Biology subjects

Moeskjaer, S.

Publications and source records attributed to Moeskjaer, S..

5 recordsLinked to original sources

bioRxiv2021

Major effect loci for plant size before onset of nitrogen fixation allow accurate prediction of yield in white clover

White clover is an agriculturally important forage legume grown throughout temperate regions as a mixed clover-grass crop. It is typically cultivated with low nitrogen input, making yield dependent on nitrogen fixation by rhizobia in root nodules. Here, we investigate the effects of clover and rhizobium genetic variation by monitoring plant growth and quantifying dry matter yield of 704 combinations of 145 clover and 169 rhizobium genotypes. We find no significant effect of rhizobium variation. In contrast, we can predict yield based on a few white clover markers strongly associated with plant size prior to nitrogen fixation, and the prediction accuracy for polycross offspring yield is remarkably high. Several of the markers are located near a homolog of Arabidopsis thaliana GIGANTUS 1, which regulates growth rate and biomass accumulation. Our work provides fundamental insight into the genetics of white clover yield and identifies specific candidate genes as breeding targets.

plant biology↗

bioRxiv2020

Amplicons and isolates: Rhizobium diversity in fields under conventional and organic management

BackgroundThe influence of farming on plant, animal and microbial biodiversity has been carefully studied and much debated. Here, we compare an isolate-based study of 196 Rhizobium strains to amplicon-based MAUI-seq analysis of rhizobia from 17,000 white clover root nodules. We use these data to investigate the influence of soil properties, geographic distance, and field management on Rhizobium nodule populations. ResultsOverall, there was good agreement between the two approaches and the precise allele frequency estimates from the large-scale MAUI-seq amplicon data allowed detailed comparisons of rhizobium populations between individual plots and fields. A few specific chromosomal core-gene alleles were significantly correlated with soil clay content, and core-gene allele profiles became increasingly distinct with geographic distance. Field management was associated with striking differences in Rhizobium diversity, where organic fields showed significantly higher diversity levels than conventionally managed trials. ConclusionsOur results indicate that MAUI-seq is suitable and robust for assessing nodule Rhizobium diversity. We further observe possible profound effects of field management on microbial diversity, which could impact plant health and productivity and warrant further investigation.

ecology↗

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

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↗