Consultas eficientes sobre ficheros TSV con SQL

Hola,
estos dias está de visita mi colega Valerie y me preguntaba si había alguna manera de seleccionar de manera eficiente filas de un fichero con millones de líneas, en su caso con columnas separadas por tabuladores (TSV). Yo le sugerí una base de datos relacional y como ella escribe sobre todo en python lo hicimos así, con sqlite:

import sqlite3

# local file with data to populate SQL db
data_file = 'data4sql.tab'

# persistent database file to be created, returns a Connection
conn = sqlite3.connect('example.sqlite.db')

# Cursor object to perform SQL commands on that connection
c = conn.cursor()

# create a table as a list of columns and their types (NULL, INTEGER, REAL, TEXT, BLOB)
# NOTE: the columns should match those in data_file
tb_name = 'mytable'
c.execute('CREATE TABLE {tn}\
             (IMG text, scaffold_id text, GC real, length integer, locus_tag text,\
             IMG_gene_id text, gene_type text, gene_start integer, gene_stop integer,\
             gene_length integer, depth real)'.format(tn=tb_name))

with open(data_file) as fin:
    for line in fin:
        cols = line.rstrip().split("\t")

        # make sure empty values are changed to NULL
        cols=[None if x=='' else x for x in cols]
        
        # Insert a row of data
        c.execute("INSERT INTO {tn} VALUES (?,?,?,?,?,?,?,?,?,?,?)".format(tn=tb_name),cols[0:11])

# save (commit) the changes
conn.commit()

# example queries, any valid SELECT SQL can be used
c.execute('SELECT * FROM {tn} WHERE depth >10'.\
        format(tn=tb_name))
for line in c.fetchall():
   print(line)

# close and exit
conn.close()

En realidad esto se debería separar en dos programas, uno para crear la base de datos y otro para hacer consultas sobe ella. El código es sencillo, pero deberás conocer un mínimo de sintaxis SQL para entender cómo crear tablas, con sus tipos, y cómo hacer consultas. Fíjate que los valores perdidos los sustituimos por un objeto None,
saludos,
Bruno y Valerie

4th International Brachypodium Conference

Hi, the 4th International Brachypodium Conference started a few hours ago in Huesca, Spain, this side of the Pyrenees. Some people will be tweeting about this with hashtag #IntBrachyConf2019

http://brachypodium2019.unizar.es

Here I will be posting my notes on the talks I attend.

  PS: The abstract book has been published at https://zaguan.unizar.es/record/79582

 

  Tuesday

Keynote by Elizabeth Kellog . I missed the first part of the talk, but she presented a whole range of data (histological, genomic, genetic) showing that the abscission zone (AZ), which is where florets in the spikelet shed, is fundamentally different in three grasses: Brachypodium, Oryza and Setaria. A key result was that only 3 genes are differently expressed in all three species, including yabby2 and myb26, and that lignin does not seem fundamental for abscission. However, later GWAS work on a wide Setaria panel found a single locus explaining abscission phenotypes, and it was a different myb transcription factor. A key question arising is why grasses have developed different genetic mechanisms to control abscission. You can read more about this at:

https://onlinelibrary.wiley.com/doi/10.1002/9781119312994.apr0619
https://www.ncbi.nlm.nih.gov/pubmed/27257006

Wednesday

Session: Natural diversity and evolution

Robert Hasterok, University of Silesia

http://brachypodium2019.unizar.es/robert-hasterok

He speaks about the evolution of the grass karyotype, which is 100-150Myr old, with a basic chr number n=5, and the species in the Brachypodium genus, with a variety of ploidy levels and chr numbers. He focus first on barcoding of annual B. stacei, B. distachyon and B. hybridum using dozens of BACs from B. distachyon to track chr regions (https://academic.oup.com/aob/article/122/3/445/5034913). Then he moves to more complex perennials, showing unpublished results. Although showing conserved syntenic chr regions, perennials have larger genomes. Regarding B. mexicanum, their data cannot so far tell whether it is allopolyploid or perhaps underwent whole-genome duplication.

