Biology subjects

Catalan, P.

Publications and source records attributed to Catalan, P..

At least 19 recordsLinked to original sources

bioRxiv2026

Genomics and adaptive divergence of the allopolyploid grass Brachypodium hybridum in a pangenotypic framework

Natural allopolyploids with multiple origins are powerful systems for analyzing genome evolution; however, population-level whole-genome studies of wild-type recurrent polyploids remain scarce. We investigated the origins and evolutionary dynamics of the allotetraploid grass Brachypodium hybridum and its diploid progenitors (B. distachyon, B. stacei) by combining whole-genome sequencing of 307 accessions from across the circum-Mediterranean region with phylogenomics, population genomics, and comparative subgenomic analyses. Nuclear and plastome phylogenies reveal three independent allopolyploidization events: an ancient Iberian origin (~1.78 Ma) and two more recent origins in the western (~0.56 Ma) and eastern (~0.24 Ma) Mediterranean. Each subgenome (D and S) evolved independently with minimal recombination. All B. hybridum lineages carry higher deleterious loads than their diploid progenitors, and the Ancient lineage carries a disproportionately heavy burden, particularly in the S subgenome. Population structure identifies three genetic groups; while the Ancient lineage remained isolated, recent western and eastern lineages exchanged migrants in the eastern Mediterranean contact zone. Brachypodium hybridum exemplifies how recurrent allopolyploidization, minimal subgenomic recombination, and environmental filtering generate and maintain genetic diversity, establishing it as a model for polyploid evolution and ecological adaptation in grasses worldwide.

plant biology↗

bioRxiv2026

Multidimensional host-associated diversification in natural Festuca_Epichloe festucae symbioses across the Iberian Peninsula

Epichloe fungal endophytes form widespread symbioses with temperate grasses, yet the extent to which diversity within endophyte species is shaped by host association remains poorly understood. Here, we characterized naturally occurring Festuca_Epichloe symbioses across diverse Iberian ecosystems using an integrative framework combining ecological, cytogenetic, phenotypic, molecular and chemical analyses. Novel associations of Epichloe festucae with Festuca trichophylla, F. lambinonii and F. yvesii were documented, together with substantial variation in infection incidence and mating-type composition among host-associated populations. Morphological traits, vegetative growth and alkaloid profiles differentiated strains according to host identity. Furthermore, multilocus phylogenetic analyses assigned all fine-leaved Festuca host isolates to Epichloe festucae, but identified a recurrent host-associated genetic structure, along with a deeper evolutionary signal, that largely corresponds to the host phylogeny. By contrast, genome size estimates varied little among Epichloe festucae strains, with all isolates exhibiting haploid genomes. Alkaloid content across the four major classes of Epichloe compounds (pyrrolopyrazines, 1-aminopyrrolizidines, ergot alkaloids and indole-diterpenes) showed only partial concordance with the presence of biosynthetic genes, indicating that functional outcomes are influenced by regulatory and environmental factors beyond biosynthetic gene presence. Chemotypic profiles clearly differentiated Epichloe festucae from E. coenophiala while demonstrating considerable functional diversity among E. festucae strains. Collectively, these complementary datasets reveal two interconnected signatures of diversification: pervasive host-associated differentiation across multiple biological dimensions and a deeper historical signal retained in phylogenetic relationships. These findings provide a foundation for future genomic, evolutionary and systematic studies to determine whether these lineages represent ongoing fungal divergence and speciation

evolutionary biology↗

bioRxiv2026

From tiny to massive: exploring genome evolution in the model 1 grass genus Brachypodium

Brachypodium is a powerful model system for investigating grass genome evolution, yet genomic resources remain concentrated in the three annual species, whereas perennial species are less sampled. Here, we present chromosome-level assemblies for two perennial species, Brachypodium mexicanum and B. arbuscula, which represent the earliest-diverging lineages of the genus and the earliest-diverging lineage of the core perennial clade, respectively. Synteny-based phylogenomics indicate that B. mexicanum is a meso-allotetraploid composed of two closely related but temporally distinct x=10 subgenomes, here designed as P and U, each carrying subgenome-specific chromosome rearrangements. We further show that the unusually large B. mexicanum genome, in contrast to the reduced genomes of most other Brachypodium species, is primarily due to transposable elements distributed across all chromosomal regions. By contrast, the diploid genome of the earliest-diverging core perennial, B. arbuscula, contains few transposable elements, whereas the most recent diverged diploid perennial B. sylvaticum shows evidence of a secondary TEs proliferation. Comparisons of lineage-specific and functionally enriched orthogroups among B. mexicanum, core perennial species and annual species suggest that ancestral hybridization between annual and perennial lineages may have contributed to the origin of allotetraploid B. mexicanum. These assemblies provide a framework for testing how polyploidy, descending dysploidy, transposable-element turnover, and life-history evolution jointly shaped genome architecture in Brachypodium.

