MethylScore, a pipeline for accurate and context-aware identification of differentially methylated regions from population-scale plant whole-genome bisulfite sequencing data

Hüther et al. (2022) Quant. Plant Biol. 3, e9

Whole-genome bisulfite sequencing (WGBS) is the standard method for profiling DNA methylation at single-nucleotide resolution. Different tools have been developed to extract differentially methylated regions (DMRs), often built upon assumptions from mammalian data. Here, we present MethylScore, a pipeline to analyse WGBS data and to account for the substantially more complex and variable nature of plant DNA methylation. MethylScore uses an unsupervised machine learning approach to segment the genome by classification into states of high and low methylation. It processes data from genomic alignments to DMR output and is designed to be usable by novice and expert users alike. We show how MethylScore can identify DMRs from hundreds of samples and how its data-driven approach can stratify associated samples without prior information. We identify DMRs in the A. thaliana 1,001 Genomes dataset to unveil known and unknown genotype–epigenotype associations.

Jiawei Wang, a postdoc in the lab from 2005 to 2011 supported by EMBO, is one of this year's Xplorer Prize awardees, recognizing his fundamental contributions to plant developmental biology, including having been a pioneer in scRNA-seq analyses of plants. Congratulations, Jiawei!

(Translated from German)

Tübingen Children's University

Max Planck researcher Detlef Weigel at the Children's University: Big beak on demand

Max Planck researcher Detlef Weigel talked about dogs, finches and the four letters of life.

29.06.2022
By Ulla Steuernagel

Watching evolution at work takes time. At the Tübingen Children's University, it went a little faster. On Tuesday, biology professor Detlef Weigel explained to the young students how biodiversity develops and why a sheepdog is a sheepdog and not a dachshund. About 180 young and old listeners followed the lecture of the renowned and award-winning plant geneticist in the Kupferbau lecture hall.

When most people think of evolution, they think of dinosaurs. After all, they are considered the losers of evolution, having become extinct about 60 million years ago. Or are there still relatives, Weigel asked the children. And they knew that lizards and crocodiles are indeed related to the dinos, and birds even their descendants.

As an evolutionary scientist, you're dealing with very large periods of time and tiny little changes. But sometimes change can happen quickly and be highly visible. Here, "Sam" took the lecture hall stage, a mongrel of Australian shepherd and poodle. This friendly-looking animal with fuzzy fur and floppy ears could no longer be seen that dogs originally descended from wolves. With dogs, breeders mixed and mix, depending on the speed of long legs (sheepdog) or assistance in hunting (dachshund).

However, the development of living creatures usually happens entirely without human intervention. Nature creates the diversity and adapts the species to the environmental conditions. Even Charles Darwin, who was born more than two hundred years ago, observed how the beaks of finches on the Galapagos Islands changed depending on which seeds they had to pick.

However, the research couple Rosemary and Peter Grant found out long after him that large beaks were not advantageous for all times. Beaks evolved according to the weather and the size of the seeds. "Evolution," the professor said, "doesn't just go in one direction." The causes of such changes play out entirely in secret: in the tiny nucleus of each cell. This is where the genetic material, the genes, sit. "Not everything is inherited," Weigel explained. No matter how much the parents go to the gym - the muscles trained here do not transfer to the next generation.

Genes are part of DNA (the deoxyribonucleic acid or English: acid for acid), two spiral-shaped strands. DNA is composed of four elements, each designated by a letter: A, T, G, C. These elements cannot combine at will: G can only combine with C, A can only combine with T, and vice versa. The DNA also does not always remain the same: "Mutations, i.e. changes, occur all the time," says Weigel. If something goes wrong, the body can often repair it itself, but not always. For example, you can get sick from too much exposure to the sun.

Incidentally, the DNA was discovered in Tübingen. Weigel recommended taking a look at Friedrich Miescher's laboratory in the castle. And as far as evolution is concerned, Weigel summarized for the children: It creates changes in genes, it can be fast or slow, it doesn't run in just one direction, and it always takes place.

Wikipedia is often a good source
For his lecture, Detlef Weigel revealed, he had to look up some things, and he did so in a place that tends to be frowned upon in schools: "I find Wikipedia quite a good source," Weigel said. His real area of research is not dogs, but inconspicuous plants. The thale cress (scientific name: Arabidopsis) is very suitable for evolutionary observers; it reproduces quickly and is extremely adaptable, coping with a wide variety of climates in Europe, as well as in Asia, Africa and even Patagonia, just outside the South Pole. It is not obvious that it is also related to wild cabbage, which in turn was once related to wild mustard. But that was a while ago: "Ten million years," said Weigel.