Liang Wu,  Zhejiang University, Hangzhou

He talks about divergent roles of FTs in flowering control in Brachypodium distachyon, building on previous published work (https://www.nature.com/articles/ncomms14320). While there are only 2 homologues in Arabidopsis thaliana, there are 6 copies in B. Distachyon. He then goes on to show experimental results on some of them. For instance, FT2 alternative splicing and dimerization seem to be involved with age flowering. Instead, FT5 is induced in short days and has a weak flowering inductivity. In fact it represses flowering in long days and it is itself repressed by CO1, although they don’t have an antibody to directly check the interaction  (https://www.nature.com/articles/s41467-019-08785-y).

Sinead Dread, U Leicester   

She talks about Brachypodium distachyon grains in a comparative (flat, little starch vs creased grain) and evolutionary context. Brachy are sister to core pooids (Bromeae, Triticeae, Aveneae, Poeae). Compared to Triticeae, brachy aleurone cannot be separated from the grain as easily. Most of these observations have been published at https://www.ncbi.nlm.nih.gov/pubmed/24723396 . They have available reference transcriptomes of the grain (that they hope to host at the EBI) which they are using to study the expression of transcription factor families relevant in the grain (FIL2/6,YABBY22/5, INO). She terminates with in situ pics showing similarities between brachy and rice.

Benoit Lefebvre, INRA Toulousse

https://www6.toulouse.inra.fr/lipm_eng/Research/Symbiotic-signalling/Members

Brachypodium distachyon genetic variability for beneficial interaction with arbuscular mycorrhizal fungi (AMF), a kind of associations that have been shown to protect against diseases in rice (Magnaporthe oryzae) and that in brachy seems to depend on the availability of both P and N in the root. They work first with ecotype Bd3-1 to set up an automated phenotyping system to assess the effect of AMF on growth. Now they are analyzing all ecotypes sequenced at the JGI. Clearly there seems to be a positive response in some ecotypes (particularly those with low biomass) and also negative on others (affects resource allocation). He has published several papers on this: https://www.ncbi.nlm.nih.gov/pubmed/28548654 , https://www.ncbi.nlm.nih.gov/pubmed/30405668,https://www.ncbi.nlm.nih.gov/pubmed/30347445.

Errol Véla,  U Montpellier

His talk is taxonomic, about the typification of names and their taxonomic assignment within the Brachypodium distachyon complex, a work they are carrying out in collaboration with the group of Pilar Catalán. He shows very nice pics of morphological traits that clearly differentiate the three annual Brachypodium species. Their main result is that B. stacei had been described earlier on a wider distribution area including France and Algerie, and should be renamed to B. rigidum.

Session: Comparative genomics and transcriptomics   

Robin Buell, Michigan State U  

http://brachypodium2019.unizar.es/speakers/robin-buell

She talks about “Life with 1000 genomes: Defining the pan-genome in maize” after a short intro on bacterial pan-genomes. Structural variation is impacted by reproductive mode, TEs, ploidy, with outcrossers so far showing more variability (maize vs potato). What’s an allele? Structural variants are usually lowly expressed, shorter, and a subset of them have roles in adaptation, and should be considered in genotype-phenotype analyses. They have done GWAS/eQTL studies to identify genes/alleles that confer higher ethanol content from corn stover. They use transcriptomes as pangenoma proxies and map accessory transcript based on LD and have confirmed the PAV patterns in whole-genome assemblies which have been produced since (http://www.plantcell.org/content/26/1/121 , https://dl.sciencesocieties.org/publications/tpg/abstracts/0/0/180069). She expects PAV genes to be able to complement absent genes in hybrids. She also shows results on clustering pangenes in terms of protein sequences, confirming that the variability is still there, with lots of unique proteins found in some cultivars (B73, PH207, PHJ89). The found a PAV explaining resistance to mosaic virus resistance, while SNPs could not provide signal. Expression data is critical to remove PAV genes not relevant in a particular condition of interest. They have built a broad expression atlas of B73 with 79 tissues: over 4K pangenes have FPKM larger than 1, apparently enriched in the seed (https://onlinelibrary.wiley.com/doi/10.1111/tpj.14184). They have also done WGNCA and found modules enriched in particular functions which include PAV genes and a few are highly connected. They use stringent criteria (I believe araound 80% identity) to remove “copies” of existing genes.