evolutionary biology↗

bioRxiv2026

Exploiting outer-membrane protein promiscuity to induce transient collateral sensitivity via efflux pump competition

In the fight against antimicrobial resistance, the identification of robust collateral sensitivity (CS) patterns could form the basis of successful sequential and combinatorial antimicrobial therapies. While most of the focus has been devoted to study stable CS due to mutations, CS can be transiently induced in Pseudomonas aeruginosa using dequalinium chloride (DC), which increases the expression of the efflux operon mexCD-oprJ. This leads to transient CS to the aminoglycoside tobramycin, whose molecular mechanism remains unclear. Using a combination of experimental results, mechanistic mathematical models and structural simulations, we show that the inactivation of NfxB by DC not only increases mexCD expression but also reduces the effective amount of the MexXY-OprM aminoglycosides efflux pump. Our data suggest that, under conditions of high MexCD production, this efflux pump can outcompete MexXY for the outer-membrane protein OprM, thereby inducing CS to tobramycin. Bayesian fits accurately reproduce measured mexCD expression and minimal inhibitory concentration (MIC) shifts across DC doses. Model predictions were validated in P. aeruginosa PA14 mutants lacking functional outer-membrane channels. Loss of OprJ preserves DC-induced CS to tobramycin, whereas loss of OprM abolishes it. These results identify competition for OprM as the proximal cause of DC-induced, transient CS and provide a generalizable framework for eliciting CS by perturbing shared components of multidrug efflux systems. This strategy suggests immediate avenues to enhance aminoglycoside efficacy while minimizing selection for stable resistance.

microbiology↗

bioRxiv2025

Deconvolution of Single Homeologous Polymorphism (SHP) drives phylogenetic analysis of allopolyploids

The genomic and evolutionary study of allopolyploid organisms involves multiple copies of homeologous chromosomes, making their assembly, annotation, and phylogenetic analysis challenging. Bioinformatics tools and protocols have been developed to study polyploid genomes, but sometimes require the assembly of their genomes, or at least the genes, limiting their use. We have developed AlloSHP, a command-line tool for detecting and extracting single homeologous polymorphisms (SHPs) from the subgenomes of allopolyploid species. This tool integrates three main algorithms, WGA, VCF2ALIGNMENT and VCF2SYNTENY, and allows the detection SHPs for the study of diploid-polyploid complexes with available diploid progenitor genomes, without assembling and annotating the genomes of the allopolyploids under study. AlloSHP has been validated on three diploid-polyploid plant complexes, Brachypodium, Brassica, and Triticum-Aegilops, and a set of synthetic hybrid yeasts and their progenitors of the genus Saccharomyces. The results and congruent phylogenies obtained from the four datasets demonstrate the potential of AlloSHP for the evolutionary analysis of allopolyploids with a wide range of ploidy and genome sizes. AlloSHP combines the strategies of simultaneous mapping against multiple reference genomes and syntenic alignment of these genomes to call SHPs, using as input data a single VCF file and the reference genomes of the known or closest extant diploid progenitor species. This novel approach provides a valuable tool for the evolutionary study of allopolyploid species, both at the interspecific and intraspecific levels, allowing the simultaneous analysis of a large number of accessions and avoiding the complex process of assembling polyploid genomes.

bioinformatics↗

bioRxiv2025

A Palearctic divide, niche conservatism and host-fungal endophyte interactions shaped the phylogeography of the grass Brachypodium sylvaticum

