Tuesday 17012023
Ian D Godwin, QAAFI, The University of Queensland. While he introduces sorghum, he recommends the book https://drunkenbotanist.com, which can be used for drinks, food and chicken fodder. In Australia it is grown in the driest area on the E. They are using gene editing to improve it and require high quality genomic resources, such as https://www.nature.com/articles/s41477-021-00925-x . They are particularly interested in high resolution PAV maps, as PAV is a main driver of diversity in this crop. Also they use a non-reference assembly for their work, although transformation still needs to be optimized. They have selected their own promoters that also work well in barley and maize. They are using these to optimize may trais, mostly plant and root architecture, but also starch composition, which is naturally in a tight protein matrix that make it undigestible (https://onlinelibrary.wiley.com/doi/full/10.1111/pbi.13284). The plants have to be tested in the field, root reach the bottom of a pot in 10 days. The obtained lies with increased protein and larger grains. They have also tested them for poultry feeding, and observed that digestible, high protein content reduces the amount of soy-based fodder required by chicken. They further improved protein digestability by knocking out gamm-kapharin. He mentions that a VRN1 homolog in Sorghum controls root angle. In questions he says they are now introgressing their edited genes in parental lines used for Sorghum hybrids.
Viviane Slon, Tel Aviv University. She extracts ancient DNA from sediments. Previous work have extracted plant and animal DNA 400K yr old (permafrost). Such experiments allow to find out first/last appearance dates in sediments, which can be correlated to past biodiversity, history, climate change and human activity. A few weeks ago researchers have been able to go back 2M yr in Greenland. About 90% of the successfully extract DNA has no BLASTN hits. To improve yield they use mammalian mtDNA capture. What does differentiate ancient DNA from modern? It is shorter, C in single-stranded ends deaminate -> T (this is actually as a sanity check by counting nt substitution pero position). They are now able to extract hominid mtDNA from the soil even when there are no bones, as they have shown in the Denisova cave (https://www.nature.com/articles/s41586-021-03675-0). They have also managed to extract nuclear DNA in Galería de las estatuas, Atapuerca (https://www.science.org/doi/10.1126/science.abf1667) and distinguished two Neanthertal populations. What next? Her lab is now developing methods to improve field sampling, the wet lab and data analyses. With this toolbox we should be able to fill the gaps in the biodiversity history, particularly for plants. With high density sampling in sediment transects we should be able to estimate changes in allele frequencies with help from coalescent theory.
Samuel P. Hazen, University of Massachusetts Amherst. Talks about their experiments to find TFs that might be controlling cell wall thickening in Brachupodium distachyon., such as the bZIP named SWIZ. This is one among other TFS that are thigmotropic, relocating and locally expressing to the nucleous when the plant is touched/perturbed (this depends on calmodulin and Ca being released). Expression lasts about 1h. They find that 7-9K genes are differentially expressed (DE) upon touching the plants and they have also discovered a couple of DNA motifs for SWIZ using ATAC-Seq analysis. They have also done de novo discovery of motifs upstream of DE genes. Adding external GA hormone represses movement to the nucleous. There’s a preprint at https://www.biorxiv.org/content/10.1101/2021.02.03.429573v2.abstract
Melissa Bredow, Department of Plant Pathology and Microbiology, Iowa State University. Frost is still an important stress for crops despite global warming. Freeze damage starts by seed ice crystal that end up piercing cell membranes. Gradual expose to cold expressed ice-binding proteins (IBP) that protect membranes upon freeze. She uses brachy as model to study the protection provided by IBPs. There are seven IBPs in B. distachyon (BdIRI1-7), none in A. thaliana. These protein are only stable < 4ºC (disordered otherwise) and theire folds are different across species. Apparently is not just cold what matters, but also bacterial (Xanthomonas, Pseudomonas sp) ice nucleation proteins that favour freeze and membrane destruction. Their current modela is that BdIRI proteins actually bind to bacterial nucleation proteins to inhibit their function.
Todd Blevins, Centre national de la recherche scientifique, University of Strasbourg. Studies the role of RNA polymerase IV in brachy, which silence transposons by transcribing non-coding RNAs that drive AGO-based silencing, as reviewed in https://www.annualreviews.org/doi/abs/10.1146/annurev-arplant-093020-035446. Mutants of these genes (nrpd1) have reduced leaf elongation via regulation of cell production and via cell cycle exit. In addition, mutation causes higher expression of some genes, including bZIP TFs, which are silenced in the wild type. These have differentially methylated promoters. This varies across ecotyopes and depends on the presence/absence of a TE. They have screened methylated sequences with Illumina and Nanopore and found very comparable results, although ONT is superior when it comes to check individual TEs, as Illumina reads multimap.
