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Commentary on Earth Biogenome project

Posted on December 01, 2019

Please take genome assembly quality into account read more

The Earth BioGenome project: Opportunities and Challenges for Plant Genomics and Conservation

Moises Exposito Alonso, Hajk Georg Drost, Hernán A. Burbano & Detlef Weigel
Plant Journal | 01 December 2019 https://doi.org/10.1111/tpj.14631

Sequencing them all. That is the ambitious goal of the recently launched Earth BioGenome Project (Lewin et al., 2018), which aims to produce reference genomes for all eukaryotic species within the next decade. In this Perspective, we discuss the opportunities of this project with a plant focus, but highlight also potential limitations. This includes the question of how to best capture all plant diversity, as the green taxon is one of the most complex clades in the tree of life, with over 300,000 species. For this, we highlight four key points: (1) the unique biological insights that could be gained from studying plants, (2) their apparent underrepresentation in sequencing efforts given the number of threatened species, (3) the necessity of phylogenomic methods that are aware of differences in genome complexity and quality, and (4) the accounting for within?species genetic diversity and the historical aspect of conservation genetics.

AraPheno and AraGWAS updates

Posted on November 19, 2019

RNA-Seq and knockout mutation data for Arabidopsis thaliana read more

AraPheno and the AraGWAS Catalog 2020: a major database update including RNA-Seq and knockout mutation data for Arabidopsis thaliana

Matteo Togninalli, Ümit Seren, Jan A Freudenthal, J Grey Monroe, Dazhe Meng, Magnus Nordborg, Detlef Weigel, Karsten Borgwardt, Arthur Korte, Dominik G Grimm

Nucleic Acids Research, gkz925, https://doi.org/10.1093/nar/gkz925

Genome-wide association studies (GWAS) are integral for studying genotype-phenotype relationships and gaining a deeper understanding of the genetic architecture underlying trait variation. A plethora of genetic associations between distinct loci and various traits have been successfully discovered and published for the model plant Arabidopsis thaliana. This success and the free availability of full genomes and phenotypic data for more than 1,000 different natural inbred lines led to the development of several data repositories. AraPheno (https://arapheno.1001genomes.org) serves as a central repository of population-scale phenotypes in A. thaliana, while the AraGWAS Catalog (https://aragwas.1001genomes.org) provides a publicly available, manually curated and standardized collection of marker-trait associations for all available phenotypes from AraPheno. In this major update, we introduce the next generation of both platforms, including new data, features and tools. We included novel results on associations between knockout-mutations and all AraPheno traits. Furthermore, AraPheno has been extended to display RNA-Seq data for hundreds of accessions, providing expression information for over 28 000 genes for these accessions. All data, including the imputed genotype matrix used for GWAS, are easily downloadable via the respective databases.

bioRxiv: Microbial biomass & disease in wild plants

Posted on November 03, 2019

Absolute microbial biomass as an indicator of disease in wild A. thaliana read more

The relationship between microbial biomass and disease in the Arabidopsis thaliana phyllosphere

Karasov et al., bioRxiv 828814, posted November 3, 2019.

A central goal in microbiome research is to learn what distinguishes a healthy from a dysbiotic microbial community. Shifts in diversity and taxonomic composition are important indicators of dysbiosis, but a full understanding also requires knowledge of absolute microbial biomass. Simultaneous information on both microbiome composition and the quantity of its components can provide insight into microbiome function and disease state. Here we use shotgun metagenomics to simultaneously assess microbiome composition and microbial load in the phyllosphere of wild populations of the plant Arabidopsis thaliana. We find that wild plants vary substantially in the load of colonizing microbes, and that high loads are typically associated with the proliferation of single taxa, with only a few putatively pathogenic taxa achieving high abundances in the field. Our results suggest (i) that the inside of a plant leaf is on average sparsely colonized with an estimated two bacterial genomes per plant genome and an order of magnitude fewer eukaryotic microbial genomes, and (ii) that higher levels of microbial biomass often indicate successful colonization by pathogens. Lastly, our results show that load is a significant explanatory variable for loss of estimated Shannon diversity in phyllosphere microbiomes, implying that reduced diversity may be a significant predictor of microbial dysbiosis in a plant leaf.

bioRxiv: Integrated sequencing approaches for microbiome analyses

Posted on October 30, 2019

Combining WGS and 16S rDNA to detect microbe-microbe interaction networks read more

Combining whole genome shotgun sequencing and rDNA amplicon analyses to improve detection of microbe-microbe interaction networks in plant leaves

Regalado, Lundberg et al., bioRxiv 823492, posted October 30, 2019.