Brachypodium sylvaticum is a perennial woodland grass selected as model species for perenniality, which is widely distributed across the Palearctic. This plant forms a symbiosis with the endophytic fungus Epichloe sylvatica. We integrate whole-genome phylogenomics, plastome analysis, environmental niche modeling (ENM), and coevolutionary analyses to investigate the diversification of B. sylvaticum and its fungal symbiont. Using 94 representative individuals spanning Eurasia and North Africa, we recovered two deeply divergent sister lineages (Eastern and Western Palearctic), with cytonuclear discordances suggesting historical plastid capture events in the western group. Admixture analysis revealed four genetic clusters, including signatures of secondary contact and hybridization in the Western lineage. Filtered ITS sequences of E. sylvatica recovered from holobiont genome skimming reads enabled phylogenetic reconstruction, revealing two fungal clades that broadly mirror their hosts evolutionary history in the West. PACo and ParaFit analyses supported partial co-divergence between hosts and endophytes. ENM projections identified climatically stable glacial refugia for both B. sylvaticum main lineages during the Last Glacial Maximum and asymmetric postglacial expansion, with moderate niche shifts in the West and stronger turnover in the East. Evidence of niche overlap and similarity indicated niche conservatism among clades, suggesting that geographic isolation, rather than adaptive divergence, was the primary driver of lineage splitting. IBD and IBE patterns significantly influenced divergences in the Western, but not the Eastern, group, highlighting contrasting demographic and ecological dynamics. Our results provide the first evidence of coevolutionary and ecological structuring in B. sylvaticum-E. sylvatica holobionts across their Western native range.

plant biology↗

bioRxiv2025

Exploring genomic diversity and reproductive strategies in three expansion phases of the superdominant Brachypodium rupestre in high mountain grasslands

Tall-grass expansion in natural plant communities is a concern under current global change scenarios. Driven by factors such as community vulnerability and the competitive abilities of tall-grass species, this phenomenon is exemplified by Brachypodium rupestre (Host) Roem. & Schult, a perennial tall-grass native to Europe. B. rupestre spreads aggressively in the grasslands of the western Pyrenees due to a disrupted regime of lack of herbivory and recurrent burnings that has persisted over several decades. This study aims to investigate whether the contrasted managements of grazing, abandonment and burnings have promoted specific reproductive traits and impacted the population genomics of B. rupestre. Nine sites varying in cover of B. rupestre classified into three expansion phases associated to different management regimes were monitored: i) scattered populations in multispecific grazed sites, ii) stand populations expanding at sites of relaxed grazing or abandonment, and iii) superdominant populations constituting dense degraded covers in recurrently burned sites. ddRADseq data showed high genomic diversity but relatively low genomic structure, likely due to substantial gene flow and the absence of wind barriers. The standardized index of association supported asexual reproduction in all populations, which is coupled with sexual reproduction. Contrasting management practices did not promote distinct genomic identities between expansion phases; rather, the genetic differentiation and divergence of populations responded to life history and spatial isolation, even within a small geographic area. The similar levels of genetic diversity and the significantly different number of clones between expansion phases suggest a complex pattern of genotypic and clonal variability, which may be influenced by environmental factors (historical disturbance regimes).

plant biology↗

bioRxiv2025

On the taxonomy and nomenclature of the annual species of the Brachypodium distachyon grass complex (Gramineae, Pooideae)

The taxonomy and nomenclature of the type materials potentially attributable to the three recognized annual species of the grass genus Brachypodium (B. distachyon, B. stacei, B. hybridum) have been investigated through statistical discriminant analysis of twelve quantitative morphological traits in eight herbarium types corresponding to heterotypic synonyms and newly designated types of each species, along with the lectotype and the epitype of B. distachyon and the holotypes of B. stacei and B. hybridum, plus 50 additional representative specimens of the currently recognized taxa, and through a comprehensive nomenclatural review. The possible taxonomic assignments of types to these species and the nomenclatural priority of Brachypodium distachyon and ten related names, B. hybridum, B. macrostachyum, B. megastachyum, B. stacei, Bromus pentastachyos, Festuca monostachyos, F. rigida, Trachynia platystachya, Triticum schimperi, and T. subtile, have been discussed. Lectotypes are designated for Festuca monostachyos, F. rigida, Triticum schimperi, and T. subtile. Based on our taxonomic and nomenclatural study, the names Festuca monostachyos and Triticum subtile can be considered conspecific and heterotypic synonyms of the Linnaean name Bromus distachyos ({equiv} Brachypodium distachyon). Furthermore, the names Brachypodium macrostachyum, Brachypodium megastachyum, Bromus pentastachyos, Festuca rigida, and Brachypodium distachyon var. platystachyon ({equiv} Trachynia platystachya) are conspecific with Brachypodium hybridum, and Triticum schimperi is conspecific with Brachypodium stacei. Since the names B. hybridum and B. stacei are in common use, but both are later heterotypic synonyms, respectively, of the names of the species with which they are conspecific, a proposal for the conservation of these two names is necessary. On the other hand, the application of the names Bromus pauper, Brachypodium geniculatum, Festuca pseudistachya, Bromus paradoxus, and Triticum flabellatum is uncertain, and as such, they are treated as nomen ambiguum. Finally, Festuca ciliata and Triticum asperum are two illegitimate names, according to Art. 52.1 of the Shenzhen Code, while Triticum brevisetum is a new synonym of Brachypodium retusum. A lectotype for the name T. brevisetum is also selected and designated in this paper.