Keiichi Mochida, RIKEN 

Starts by summarizing virtues of hybrid crops in terms of vigor or biomass, as happens with B. hybridum.  He then moves to the transcriptome analysis of gene regulatory network reveals differential organization of rhythmic transcriptome between sub-genomes in the allopolyploid grass B. hybridum. This work has been published at https://academic.oup.com/gigascience/article/7/4/giy020/4924998. The main message is that in their experiment they found thousands of genes (about 20% of genes) with differential expression when comparing the hybrid and the parental diploids (B. distachyon, B. stacei).

Alexander Betekhtin, U Silesia in Katowice

He talks about his work on CRISPR/Cas9-based targeted mutagenesis in B. distachyon and B. hybridum and its application to study the model grass genome organization, a field in which they have relevant experience (https://www.ncbi.nlm.nih.gov/pubmed/29893795). Their hypothesis is that genome stability depends on the CDKG/Ph1 pathway, as seen in bread wheat and Arabidopsis thaliana. They are 4 copies of this genes. They induce mutants in several of them and are now trying to understand the cytogenetic phenotypes. 

János Györgyey, Hungarian Academy of Sciences  

He explains he moved from wheat work on root architecture to brachy and then starts talking about the LOB-domain transcription factor gene family in B. distachyon, a work they published at https://www.ncbi.nlm.nih.gov/pubmed/27686461. LOB stands for lateral organ boundary. These TFs contain a Leu zipper domain as part of the larger LOB domain (https://www.sciencedirect.com/science/article/abs/pii/S1360138510002050). They are characterizing the expression of all the gene copies of this family across tissues.

Bruno Contreras Moreira, Ensembl Plants, EBI

My talk is “A pan-genome perspective on the co-expression response of genes to drought in the model grass B. distachyon”, which was mainly the work of Rubén Sancho, a former PhD student. Here we analysed the osmotic stress responses of 33 B. distachyon ecotypes under two conditions, mild drought (D) and well-watered (control, C). Leaf transcripts were sequenced and pseudo-aligned to the Bd21 reference genome with a double purpose: i) to estimate their abundance and, ii) to assess the proportions of core and accessory genes expressed in response to drought. We built weighted co-expression networks from the transcriptome data and were able to dissect two distinct network topologies in drought and control conditions, respectively. While transcripts of control plants could be clustered in 30 modules with 839 hub genes, plants under mild drought yielded 38 modules with 628 genes annotated as hubs. By comparing the resulting modules we identified five exclusive D modules containing over-expressed genes enriched in Gene Ontology terms such as proline synthesis, response to water deprivation, phosphate starvation and temperature stimulus. In those exclusive D modules we performed de novo DNA motif discovery in upstream sequences and identified putative cis-regulatory elements of an ABA inducible leucine zipper transcription factor. In addition, we observed that some genes in these modules display different expression levels among tolerant and susceptible ecotypes. Finally, pan-genome analysis indicated that most expressed transcripts are encoded by core genes, present in all ecotypes, while 14%, including some hubs, correspond to accessory genes.

Charles Solomon, U Leicester

He talks about his PhD project on programmed cell death in developing B. distachyon caryopsis. He takes us on a nice comparison of caryopsis development in brachy, A. thaliana and crops such as wheat and barley. His experiments involve histological sections, dyes and RNA-seq to track the expression of particular gene families, such as proteases A1, C1/13/14, in vegetative and grain tissues.

Session: Development and growth   

David des Marais, MIT

He talks about natural diversity in patterns of biomass allocation in annual (live fast, die young) and perennial (bet-hedging) Brachypodium species. Most human calories are coming from annuals, but there are some important perennials as well (ie sugarcane). Perennials must compute how many meristems to commit; some also produce rhizomes. In their experiment they see that perennial brachy species produce more seeds, but annuals grow faster (dry mass over days in a single session).  This also holds for relative growth rate, which can be decomposed as the product of leaf area x leaf mass ratio x net assimilation rate. They also see that dark photosynthesis significantly faster in B. distachyon vs perennials. He gets asked whether comparing to B. mexicanum, being also polyploid, makes sense. General idea: there’s more than one way to evolve a perennial into an annual.

