Hi, these are my notes on the Cereal Bioinformatics Session, plus the keynote by Keith Edwards, at Monogram 2019.
The rest of the notes are at https://bioinfoperl.blogspot.com/2019/05/monogram19-2.html?m=1
The rest of the notes are at https://bioinfoperl.blogspot.com/2019/05/monogram19-2.html?m=1
Cristobal Uauy, JIC
Speaks
about http://wheat-expression.com and explains the different
references, from TGAC to RefSeq v1.0 (with 01 in the middle of gene names) and v1.1
(02 instead, as in TraesCS3D02G273600,
used in http://plants.ensembl.org/Triticum_aestivum/Info/Index). He asks users to cite the papers
not just the Web site. He mentions also the gene expression browser http://bar.utoronto.ca/efp_wheat/cgi-bin/efpWeb.cgi , http://www.polymarker.info to design polyploid-aware primers and the in silico wheat TILLING
integrated in Ensembl Plants (http://www.wheat-tilling.com is legacy on previous gene models,
but still useful in some cases). He wraps up by describing http://www.wheat-training.com , which links out to all resources and wheat
populations as well.
Guy Gnaamati, EMBL-EBI
Describes
the RefSeq v1.0 assembly with the v1.1 gene annotation in Ensembl Plants, the updated marker
display (http://plants.ensembl.org/Triticum_aestivum/Variation/Explore?r=4A:714193214-714194214;v=BA00249348;vdb=variation;vf=194242) and their linked SIFT predictions. He summarizes the outcome of the
ensembl4breeders event (see table in poster belowttps://twitter.com/ensemblgenomes/status/1098902364998782976https://twitter.com/ensemblgenomes/status/1098902364998782ttps://twitter.com/ensemblgenomes/status/1098902364998782976https://twitter.com/ensemblgenomes/status/1098902364998782976), and singles out pangenomes and the wheat test case as a
prototype to develop that within Ensembl. He finishes advertising the upcoming
Plant Genomes in a Changing Environment conference in October, 2019 (https://coursesandconferences.wellcomegenomecampus.org/our-events/plant-genomes-2019)
Leif Skot, IBERS
He talks
about breeding targets in outperennial ryegrass (Lolium perenne ) and genomic predictions based on a 50yr running
breeding experiment with linear biomass, yield gains with no signs of
inbreeding depression yet. There seems to be a physically-anchored genome
assembly under way (https://gtr.ukri.org/projects?ref=BB%2FG012342%2F1), but not ready yet; there are
though synteny-based (https://www.ncbi.nlm.nih.gov/pubmed/26408275) and de novo (https://link.springer.com/chapter/10.1007/978-3-319-28932-8_19) assemblies.
Craig Simpson, JHI
They are
using Salmon/kallisto to quantify barley transcriptomes, knowing that current
barley gene models are still poor. Their aim is also to build a reference
transcriptome (BarRTv1) with https://ccb.jhu.edu/software/stringtie guided by Morex assembly. They
analyze 11 RNAseq datasets, with over 800 Illumina samples. They filter out
low-expression transcripts (less than 0.3TPM)
and use gmap to map back to Morex reference. They try to validate their
expression values with RT-PCR and realize how difficult is to map multiple
isoforms to a single PCR read. By correlating with RT-PCR results they defined
optimal StringTie params: -c 2.5 - 50 –f 0, yielding over 60K genes and 177K
transcripts, less than the original, which have been imported into a database
by Linda Milne. They plan to do BarRTv2 with PacBio Iso-seq. He says there are
many genes with a single dominant isoforms but also many others with 2-4
dominant isoforms, which could be nice to annotate in resources such as
Ensembl. This data is still unpublished.
Kumar Gaurav, JIC
He talks
about wild parents of wheat and their recent R-gene enrichment sequencing work
to show they contain useful disease resistance genes. They belong to the Open
Wild Wheat consortium, and have sequenced 260 Aegilops tauschii individuals
with 10-30x cover (10Tb, available under Toronto agreement, seeds from JRU, JCI).
They are performing diversity studies and mention wheat lineages 1 and 2.
Anthony Hall, JIC
He talks
about a pan-genome of wheat elite cultivars as a way to gain access to hidden
variability (SV, TE, promoters). This is the 10+ project, with NRGene RefSeq
and W2RAP (https://github.com/bioinfologics/w2rap) assemblies. They know they are not
covering all wheat variability out there. The assemblies are ready, they are
now finishing the annotations with both de novo and validated gene models using
a pan-transcriptome. A BLAST server is already available at https://webblast.ipk-gatersleben.de/wheat_ten_genomes .