plant biology↗

bioRxiv2024

Genic and phylogenomic discordances reveal conflicting hybridization episodes in temperate Loliinae grasses

The grass subtribe Loliinae has great ecological and economic importance, as it includes community-dominant species of world mountain grasslands and the most extensively cultivated pasture, fodder and lawn grasses (fescues, ryegrasses). Resolving the phylogeny of recently evolved Loliinae lineages has proven challenging due to frequent introgressions and polyploidizations that occurred throughout their history. Evolutionary reconstruction based on genome-wide data sets is useful for large groups of species, enabling recovering phylogenetic trees, contrasting their topologies, unraveling the origins of the discordances, and testing hypotheses on their reticulate history. Here we present the first target-capture phylogeny of Loliinae using 234 single-copy nuclear coding loci for a large sample of 132 representative taxa, covering all its 29 evolutionary lineages. Additionally, we have completed organelle (plastome) sequences to elucidate the hybridogenic speciation history of the Loliinae from complementary genome sources. Concatenated maximum likelihood and multispecies coalescent trees of single-copy genes showed well-supported relationships for major lineages, which were generally consistent across analyses and genomes, and with previous taxonomic and phylogenetic findings. However, they also revealed high levels of both nuclear and cyto-nuclear discordances. The time-calibrated phylogeny of target-capture data supports an early Miocene origin for Loliinae and Mid-Late Miocene splits for its main broad-leaved and fine-leaved lineages, while current species-rich groups radiated in Plio-Pleistocene times. Hybridization and topological incongruence tests between the nuclear single-copy genes and plastome-based trees using multiple approaches and different sampling subsets confirmed the rampant introgression experienced by Loliinae at deep and shallow nodes. However, hybridization rates differed from lineage to lineage within the major clades and were not correlated with time or ploidy but rather depended on the "hybridogenous" nature of particular lineages. Our analyses detected high hybridization rates in four broad-leaved (Subulatae-Hawaiian, Tropical-South African, Mexico-Central-South American and Leucopoa p.p.) and five fine-leaved Loliinae lineages (American II, Aulaxyper, Afroalpine, American-Neozeylandic) containing rogue species that probably originated from trans-clade crosses and are more likely to hybridize greatly. In contrast, they recovered low hybridization rates in four broad-leaved (Schedonorus-Lolium, Subbulbosae, Drymanthele-Pseudoscariosae-Lojaconoa, Leucopoa pp) and six fine-leaved lineages (Festuca, Psilurus-Vulpia, American I, Exaratae-Loretia, American-Vulpia-Pampas, Eskia), with species derived from single ancestors that hybridize only with close congeners. The levels of intragenomic nuclear discordance could have been magnified by the prevalence of allopolyploids in the Loliinae and by methodological bias in the selection of orthologs; however, our nuclear and plastome trees have revealed key hybrid origins in these grasses. [allopolyploidization, lineage-specific hybridization rates, nuclear and cyto-nuclear discordances, Festuca and related genera, phylogenomics, nuclear single-copy genes, plastome].

evolutionary biology↗

bioRxiv2024

Genomic and evolutionary evidence for drought adaptation of grass allopolyploid Brachypodium hybridum