Daniel Woods, UC Davis  

He starts by describing his current work in comparing genotypes of both brachy and wheat in terms of flowering-related traits, which builds from early work (https://www.ncbi.nlm.nih.gov/pubmed/23619014). His goal is to accelerate flowering gene discovery; he’s fished so far 14 genes! He goes on to tell a story about a splice site mutant in a predicted DNA polymerase subunit Cdc-27 (ZAO1) that caused rapid flowering of B. distachyon. He discovered ZAO1 is a plant-specific gene, but there are other AAO genes elsewhere. ZAO1 mutants seem to have altered the expression of few genes, including most flowering control genes and MADS-box TFs. He’s now doing Y2H assays in both brachy and wheat to fish proteins interacting with ZAO1.

John Doonan, Aberystwyth U, Wales   

He talks about grain trait variation in Brachypodium, which has lower starch content than crop grasses. He describes a QTL analysis of populations from several ecotypes of B. distachyon and different traits. The best peak on shattering maps next to a gene homologous to a shattering gene described in rice. They are now working on phenotyping as part of EPPN (https://eppn2020.plant-phenotyping.eu) and verifying the candidate genes.

Michael Raissig, U Heidelberg

His talk is about evolutionary innovations of stomatal form and function in Brachypodium. Grasses have bell-shaped guard cells that are fundamentally different than those in dicots, opening significantly faster (https://science.sciencemag.org/content/355/6330/1215). A stomata requires 6 cycles of cell division/differentiation.  If I got that correctly, his lab is currently going through a large mutant collection to identify more genes involved in stomata development.

Richard Sibout, INRA Nantes

His talk intends to highlight the role of vascular tissues in grasses. In this context his lab are studying mutants in B. distachyon that affect the vascular development and auxine content, such as as vac1.  When they mapped the mutant, it turns out it affects a Leucine Rich Repeat Receptor Kinase (LRRRK) that regulates vasculature patterning, phloem-xylem polarity and cell wall composition. He shows beautiful pics but there is no paper or preprint to get them just yet.

Thiel Lehman, U Zurich 

He explains that some B. distachyon genes (BdRSL) have previously been shown to rescue A. thaliana root hair mutants (https://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1006211). He then moves on to talk about the molecular and cell biological characterization of another gene, the  BUZZ cell division kinase, which is also involved in root hair development are somehow causes misexpression of BdRSL genes.

  

Session: Tolerance and adaptation to abiotic stresses

Pubudu Handakumbura, U Massachusetts Amherst

She talks about genotypic and phenotypic diversity for drought tolerance in B. distachyon. She shows significant differences among ecotypes in their responses to freshwater limitation, with very little shared proteins/metabolites (6 ecotypes) being expressed. Metabolite response is strong in the root and moderate in the leaf.

Mhemmed Gandour, U Sidi Bouzid, Tunisia

He talks about screening B. hybridum genotypes for drought tolerance. His data shows high germination rates in dry conditions and conversely a significant reduction under max soil moisture. They have also measured water content in the leaf and root.

Shira Penner, Tel Aviv U  

https://labsapir.wixsite.com/labsapir/people

She describes her PhD work with around 30 Brachypodium populations with variant ploidy along the aridity gradient in Israel (from 700l N to 200l S) in order to assess their adaptation to stress. After analyzing her common garden results she believes those plants escape drought but face competition and finishes with a hint that endophytes might increase fitness. They could not separate B. distachyon from B. stacei plants, both diploids.

Johannes Metz, U Hildesheim , U Potsdam

Following the previous talk, he speaks about ecology of annual Brachypodium in Israel, sampling populations at the same elevation on a precipitation gradient. He focus only on B. hybridum and finds that arid genotypes have less roots and are less plastic, with no significant bet-hedging (https://www.sciencedirect.com/science/article/abs/pii/S1433831917300872 , https://www.sciencedirect.com/science/article/pii/S1439179117302311).