Detlef Weigel with Sam, a family-friendly mix of Australian Shepherd dog and poodle. Picture: Ulrich Metz

Contrasting patterns of microbial dominance in the Arabidopsis thaliana phyllosphere

Derek S. Lundberg et al. (2022) bioRxiv 438366 https://doi.org/10.1101/2021.04.06.438366

Sphingomonas is one of the most abundant bacterial genera in the phyllosphere of wild Arabidopsis thaliana, but relative to Pseudomonas, the ecology of Sphingomonas and its interaction with plants remains elusive. We analyzed the genomic features of over 400 Sphingomonas isolates collected from local A. thaliana populations, which revealed high intergenomic diversity, in contrast to genetically much more uniform Pseudomonas isolates found in the same host populations. Variation in Sphingomonas plasmid complements and additional genomic features suggest high adaptability of this genus, and the widespread presence of protein secretion systems hints at frequent biotic interactions. While some of the isolates showed plant-protective properties in lab tests, this was a rare trait. To begin to understand the extent of strain sharing across alternate hosts, we employed amplicon sequencing and a novel bulk-culturing metagenomics approach on both A. thaliana and neighboring plants. Our data reveal that Sphingomonas and Pseudomonas both thrive on other diverse plant hosts, but that Sphingomonas is a poor competitor in dying or dead leaves.

Deep haplotype analyses of target-site resistance locus ACCase in blackgrass enabled by pool-based amplicon sequencing

Sonja Kersten et al. (2022) bioRxiv 496946 doi.org/10.1101/2022.06.22.496946

Rapid adaptation of weeds to herbicide applications in agriculture through resistance development is a widespread phenomenon. In particular, the grass Alopecurus myosuroides is an extremely problematic weed in cereal crops with the potential to manifest resistance in the course of only a few generations. Target-site resistances (TSRs), with their strong phenotypic response, play an important role in this rapid adaptive response. Recently, using PacBio's long-read amplicon sequencing technology in hundreds of individuals, we were able to decipher the genomic context in which TSR mutations occur. However, sequencing individual amplicons is both costly and time consuming, thus impractical to implement for other resistance loci or applications. Alternatively, pool-based approaches overcome these limitations and provide reliable allele frequencies, albeit at the expense of not preserving haplotype information. In this proof-of-concept study, we sequenced with PacBio High Fidelity (HiFi) reads long-range amplicons (13.2 kb) encompassing the entire ACCase gene in pools of over hundred individuals, and resolved them into haplotypes using the clustering algorithm PacBio amplicon analysis (pbaa), a new application for pools and for plants. From these amplicon pools, we were able to recover most haplotypes from previously sequenced individuals of the same population. In addition, we analyzed new pools from a Germany-wide collection of A. myosuroides populations and found that TSR mutations originating from soft sweeps of independent origin were common. Forward-in-time simulations indicate that TSR haplotypes will persist for decades even at relatively low frequencies and without selection, pointing to the importance of accurate measurement of TSR haplotype prevalence for weed management.

PICLN modulates alternative splicing and ensures adaptation to light and temperature changes in plants

Julieta L. Mateos et al. (2022) bioRxiv 496170 doi.org/10.1101/2022.06.14.496170

Plants undergo transcriptome reprogramming to adapt to daily and seasonal fluctuations in light and temperature conditions. While most efforts have focused on the role of master transcription factors, the importance of splicing factors modulating these processes is now emerging. Efficient pre-mRNA splicing depends on proper spliceosome assembly, which in plants and animals requires the PRMT5-methylosome complex. PICLN is part of the PRMT5-methylosome complex in both humans and Arabidopsis thaliana, and we show here that the human PICLN ortholog rescues phenotypes of A. thaliana picln mutants. Altered photomorphogenic and photoperiodic responses in A. thaliana picln mutants are associated with changes in pre-mRNA splicing, which partially overlap with those in prmt5 mutants. Mammalian PICLN also acts in concert with the Survival Motor Neuron (SMN) complex component GEMIN2 to modulate the late steps of UsnRNP assembly, and many alternative splicing events regulated by PICLN but not PRMT5 are controlled

by A. thaliana GEMIN2. As with GEMIN2 and SME1/PCP, low temperature, which increases PICLN expression, aggravates morphological and molecular defects of picln mutants. Taken together, these results establish a key role for PICLN in the regulation of pre-mRNA splicing and in mediating plant adaptation to daily and seasonal fluctuations in environmental conditions.