Climate change increases the frequency and severity of drought worldwide, threatening the environmental resilience of cultivated grasses. However, the genetic diversity in many wild grasses could contribute to the development of climate-adapted varieties. Here, we elucidated the impact of polyploidy on drought response using allotetraploid Brachypodium hybridum (Bh) and its progenitor diploid species B. stacei (Bs). Our findings suggest that progenitor species genomic legacies resulting from hybridization and whole-genome duplications conferred greater ecological adaptive advantages to Bh over Bs. Genes related to stomatal regulation and immune response from S-subgenomes were under positive selection during speciation, underscoring their evolutionary importance in adapting to environmental stresses. Biased expression in polyploid subgenomes [B. stacei-type (Bhs) and B. distachyon-type (Bhd)] significantly influenced differential gene expression, with the dominant subgenome exhibiting more differential expression. B. hybridum adapted a drought escape strategy characterized by higher photosynthetic capacity and lower WUEi than Bs, driven by a highly correlated co-expression network involving genes in the circadian rhythm pathway. In summary, our study showed the influence of polyploidy on ecological and environmental adaptation and resilience in model Brachypodium grasses. These insights hold promise for informing the breeding of climate-resilient cereal crops and pasture grasses.

evolutionary biology↗

bioRxiv2024

Nuclear phylogenomics of grasses (Poaceae) supports current classification and reveals repeated reticulation

O_LIGrasses (Poaceae) comprise around 11,800 species and are central for human livelihoods and terrestrial ecosystems. Knowing their relationships and evolutionary history is key to comparative research and crop breeding. Advances in genome-scale sequencing allow for increased breadth and depth of phylogenomic analyses, making it possible to infer a new reference species tree of the family. C_LIO_LIWe inferred a comprehensive species tree of grasses by combining new and published sequences for 331 nuclear genes from genome, transcriptome, target enrichment and shotgun data. Our 1,153-tip tree covers 79% of grass genera (including 21 genera sequenced for the first time) and all but two small tribes. We compared it to a 910-tip plastome tree. C_LIO_LIThe nuclear phylogeny matches that of the plastome at most deep branches, with only a few instances of incongruence. Gene tree-species tree reconciliation suggests that reticulation events occurred repeatedly in the history of grasses. C_LIO_LIWe provide a robust framework for the grass tree of life to support research on grass evolution, including modes of reticulation, and genetic diversity for sustainable agriculture. C_LI

plant biology↗

bioRxiv2024

Full factorial construction of synthetic microbial communities

Constructing combinatorially complete species assemblages is often necessary to dissect the complexity of microbial interactions and to find optimal microbial consortia. At the moment, this is accomplished through either painstaking, labor intensive liquid handling procedures, or through the use of state-of-the-art microfluidic devices. Here we present a simple, rapid, low-cost, and highly accessible liquid handling methodology for assembling all possible combinations of a library of microbial strains, which can be implemented with basic laboratory equipment. To demonstrate the usefulness of this methodology, we construct a combinatorially complete set of consortia from a library of eight Pseudomonas aeruginosa strains, and empirically measure the community-function landscape of biomass productivity, identify the highest yield community, and dissect the interactions that lead to its optimal function. This easy to implement, inexpensive methodology will make the assembly of combinatorially complete microbial consortia easily accessible for all laboratories.

ecology↗

bioRxiv2023

Scattered differentiation of unlinked loci across the genome underlines ecological divergence of the selfing grass Brachypodium stacei

Ecological divergence without geographic isolation, as an early speciation process that may lead finally to reproductive isolation through natural selection, remains one of the most interesting issues in evolutionary biology. However, the patterns of the underlying genetic divergences across the genome vary between different groups. Here we report that Brachypodium stacei, an inbreeding grass species, has been involved in sympatric ecological divergence without geographic isolation. Genomic, transcriptomic, and metabolomic analyses suggest that diploid B. stacei diverged sympatrically in two slopes with contrasting biomes at Evolution Canyon I (ECI), Mount Carmel, Israel, where gene flow has continued freely but reduced with the time. This ecological divergence involved the scattered divergence of many unlinked loci across the total genome that include both coding and non-coding regions. We also identified significantly differential expressions of ABA signaling pathway genes, and contrasting metabolome composition between the arid-vs forest-adapted B. stacei ECI populations. These results suggest that many small loci involved in environmental responses act additively to account for the ecological usages of this species in contrasted environments with gene flow. SignificanceEcological divergence provides evidence for the origin of species through natural selection that has governed evolutionists attention since Darwin. In this study, we present multiple-omics analyses of two plant populations growing sympatrically in contrasted environments and revealed their distinct differentiation across all examined data. These two populations share the most recent ancestor compared with other populations and their divergence started in the early Holocene. We revealed that gene flow had continued but with a progressive reduction over time. The genetic divergences are scattered across the total genome involving many unlinked coding and non-coding regions. These findings highlight the significance of natural selection in the ecological divergence that may finally lead to species formation without geographic isolation.