Eviatar Nevo, U Haifa   

http://brachypodium2019.unizar.es/eviatar-nevo
https://www.youtube.com/watch?v=UhNzH39zLbk
Videoconference on Evolution Canyon: sympatric evolution through niche adaptation.

Thursday

Session: Regulatory elements, networks and epigenomics

Anne Roulin, U Zurich   

http://brachypodium2019.unizar.es/anne-roulin

She talks about population genomics of transposable elements (TE) in B. distachyon. The effects of TE jumps can be disruptions, the creation of new promoters or rather the epigenetic silencing of neighbor regions. She shows that TEs in B. distachyon are not concentrated exclusively in the centromeres, and rather colonize all chromosome regions. Her team has developed a pipeline to analyze TE insertions polymorphism (TIPs), and can now compare the rate of fixation of TIPs and SNPs in the 3 Mediterranean populations on B. distachyon. The results were published at https://academic.oup.com/gbe/article/10/1/304/4769669 . She concludes that both recent activity of TE families and purifying selection explain the current distribution of TEs along the pangenome. Then she moves a more recent study on the effect on the expression/silencing of neighbor genes in parallel in brachy and A. thaliana. They observe families of TE that have a distance-related effect while other do not.

Mexia Li, KU Leuven  

Her talk is about RNA interactome capture (RIC) in B. distachyon, a protocol that has only been tested in Arabidopsis so far (https://www.ncbi.nlm.nih.gov/pubmed/29339797) and that she says still needs to be optimized in plants (https://www.life-science-alliance.org/content/1/3/e201800088). Her results reveal a collection of core RBPome of RNA binding proteins conserved in A. thaliana and B. distachyon and by extension in flowering plants.

Joshua Coomey, U Mass Amherst

He talks about a transcription factor, SECONDARY WALL INTERACTING bZIP (SWIZ), which regulates secondary cell wall biosynthesis in B. distachyon in (thigmomorphogenic?) response to mechanical stress. In particular SWIZ overexpression produces thicker walls and is translocated to the nucleus in the root after stress (in histological preparations and confocal videos). This behavior seems to be linked to GA synthesis rates. Using DAP-seq they have characterized the bZIP-like motif of SWIZ, which binds to 3500 loci in the genome (800 have the consensus), similar to AtbZIP52: CAGn*CTG.  

Michael Thieme , U Zurich

Follows on a previous talk by Anne Roulin. His is about stress-induced mobilization of transposable elements (TE) in natural accessions of B. distachyon. This work is after previous work on rice and A. thaliana ONSEN LTR TE (https://genomebiology.biomedcentral.com/articles/10.1186/s13059-017-1265-4), but he says A. thaliana is not really the best plant to study the effect of TEs on natural populations. He is now performing mobilome-seq after applying stress using a published protocol (https://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1006630).  Preliminary results suggest TEs get mobilized in some ecotypes but not others after applying the same stress condition.

Christoph Stritt, U Zurich 

He talks about this study on the high sequence turnover and GC between retrotransposon copies, which possibly indicate frequent ectopic recombination. I had already cited his work (https://academic.oup.com/gbe/article/10/1/304/4769669). There are in total 11 (7 copia + 4 gipsy) LTR lineages in the B. distachyon genome, which vary widely in age and abundance. Among them, the Angela lineage is the most dynamic and responsible for a within-species polymorphisms, while the Retand lineage is significantly richer in GC% than the genome.  

Kirankumar Mysore, Noble Research Institute    

He describes an insertional mutagenesis in B. distachyon Bd21-3 using the Tnt1 retrotransposon, based on https://www.ncbi.nlm.nih.gov/pubmed/29039003, and its potential use to identify novel sources of disease resistance. On average, each line test has 12 Tnt1 insertions, of which 4 are genic. They estimate they need 22K TnT1 lines to target any gene with 0.95 probability.

