Biology subjects

Andersen, S. U.

Publications and source records attributed to Andersen, S. U..

26 records · Page 2Linked to original sources

bioRxiv2020

VC1 catalyzes a key step in the biosynthesis of vicine from GTP in faba bean

Faba bean is a widely adapted and high-yielding legume cultivated for its protein-rich seeds1. However, the seeds accumulate the anti-nutritional pyrimidine glucosides vicine and convicine, which can cause haemolytic anaemia--favism--in the 400 million individuals genetically predisposed by a deficiency in glucose-6-phosphate dehydrogenase2. Here, we identify the first enzyme associated with vicine and convicine biosynthesis, which we name VC1. We show that VC1 co-locates with the major QTL for vicine and convicine content and that the expression of VC1 correlates highly with vicine content across tissues. We also show that low-vicine varieties express a version of VC1 carrying a small, frame-shift insertion, and that overexpression of wild-type VC1 leads to an increase in vicine levels. VC1 encodes a functional GTP cyclohydrolase II, an enzyme normally involved in riboflavin biosynthesis from the purine GTP. Through feeding studies, we demonstrate that GTP is a precursor of vicine both in faba bean and in the distantly related plant bitter gourd. Our results reveal an unexpected biosynthetic origin for vicine and convicine and pave the way for the development of faba bean cultivars that are free from these anti-nutrients, providing a safe and sustainable source of dietary protein.

biochemistry↗

bioRxiv2019

Evaluation of yield, yield stability and yield-protein trade-off in commercial faba bean cultivars

Faba bean is a legume crop with high protein content and large potential for cultivation in the Northern latitudes. However, it has a reputation for being an unstable crop with large inter-annual variability, mostly explained by yearly variation in rainfall. Consequently, the objective is to breed cultivars with high seed yield and high yield stability. In this study, 17 commercial cultivars of faba bean were evaluated for seed yield, yield stability and trade-off between seed yield and protein content in four locations in Denmark and Finland during 2016-2018. We found that location and year effects accounted for 72% of the total seed yield variation. Cultivar by environment interactions (GxE) were found to be small and did not cause re-ranking of cultivars in different environments. Yield stability contributed little to the mean yield of the cultivars because high-yielding cultivars consistently outperformed the lower yielding genotypes, even under the most adverse conditions. The latter was also the case for total protein yield quantified as total yield multiplied by seed protein percentage. Although we found a strong negative correlation of -0.64 between yield and protein content, a few cultivars produced high yields while maintaining a relatively high protein content, suggesting that these traits may to some degree be genetically separable.

plant biology↗

bioRxiv2019

Syntenizer 3000: Synteny-based analysis of orthologous gene groups

MotivationThe amorphous nature of genes combined with the prevalence of duplication events makes establishing correct genetic phylogenies challenging.\n\nSince homologous gene groups are traditionally formed on basis of sequence similarity, both orthologs and paralogs are often placed in the same gene group by existing tools. Certain tools such as PoFF take syntenic relationship of genes into consideration when forming gene groups. However, a method to form gene groups consisting of only true syntelogs has not yet been developed.\n\nIn order to obtain orthologous gene groups consisting of the most likely syntelogs we need a method to filter out paralogs. If one strain has two or more copies of the same gene in a gene group we want to keep only the true syntelog in the group, and remove the paralogous copies by distinguishing between the two using synteny analysis.\n\nResultsWe present a novel algorithm for measuring the degree of synteny shared between two genes and successfully disambiguate gene groups. This synteny measure is the basis for a number of other useful functions such as gene neighbourhood visualisation to inspect suspect gene groups, strain visualisation for assessing assembly quality and finding genomic areas of interest, and chromosome/plasmid classification of contigs in partially classified datasets.\n\nAvailabilityThe latest version of Syntenizer 3000 can be downloaded from the GitHub repository at https://github.com/kamiboy/Syntenizer3000/\n\nConsult the manual.pdf file in the repository for instructions on how to build and use the tool, as well as a in depth explanation of the algorithms utilised.

bioinformatics↗

bioRxiv2019

Identification of novel genes involved in phosphate accumulation in Lotus japonicus through Genome Wide Association mapping of root system architecture and anion content

Phosphate is a key nutrient for plants and as it is needed in high quantities. It is highly immobile in the soil and represents a major limiting factor for plant productivity. Plants have evolved different solutions to forage the soil for phosphate and to adapt to phosphate limitation ranging from a profound tuning of their root system architecture and metabolic profile to the evolution of widespread mutualistic interactions, such as those with arbuscular mycorrhizal fungi (AM symbiosis). Despite the prevalence of AM symbiosis throughout land plants, most studies aimed at identifying genes that regulate plant responses to phosphate have been conducted in species incapable of AM symbiosis, such as Arabidopsis. Here we elucidated plant responses and their genetic basis to different phosphate levels in a plant species that is widely used as a model for AM symbiosis: Lotus japonicus. Rather than focusing on a single model strain, we measured root growth and anion content in response to different levels of phosphate in a large panel of Lotus japonicus natural accessions. This allowed us not only to uncover common as well as divergent responses within this species, but also enabled Genome Wide Association Studies by which we identified new genes regulating phosphate homeostasis in Lotus. Under low phosphate conditions, we uncovered a correlation between plant biomass and the decrease of plant phosphate concentration in plant tissues, suggesting a dilution effect. Altogether our data of the genetic and phenotypic variation within a species capable of AM complements studies that have been conducted in Arabidopsis, and advances our understanding of the continuum of genotype by phosphate level interaction that exists throughout dicot plants. Author SummaryPhosphate represents a major limiting factor for plant productivity. Plants have evolved different solutions to adapt to phosphate limitation ranging from a profound tuning of their root system architecture and metabolic profile to the evolution of widespread mutualistic interactions, such as arbuscular mycorrhizal symbiosis. Here we elucidated plant responses and their genetic basis to different phosphate levels in model legume plant species, Lotus japonicus, a plant commonly used for studying arbuscular mycorhizal symbiosis. We investigated Lotus responses to phosphate levels by combining high throughput root system architecture phenotyping and nutrient measurements with a natural variation approach. We investigated relations between root phenotypic responses and nutrient accumulation and we uncovered, under low phosphate conditions, a correlation between plant biomass and the decrease of plant phosphate concentration in plant tissues, suggesting a dilution effect. By means of Genome Wide Association mapping and integration of multiple traits, we identified new genes regulating phosphate homeostasis in Lotus.