evolutionary biology↗

bioRxiv2023

Frequent emergence of resistance mutations following complex intra-host genomic dynamics in SARS-CoV-2 patients receiving Sotrovimab

The emergence of the Omicron variant of SARS-CoV-2 represented a challenge to the treatment of COVID-19 with monoclonal antibodies. Only Sotrovimab maintained partial activity, allowing it to be used in high-risk patients infected with the Omicron variant. However, the reports of resistance mutations to Sotrovimab call for efforts to better understand the intra-patient emergence of this resistance. A retrospective genomic analysis was conducted on respiratory samples from immunocompromised patients infected with SARS-CoV-2 who received Sotrovimab at our hospital between December 2021 and August 2022. The study involved 95 sequential specimens from 22 patients (1-12 samples/patient; 3-107 days post-infusion (Ct [≤] 32)). Resistance mutations (in P337, E340, K356, and R346) were detected in 68% of cases; the shortest time to detection of a resistance mutation was 5 days after Sotrovimab infusion. The dynamics of resistance acquisition were highly complex, with up to 11 distinct amino acid changes in specimens from the same patient. In two patients, the mutation distribution was compartmentalized in respiratory samples from different sources. This is the first study to examine the acquisition of resistance to Sotrovimab in the BA.5 lineage, enabling us to determine the lack of genomic or clinical differences between Sotrovimab resistance in BA.5 relative to BA.1/2. Across all Omicron lineages, the acquisition of resistance delayed SARS-CoV-2 clearance (40.67 vs 19.5 days). Close, real-time genomic surveillance of patients receiving Sotrovimab should be mandatory to facilitate early therapeutic interventions.

microbiology↗

bioRxiv2021

Day length-dependent thermal COP1 dynamics integrate conflicting seasonal cues in the control of Arabidopsis elongation

As the summer approaches, plants experience enhanced light inputs and elevated temperatures, two environmental cues with an opposite morphogenic impact. How plants integrate this conflicting information throughout seasons remains unclear. Key components of the plant response to light and temperature include phytochrome B (phyB), PHYTOCROME INTERACTING FACTOR 4 (PIF4), EARLY FLOWERING 3 (ELF3) and CONSTITUTIVE PHOTOMORPHOGENIC 1 (COP1). Here, we used hypocotyl lengths of single and double mutant/over-expression lines to fit a mathematical model incorporating known interactions of these genes. The fitted model recapitulates day length-dependent thermoelongation of all lines studied, and correctly predicts temperature responsiveness of new genotypes. Whilst previous works pointed to a lightindependent thermal function of COP1, simulations of our model suggested that COP1 has a role in temperature-signaling only during daytime. Based on by this prediction, we show that COP1 overexpression increases thermal response in continuous white light, while it has little effect in darkness. Defective thermal response of cop1-4 mutants is epistatic to phyB-9 and elf3-8, indicating that COP1 activity is essential to the transduction of phyB and ELF3 thermosensory function. Our model accurately captures phyB, ELF3 and PIF4 dynamics, providing an excellent toolbox for identification of best allelic combinations towards optimized crops resilience to climate change at different geographical latitudes.