Session: Polyploidy and perenniality

Pamela Soltis, U Florida

http://brachypodium2019.unizar.es/pamela-soltis

She talks about polyploidy as integrator across levels of biological organization: from cells to ecosystems. She talks mainly about her microevolution work on Tragopogon, which has unveiled a variety on mechanisms of novelty in polyploids: non-additive gene content (gene loss), expression, karyotupes, mosaics, etc. Then she moves to the macroevolutionary scale, starting with this tree: https://genomevolution.org/wiki/index.php?title=Whole_genome_duplication, which summarizes whole genome duplications (WGD) events. She claims that all genomes probably contain ancient WGD which have diploidized later on. We would just need to recognize them to better understand species. Not all WGD can be associated to radiation events in evolutionary time. They have published a paper in this: https://www.ncbi.nlm.nih.gov/pubmed/27234228

Ruben Sancho, U Zaragoza, EEAD-CSIC, Arnold Arboretum  

His talk is about his PhD work on i) reference-genome syntenic mapping and ii) multigene-based phylogenomics to reveal the ancestry of homeologous subgenomes in Brachypodium allopolyploids. This work is still unpublished and proposes plausible hypothesis for the evolutionary processes that produced the different allopolyploid species.

Virginia Markham, JGI, UC Berkeley

She presents her work on chr territories with Hi-C data on B. hybridum. After analyzing that data she sees both D & S subgenomes clearly segregated, with very little contacts. She reports that neither subgenome dominates in terms of gene expression, although it is known that there is nucleolus dominance in the hyrid. She observed that chromatine topology in the diploid parents D&S is conserved in the hybrid as well. There is one outstanding region in the chromatine which resembles a transposon trap/hotspot described in A. thaliana?

Antonio Manzaneda, U Jaén   

He presents his team’s work on homoeologous gene expression and subgenome dominance in response to water stress in the allotetraploid B. hybridum, which they have published at https://www.ncbi.nlm.nih.gov/pubmed/29893879. The used 3 lines (Bd-30-1), Larva-20 (B. hybridum) and Alsur-1 (B. stacei). They observe greater expression changes with respect to the diploid parents under stress. He suspects these differences are epigenetic, but they haven’t checked yet.

Natalia Borowska-Zuchowska, U Silesia

She talks about nucleolar dominance (35S rRNA genes) in allotetraploid B. hybridum, which was observed for the first time in roots: https://www.ncbi.nlm.nih.gov/pubmed/18438442.  More recently they have seen that stacei nucleoli are switched off during much of the life cycle, are methylated and stay at the outside margin of the nucleous: https://www.ncbi.nlm.nih.gov/pubmed/30481334. They also observe variance in the content of 35S genes in different B. hybridum ecotypes. They hypothesize that the stacei nucleoli might have pseudogenized instead of being silenced due to dominance.

Nir Sade, Tel Aviv U

He talks about his work on the perennial model grass B.  sylvaticum under stress tolerance. He tests two accessions from Tunisia & Norway in terms of their ability to produce biomass. He’s published some of this recently: https://www.ncbi.nlm.nih.gov/pubmed/29322303. Using WGNCA he identified a candidate HdZIP TF that might regulate winter hardiness.

Friday

Session: Ecology and Environment

David Lowry, Michigan State U

http://brachypodium2019.unizar.es/david-lowry

He speaks about environmental gradients and the genetic and physiological basis of local adaptation and how his team and collaborators have chosen switchgrass (Panicum virgatum) as the “worst ever model species” (outcrossing, long cycle, perennial, really tall, large genome). He shows a figure correlating switchgrass latitude of collection point (X) and days to flowering (Y), taken from https://www.jstor.org/stable/10.1086/675760. By using outbred mapping populations and cloning plants in a latitudinal gradient in the US they are now studying QTL X environment interaction (https://www.pnas.org/content/116/26/12933) and puzzling rust resistance phenotypes.

Megan Korte, U Groningen

She talks about her PhD work on facilitation (positive species interaction) as a driver of within population variation in Brachypodium. She finds that nurse shrubs modify the microclimate and affect the abundance of brachy plants that she’s genotyping.