Birkett Clay, USDA-ARS. Talks about integrating into https://breedbase.org Practical Haplotype Graphs built from exome data for wheat and barley. He uses code at https://github.com/TriticeaeToolbox/PHGv2 and imputation protocols at https://wheat.triticeaetoolbox.org/static_content/files/imputation.html. Imputation accuracy at the PHG in barley is > 93% if #markers > 2000. Details and converted VCF files are available at https://files.triticeaetoolbox.org . They display the resulting PHG with JBrowse (https://triticeaetoolbox.org/jbrowse). The PHG is built on a single reference genome, so you might need to select the appropriate reference to optimize imputation (or build a mosaic reference). Creating the PHG is computationally intensive, but the imputation is quite fast.
Karen A Sanguinet, Washington State University. She talks about buzz mutants that affect root biomass and hair formation in brachy. The A. thaliana ortholog rescue the mutant phenotype. She saw that BUZZ expression responds to N availability, although primary root growth is not N-responsive. It is expressed in the root epidermis.
Kapeel Chougule, Cold Spring Harbor Laboratory. Presents (PanOryza) efforts to consistently annotate gene models in the rice pangenome. Canonical isoforms are called with TRaCE (https://academic.oup.com/bioinformatics/article/38/1/261/6326792). At Gramene they have rice subsite and plan to build pan-gene indexes.
Andrew Olson, Cold Spring Harbor Laboratory. After a little history of the Gramene project (2022), he presents the pangenome sites (2021-22), which currently represent the larger bulk of new genes being added to Gramene (maize, rice, Vitis and Sorghum). He goes to summarize all the tasks involved in setting up and maintaining the sites, the import of data from Ensembl Plants (https://plants.ensembl.org) and Expression Atlas, and mentions they are now following the standards agreed at https://data.nal.usda.gov/ag-data-commons-collection-development-policy.
Sushma Naithani, Dept. of Botany and Plant Pathology, Oregon State University. She presents her work on curating plant reactome pathways using omic datasets (https://plantreactome.gramene.org). These pathways are linked to genes in Ensembl Plants and Gramene, which in turn often link to gene expression data. The curation protocols are illustrated at https://peerj.com/articles/11052. Currently they 126 species and 326 pathways, which have been project to 39K genes.
My turn. I presented our recent work "Building pangene sets from plant genome alignments confirms presence-absence variation", from the PanOryza project. The preprint can be read at https://www.biorxiv.org/content/10.1101/2023.01.03.520531v1 and code and documentation obtained here: https://github.com/Ensembl/plant-scripts/tree/master/pangenes.
[Source: Agata]
Jonathan Cahn, HHMI-Cold Spring Harbor Laboratory. Talks about regulatory elements in maize inferred from diverse omics datasets (ie ChIP-seq, H3K4-me1) as part of http://www.maizecode.org, which follows ENCODE guidelines. Raw data can be downloaded, I cannot see the DNA motifs though. Superenhancers are delimited by methylated areas and enriched in H3K27ac and accumulate binding sites.The results of this project are described at https://www.frontiersin.org/articles/10.3389/fpls.2020.00289/full. Shows really nice plots made with https://cran.r-project.org/web/packages/ggalluvial
Sarah Dyer, EMBL-EBI. Talks summarizes the current status of the wheat pangenome at Ensembl Plants: https://plants.ensembl.org/Triticum_aestivum/Info/Strains?db=core. The main addition since last time I checked is that now wheat genes have a cultivar-based Compara section, where you can see orthology to genes in other pangenome wheats, ie: https://plants.ensembl.org/Triticum_aestivum/Gene/Strain_Compara_Tree?g=TraesCS3D02G273600;r=3D:379535906-379539827
Josh Clevenger, HudsonAlpha Institute for Biotechnology. https://www.hudsonalpha.org/khufudata/plant-improvement
On Twitter I heard about a talk I missed by Katie Jenike were she presented Panagram, K-mer based software for alignment-free visualization & analysis of pan-genomes. There’s code (https://github.com/kjenike/panagram) and even slideas at https://twitter.com/mike_schatz/status/1615440857980899328
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