Microorganisms from all domains of life establish associations with plants. Although some harm the plant, others antagonize pathogens or prime the plant immune system, acquire nutrients, tune plant hormone levels, or perform additional services. Most culture-independent plant microbiome research has focused on amplicon sequencing of 16S rDNA and/or the internal transcribed spacer (ITS) of rDNA loci, but the decreasing cost of high-throughput sequencing has made shotgun metagenome sequencing increasingly accessible. Here, we describe shotgun sequencing of 275 wild Arabidopsis thaliana leaf microbiomes from southwest Germany, with additional bacterial 16S rDNA and eukaryotic ITS1 amplicon data from 176 of these samples. The shotgun data were dominated by bacterial sequences, with eukaryotes contributing only a minority of reads. For shotgun and amplicon data, microbial membership showed weak associations with both site of origin and plant genotype, both of which were highly confounded in this dataset. There was large variation among microbiomes, with one extreme comprising samples of low complexity and a high load of microorganisms typical of infected plants, and the other extreme being samples of high complexity and a low microbial load. We use the metagenome data, which captures the ratio of bacterial to plant DNA in leaves of wild plants, to scale the 16S rDNA amplicon data such that they reflect absolute bacterial abundance. We show that this cost-effective hybrid strategy overcomes compositionality problems in amplicon data and leads to fundamentally different conclusions about microbiome community assembly.

bioRxiv: GWAS without complete genomes

Posted on October 25, 2019

No genome required: Finding causal genetic variants not present in a reference genome read more

Finding genetic variants in plants without complete genomes

Voichek, Y., & Weigel, D., bioRxiv 818096, posted October 25, 2019.

Structural variants and presence/absence polymorphisms are common in plant genomes, yet they are routinely overlooked in genome-wide association studies (GWAS). Here, we expand the genetic variants detected in GWAS to include major deletions, insertions, and rearrangements. We first use raw sequencing data directly to derive short sequences, k-mers, that mark a broad range of polymorphisms independently of a reference genome. We then link k-mers associated with phenotypes to specific genomic regions. Using this approach, we re-analyzed 2,000 traits measured in Arabidopsis thaliana, tomato, and maize populations. Associations identified with k-mers recapitulate those found with single-nucleotide polymorphisms (SNPs), however, with stronger statistical support. Moreover, we  identified new associations with structural variants and with regions missing from reference genomes. Our results demonstrate the power of performing GWAS before linking sequence reads to specific genomic regions, which allow detection of a wider range of genetic variants responsible for phenotypic variation.

Out in PNAS: Convergent evolution of herbicide resistance

Posted on September 30, 2019

We describe how glyphosate resistance evolves in waterhemp read more

Multiple modes of convergent adaptation in the spread of glyphosate-resistant Amaranthus tuberculatus

Kreiner et al., PNAS, published September 30, 2019

While evolution has been thought of as playing out over millions of years, adaptation to new environments can occur very rapidly, presenting us with key opportunities to understand evolutionary dynamics. One of the most amazing examples of real-time evolution comes from agriculture, where due to the intense use of a few herbicides, many plant species have evolved herbicide resistance to become aggressive weeds. An important question has been whether herbicide resistance arises only rarely and then spreads quickly, or whether herbicide resistance arises all the time de novo. Our work with glyphosate resistance in US Midwestern and Canadian populations of Amaranthus tuberculatus reveals the answer to be, “it depends,” as we surprisingly find examples for both modes of evolution.

 

 

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