Pedro Rey, U Jaén  

He talks about his work about the influence of leaf functional trait variation on the response to insect herbivory in the B. distachyon species complex. Grasshoppers are the main invertebrate herbivorous. In their experiments they observe natural variation across populations in their tolerance to insects which appear genetic-based, not geographical, with B. stacei being less tolerant than the other two species.

Xavier Picó, Estación Biológica Doñana-CSIC 

He talks about the value of regional collections of natural populations to unravel the ecological and genetic basis of adaptive variation in Arabidopsis thaliana on their sampled population in Iberia and Morocco. They have done natural transplant experiments to show that Northern populations can adapt to warmer southern conditions (https://www.ncbi.nlm.nih.gov/pubmed/29947421). He insists on the idea that increasing sampling efforts is required to detect adaptative alleles which are geographically localized. In his experience min T is the key variable explaining natural variation.

Agnieszka Gladala-Kostarz, Aberystwyth U

She talks on her work assessing the impact of wind stress/mechanical stimulation on the growth and composition of B. distachyon stems. This response is mediated in part by pectin methylase activity and saccharification. She carried out her work with two contrasting ecotypes.

Luis Mur, Aberystwyth U

He describes recent collaborative efforts (Harmonia7) to analyze the genetic, epigenetic and metabolomic differentiation of Turkish B. distachyon accessions into two geographically distinct populations. Their main finding is that genotypes from separate regions have specific responses. By analyzing RNAseq data they conclude that epialleles affect expression; he explains the VRN1 locus as an example to show that SNP variation correlates with CpG variation. His main message is that genetic, epigenetic and metabolomics variation seems to be linked in two populations.

Session: Adaptation to abiotic and biotic constrains 

    

Borjana Arsova, Julich

http://brachypodium2019.unizar.es/borjana_arsova

She talks on the dynamic patterns of root nutrient uptake (N, P, Zn) as observed using non-invasive phenotyping, molecular approaches and beneficial microbes, which her group has started to publish at https://www.ncbi.nlm.nih.gov/pubmed/31127613. In conditions with limited N they observe brachy plants grow better when controlled amounts of growth-promoting bacteria are added. She also shows very nice root images of the beneficial barley fungal endophyte Sebacina vermifera.

Yusuke Kouzai, RIKEN, Japan   

He works on B. distachyon sheath blight pathogen, Rhizoctonia solani. His results, including transcriptomics on Bd3-1 and Tek-3 ecotypes, suggest that activation of WRKY-dependent immunity facilitates native resistance. He looks for dynamically expressed genes (DYGs, defined in terms of i) RPM > 5 and ii) RPM ratio max/min > 2) during infection. The WRKY genes are downstream of salicylic acid signaling and were characterized as hubs in those genotypes but not in Bd21. The compute pathogen biomass with qPCR.

Macarena Mellado-Sanchez, U Hertfordshire

She talks about the SNF2 family of chromatin remodelers, which are conserved in B.  distachyon, rice and A. thaliana. She has done transcriptome analysis to monitor the expression levels of family genes in a variety of tissues and has observed that most of them  are involved in the response to combinatorial abiotic stresses.

Emma Aronson,  UC Riverside, USA

She talks about B. distachyon and B. hybridum root, rhizosphere and bulk soil bacterial communities differ between native (where they mix with other species) and invaded ranges (where they seem to colonize whole hillsides, as in CA, USA). She shows PCA plots indicating that bulk soil and rhizospheres retrieve different root microbiomes. She shows the native microbiomes of Bdis and Bhyb are similar (but apparently more different between them than with respect to Bromus if I got that correctly). She also shows data that suggests microbiomes can change substantially in successive years.

Rajiv Kumar Tripathi, McGill U   

He describes his unpublished work on the molecular characterization of SPL/miR156, a regulator of 10 BdSBP genes (out of 18). He has done computational, transcriptomic and molecular biology work with mutants.

Marlon De la Peña Cuao, U País Vasco

His work is on using B. distachyon as a model to study ammonium assimilation, nutrition and stress in cereals. He chooses a 2.5mM [NH4] in his experiments and observes changes in the expression of enzymes involved in Met biosynthesis. He then did a large-scale hydroponic experiment with 52 ecotypes and found significant variability drove ongoing transcriptomic experiments to see differences in expressed genes.  