Micha Bayer, JHI
He talks about the barley variome sampled from exome capture of 823 barley genotypes, covering mainly SNP and small indels. He discusses the depth vs breadth dilemma when managing diversity in germplasm. Their cultivars come from WHEALBI, EXCAP, B1K Israel, WBDC and other projects.
Less than 5% of their final variant come from exons, with most coming from introns and UTRs. 96% are off-target variants with low read depth, with sufficient calling quality. Population level analyses distinguish wild and cultivated barleys, with low recombination around centromeres. They use SnpEff and are looking at fixed loss-of-function alleles in domesticated barleys. He mentions 20-30% of reads do not map the reference with max 4% mismatches.
After his talk, there’s a discussion on how to name genes in the context of pan-genomes. Cristobal says the role in Ensembl will be critical in this context.
Sebastian Raubach, JHI
After his talk, there’s a discussion on how to name genes in the context of pan-genomes. Cristobal says the role in Ensembl will be critical in this context.
Talks about
Germinate v3 https://ics.hutton.ac.uk/get-germinate, a one-stop database schema for
plant genetic resources, with powerful visualizations. It supports BrAPI,
Multi-Crop Passport Descriptors (MCPD) and Dublin Core Metadata Initiative
(DCMI). It comprises 3 modules: Scan (bar codes), Data Import and Germinate. It
is used by 100+ groups working on different crops around the world, including
wheat and maize at CIMMYT. Data can be exported to Helium, Flapjack, R, Excel,
BraPI, google maps. It supports custom, restricted data access.
Keywan Hassani-Pak, Rohampstead
He talks
about KnetMiner3.0 (http://knetminer.rothamsted.ac.uk) and does a quick 5-minute off-line
demo. He shows case the evidence view, which is an enrichment analysis, and the
keyword search to get more specific search results.
He then
makes a DFW progress report on behalf of Rob Davey (EI), including https://grassroots.tools, which is about making data
publicly available, and http://cyverseuk.org
Paul Wilkinson, U Bristol
He talks
about http://www.cerealsdb.uk.net/cerealgenomics/CerealsDB/indexNEW.php, built with Perl and PHP on top a
database. He focuses specifically on the most recently added features,
including a QTL database made in collaboration with the JIC and EI (which links
out to Ensembl Plants), online dendrograms (http://www.cerealsdb.uk.net/cerealgenomics/CerealsDB/35K_dendrogram.php) and an introgression plotter. The
latter will become available soon and allows visualizing genomic regions
introgressed in crosses. It produces nice circular plots and heatmaps.
Mario Caccamo, NIAB
He starts
by talking about http://wheatis.org, which is part of the 2011 launched wheat
initiative. There are 5 nodes across EU and US, including Ensembl Plants and
Gramene. He then moves to the recent work regarding a group of experts around
wheat gene nomenclature with the Wheat Gene Catalogue https://shigen.nig.ac.jp/wheat/komugi/genes/symbolClassList.jsp
Roughly,
10-15% of the loci in the catalogue correspond to current gene models, not
always on a 1-to-1 relation.
Kim Hammond-Kosack, Rothampsted
She talks
about PHI-base (http://www.phi-base.org) on pathogens-host interactions.
Hosts are plants half of the time, not only cereals. Main use is to lookup of
mutant-phenotypes relationships. They use a scale of 9 phenotypes, including
negative results. They have a tool (PHI-canto) to allow users to annotate their
own results with controlled vocabularies. It complies with FAIR Data
principles.
Keith Edwards, U Bristol (plenary talk)
He talks about
the genomic challenges in wheat and how we are discovering the actual diversity
of wheats thanks to the marker technologies. This is in contrast to what was thought
earlier, that they lacked variability. Today the can scan 98K KASP markers in 1
day and we now that this species, despite being only 10K yr old and having gone
through 1-2 hybridizations, has a massive diversity. This is probably due to hybrid
swarms, populations of hybrids that interbreed and backcross with their parents
(diploid & tetraploids). He shows two examples of extensive introgressions in
chromosomes of elite cultivar Cadenza and two ancient wheats: Watkins 199 and Chaff 1790 from Rothampsted.
He concludes that variation was already there 10K yr ago, is not new, and that
there is forced gene flow between wheat and its parents and close species,
mostly the tetraploids. These introgressed regions do not usually recombine, as
they are too divergent (over 0.5%), and impose a LEGO-like genome, with recombination
restricted to certain windows.
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| Source: http://www.earlham.ac.uk/articles/earlham-institute-lego-sequencer |