plant biology↗

bioRxiv2021

Evolution and functional dynamics of dehydrins in model Brachypodium grasses

Dehydration proteins (dehydrins, DHNs) confer tolerance to water-stress deficit to plants, thus playing a fundamental role in plant response and adaptation to water-deprivation stressful environments. We have performed a comparative genomics and evolutionary study of DHN genes in four model Brachypodium grass species, and a drought-induced functional analysis in 32 ecotypes of the flagship species B. distachyon, to gain insight into the origins and dynamics of these proteins and the correlated drought-mediated phenotypic responses in ecotypes showing different hydric requirements. Genomic sequence analysis detected 10 types of dehydrin genes (Bdhn) across the Brachypodium species, totalling 47 genes. Domain and conserved motif contents of peptides encoded by Bdhn genes revealed eight protein architectures, YS{phi}K2 being the most common architecture. Bdhn genes were spread across several chromosomes and more frequent in syntenic chromosomes 3 and 4 of B. distachyon, 4 and 5 of B. stacei and 4 of B. sylvaticum. Tandem and segmental duplication events were detected for four Bdhn genes. Selection analysis indicated that all the Bdhn genes were constrained by purifying selection. Three upstream cis-regulatory motifs (BES1, MYB124, ZAT) were consistently detected in several Bdhn genes. Functional analysis in 32 natural accessions of B. distachyon demonstrated that only four Bdhn genes (Bdhn1, Bdhn2, Bdhn3, Bdhn7) were expressed in mature leaves and that all of them were significantly more highly expressed in plants under drought conditions. These genes corresponded to wheat orthologs that were also significantly more expressed under drought stress. Brachypodium dehydrin expression was significantly correlated with drought-response phenotypic traits (plant biomass, leaf carbon and proline contents and WUE increases, leaf water and nitrogen content changes) being more pronounced in drought-tolerant ecotypes. Bdhn expression, associated phenotypic trait changes and climate niche variation did not show significant phylogenetic signal when tested in the B. distachyon genealogical-species tree. By contrast, some of them showed low or marginal significant phylogenetic signal when tested in the B. distachyon Bdhn tree, suggesting that Bdhn gene evolution is partially related to adaptation to drought in this species. Our results demonstrate that dehydrin composition and regulation is a key factor determining the acquisition of water-stress tolerance in grasses.

genetics↗

bioRxiv2021

Patterns of gene co-expression under water-deficit treatments and pan-genome occupancy in Brachypodium distachyon.

Natural populations are characterized by abundant genetic diversity driven by a range of different types of mutation. The tractability of sequencing complete genomes has allowed new insights into the variable composition of genomes, summarized as a species pan-genome. These analyses demonstrate that many genes are absent from the first reference genomes, whose analysis dominated the initial years of the genomic era. Our field now turns towards understanding the functional consequence of these highly variable genomes. Here, we analyzed weighted gene co-expression networks from leaf transcriptome data for drought response in the purple false brome Brachypodium distachyon and the differential expression of genes putatively involved in adaptation to this stressor. We specifically asked whether genes with variable "occupancy" in the pan-genome - genes which are either present in all studied genotypes or missing in some genotypes - show different distributions among co-expression modules. Co-expression analysis united genes expressed in drought-stressed plants into nine modules covering 72 hub genes (87 hub isoforms), and genes expressed under controlled water conditions into 13 modules, covering 190 hub genes (251 hub isoforms). We find that low occupancy pan-genes are under-represented among several modules, while other modules are over-enriched for low-occupancy pan-genes. We also provide new insight into the regulation of drought response in B. distachyon, specifically identifying one module with an apparent role in primary metabolism that is strongly responsive to drought. Our work shows the power of integrating pan-genomic analysis with transcriptomic data using factorial experiments to understand the functional genomics of environmental response.

plant biology↗

bioRxiv2021

Tracking the Ancestry of Known and 'Ghost' Homeologous Subgenomes in Model Grass Brachypodium Polyploids

Unraveling the evolution of plant polyploids is a challenge when their diploid progenitor species are extinct or unknown or when their progenitor genome sequences are unavailable. The subgenome identification methods cannot adequately retrieve the homeologous genomes that are present in the allopolyploids if they do not take into account the potential existence of unknown progenitors. We addressed this challenge in the widely distributed dysploid grass genus Brachypodium, which is a model genus for temperate cereals and biofuel grasses. We used a transcriptome-based phylogeny and newly designed subgenome detection algorithms coupled with a comparative chromosome barcoding analysis. Our phylogenomic subgenome detection pipeline was validated in Triticum allopolyploids, which have known progenitor genomes, and was used to infer the identities of three extant and four ghost subgenomes in six Brachypodium polyploids (B. mexicanum, B. boissieri, B. retusum, B. phoenicoides, B. rupestre and B. hybridum), of which five contain undescribed homeologous subgenomes. The existence of the seven Brachypodium progenitor genomes in the polyploids was confirmed by their karyotypic barcode profiles. Our results demonstrate that our subgenome detection method is able to uncover the ancestral genomic components of both allo- and autopolyploids.

plant biology↗