Session: Crop and biomass crop translation

Klaus Mayer

http://brachypodium2019.unizar.es/klaus-mayer

His talk “From genome to genomes. Charting the genome landscape(s) of western civilization” starts by reminding the domestication of wheat and barley on the fertile crescent. Why has the wheat assembly taken so long? Complete wheat LTR are 8-20Kb, compared to 300b of Alu repeats. The genome of B. distachyon in 2010 was a major step forward due to the synteny, followed by barley a couple of years later, paving the way to genome zippers (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3101540). He also mentions the breakthrough of DeNovoMAGIC2.0 to assemble wheat with a combination of sequencing libraries with different insert sizes and complementary data. He mentions the ongoing pangenome work and discusses findings the modern (war) history captured in the wheat genome diversity explored at https://www.nature.com/articles/s41588-019-0393-z

Manuel Becana, EEAD-CSIC, Zaragoza  

He takes on a nice review around hemoglobins of vascular plants both in model plants and crops. He starts with rhizobia and legumes, then moves to Frankia and actinorhiza species such as Alnus. Finally he presents non-symbiotic hemoglobins, which actually likely are the evolutionary precursors of the former. He concludes by showing recent results showing that monocots, including B. distachyon, have two copies of class 1 hemoglobines.

Miguel Alfonso-Lozano, EEAD-CSIC, Zaragoza  

He talks about his work on the functional analysis of fatty acid elongase TaFAE1 gene from biofuel feedstock pennycress (Thlaspi arvense). Their results reveal differences in seed-oil biosynthesis among Brassicaceae.  

Ernesto Igartua, EEAD-CSIC, Zaragoza  

Diversification of cultivated barley and selection footprints in the landraces of the Iberian Peninsula. He presents recently published work on environmental adaptation of landraces (https://onlinelibrary.wiley.com/doi/full/10.1111/mec.15009) from the Spanish barley core collection at http://www.eead.csic.es/barley . He shows plots that support that Temperature-related variables are the best to explain the population stratification on the landraces. 23 regions associated to env variables are now being further dissected within an exome capture panel of over 70 lines. Finally, he shows the allele frequencies on major flowering control genes that separate the landraces subpopulations (PpdH1-2, VrnH1-3,Btr).

Aurora Díaz, CITA, Zaragoza  

She talks about developing a molecular passport for a new Zea weed emerged in the maize fields of Huesca and Lleida in Spain, which is molecularly related to teosinte (ssp. mexicana and parviglumis). Her results shows that more work and data are required to fully disentangle the evolutionary origins of this weed.

Thomas Girin, INRA Versailles  

His talk is about using B. distachyon Bd21-3 to do fundamental research on ways to improve N Use Efficiency in cereals, so that farmers can reduce the amount of fertilizers. He shows results on tillering stimulation with NO3 addition and explains that brachy plants keeps producing tillers even after flowering, unlike barley and wheat.

John Vogel, JGI & UC Berkeley

http://brachypodium2019.unizar.es/speakers/john-vogel/

His talk “More, more, more, the genus Brachypodium as a sequence-enabled functional genomics model” starts by inviting everyone one to use JGI facilities (20% of current 1K users are from EU). He goes on to list the upcoming sequence resources. He singles out the Bd1-1 assembly, with 99.96% of the sequences in 16 contigs and the highest BUSCO score for a diploid at JGI.

He then moves on to discuss the implications of PAV for polyploids and how he and collaborators are trying to analyze that with B. hybridum, Bdis and Bsta. He mentions software polyCRACKER which can be used to separate subgenomes in polyploids with no prior knowledge, based on K-mer composition (https://www.biorxiv.org/content/10.1101/484832v2), which was used to annotate and track transposable elements before and after the hybridization. The PAV pattern in Bhyb is comparable to some Bdis lines.

Finally he talks about his recent efforts to develop model lab microbiomes (http://eco-fab.org) which would help produce reproducible microbiome research, as long the microbes that you want to mix can be grown in the lab (he quotes about 80% for plant-associated bacteria).