plant biology↗

bioRxiv2019

MAUI-seq: Multiplexed, high-throughput amplicon diversity profiling using unique molecular identifiers

BackgroundSequencing and PCR errors are a major challenge when characterising genetic diversity using high-throughput amplicon sequencing (HTAS). ResultsWe have developed a multiplexed HTAS method, MAUI-seq, which uses unique molecular identifiers (UMIs) to improve error correction by exploiting variation among sequences associated with a single UMI. We show that two main advantages of this approach are efficient elimination of chimeric and other erroneous reads, outperforming DADA2 and UNOISE3, and the ability to confidently recognise genuine alleles that are present at low abundance or resemble chimeras. ConclusionsThe method provides sensitive and flexible profiling of diversity and is readily adaptable to most HTAS applications, including microbial 16S rRNA profiling and metabarcoding of environmental DNA.

ecology↗

bioRxiv2019

The genomic architecture of introgression amongsibling species of bacteria

BackgroundGene transfer between bacterial species is an important mechanism for adaptation. For example, sets of genes that confer the ability to form nitrogen-fixing root nodules on host plants have frequently moved between Rhizobium species. It is not clear, though, whether such transfer is exceptional, or if frequent inter-species introgression is typical. To address this, we sequenced the genomes of 196 isolates of the Rhizobium leguminosarum species complex obtained from root nodules of white clover (Trifolium repens). ResultsCore gene phylogeny placed the isolates into five distinct genospecies that show high intra-genospecies recombination rates and remarkably different demographic histories. Most gene phylogenies were largely concordant with the genospecies, indicating that recent gene transfer between genospecies was rare. In contrast, very similar symbiosis gene sequences were found in two or more genospecies, suggesting recent horizontal transfer. The replication and conjugative transfer genes of the plasmids carrying the symbiosis genes showed a similar pattern, implying that introgression occurred by conjugative plasmid transfer. The only other regions that showed strong phylogenetic discordance with the genospecies classification were two small chromosomal clusters, one neighbouring a conjugative transfer system. Phage-related sequences were observed in the genomes, but appeared to have very limited impact on introgression. ConclusionsIntrogression among these closely-related species has been very limited, confined to the symbiosis plasmids and a few chromosomal islands. Both introgress through conjugative transfer, but have been subject to different types of selective forces.

genomics↗

bioRxiv2018

Extreme genetic signatures of local adaptation during plant colonization

Colonization of new habitats is expected to require genetic adaptations to overcome environmental challenges. Here we use full genome re-sequencing and extensive common garden experiments to investigate demographic and selective processes associated with the recent colonization of Japan by Lotus japonicus. We carefully track the colonization process where L. japonicus gradually spread from subtropical conditions to much colder climates in northern Japan. We characterize the loss of diversity during this process and identify genomic regions with extreme genetic differentiation. Next, we perform population structure-corrected association mapping of phenotypic traits measured in a common garden and discover a number of genome-wide significant associations. Contrasting these analyses, we find that there is a strong concordance between phenotypic variation and extreme differentiation for overwintering and flowering time traits. Our results provide evidence that these traits were direct targets of selection by local adaptation during the colonization process and point to associated candidate genes.

evolutionary biology↗

bioRxiv2017

Organ-Specific NLR Resistance Gene Expression Varies With Plant Symbiotic Status

Nucleotide-binding site leucine-rich repeat resistance genes (NLRs) allow plants to detect microbial effectors. We hypothesized that NLR expression patterns would reflect organ-specific differences in effector challenge and tested this by carrying out a meta-analysis of expression data for 1,235 NLRs from 9 plant species. We found stable NLR root/shoot expression ratios within species, suggesting organ-specific hardwiring of NLR expression patterns in anticipation of distinct challenges. Most monocot and dicot plant species preferentially expressed NLRs in roots. In contrast, Brassicaceae species, including oilseed rape and the model plant Arabidopsis thaliana, were unique in showing NLR expression skewed towards the shoot across multiple phylogenetically distinct groups of NLRs. The Brassicaceae NLR expression shift coincides with loss of the endomycorrhization pathway, which enables intracellular root infection by symbionts. We propose that its loss offer two likely explanations for the unusual Brassicaceae NLR expression pattern: loss of NLR-guarded symbiotic components and elimination of constraints on general root defences associated with exempting symbionts from targeting. This hypothesis is consistent with the existence of Brassicaceae-specific receptors for conserved microbial molecules and suggests that Brassicaceae species are rich sources of unique antimicrobial root defences.

plant biology↗