientation cues do not modulate visuo-tactile temporal integration

Body ownership relies on spatiotemporal correlations between multisensory signals and visual cues specifying oneself such as body form and orientation. The mechanism for the integration of bodily signals remains unclear. One approach to model multisensory integration that has been influential in the multisensory literature is Bayesian causal inference. This specifies that the brain integrates spatial and temporal signals coming from different modalities when it infers a common cause for inputs. As an example, the rubber hand illusion shows that visual form and orientation cues can promote the inference of a common cause (ones body) leading to spatial integration shown by a proprioceptive drift of the perceived location of the real hand towards the rubber hand. Recent studies investigating the effect of visual cues on temporal integration, however, have led to conflicting findings. These could be due to task differences, variation in ecological validity of stimuli and/or small samples. In this pre-registered study, we investigated the influence of visual information on temporal integration using a visuo-tactile temporal order judgement task with realistic stimuli and a sufficiently large sample determined by Bayesian analysis. Participants viewed videos of a touch being applied to plausible or implausible visual stimuli for ones hand (hand oriented plausibly, hand rotated 180 degrees, or a sponge) while also being touched at varying stimulus onset asynchronies. Participants judged which stimulus came first: viewed or felt touch. Results show that visual cues do not modulate visuo-tactile temporal order judgements. This is not in line with the idea that bodily signals indicating oneself influence the integration of multisensory signals in the temporal domain. The current study emphasises the importance of rigour in our methodologies and analyses to advance the understanding of how properties of multisensory events affect the encoding of temporal information in the brain.

neuroscience↗

bioRxiv2017

Parallel loss of symbiosis genes in relatives of nitrogen-fixing non-legume Parasponia

Rhizobium nitrogen-fixing nodules are a well-known trait of legumes, but nodules also occur in other plant lineages either with rhizobium or the actinomycete Frankia as microsymbiont. The widely accepted hypothesis is that nodulation evolved independently multiple times, with only a few losses. However, insight in the evolutionary trajectory of nodulation is lacking. We conducted comparative studies using Parasponia (Cannabaceae), the only non-legume able to establish nitrogen fixing nodules with rhizobium. This revealed that Parasponia and legumes utilize a large set of orthologous symbiosis genes. Comparing genomes of Parasponia and its non-nodulating relative Trema did not reveal specific gene duplications that could explain a recent gain of nodulation in Parasponia. Rather, Trema and other non-nodulating species in the Order Rosales show evidence of pseudogenization or loss of key symbiosis genes. This demonstrates that these species have lost the potential to nodulate. This finding challenges a long-standing hypothesis on evolution of nitrogen-fixing symbioses, and has profound implications for translational approaches aimed at engineering nitrogen-fixing nodules in crop plants.

plant biology↗