Biology subjects

Contreras-Moreira, B.

Publications and source records attributed to Contreras-Moreira, B..

18 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

A pangenome-graph approach for mapping and imputing barley sequences

Barley (Hordeum vulgare) is a key cereal crop with exceptional adaptation to diverse environments. With a large, highly repetitive diploid genome, barley presents challenges for pangenome representation. Starting from the reference genome MorexV3, we describe the construction of a barley graph (Pan20) representing the global diversity of landraces and cultivars captured in the public pangenome V1. For mapping arbitrary sequences, a greedy strategy is proposed that combines GMAP alignment followed by intersection with a Practical Haplotype Graph (PHG). This enables presence-absence variation detection and provides a consistent MorexV3 physical coordinate system across genotypes, enabling comparative analysis and visualization. For imputation of genomic data, the PHG approach relies on k-mer pseudo-alignment against the graph. Benchmarks show that Pan20 can accurately align barley genomic and transcriptomic sequences, including those not present in the Morex reference, revealing that a third of long genomic sequences map on non-reference genomes. Moreover, experiments with Genotyping by Sequencing and low-pass sequencing data indicate that FASTQ files can be efficiently mapped and imputed against the graph, preserving local haplotype context. This flexible and scalable graph framework allows barley researchers to explore genetic diversity beyond a single reference and facilitates analysis of diversity panels at the haplotype level, going beyond SNPs. Documentation and a Docker container are available at https://github.com/eead-csic-compbio/barleygraph. The graph sequence mapping utility was added to the Web application https://barleymap.eead.csic.es.

genomics↗

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↗

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

Vernalization regulatory network identifies potential novel functions for ZCCT genes within HvVRN2

O_LIFlowering is a key yield determinant, controlled by environmental and genetic factors. Vernalization requirement, a prolonged cold period to promote flowering, is determined in barley (Hordeum vulgare L.) by the allele in HvVRN1 and the presence of locus HvVRN2, which consists of two ZCCT genes: HvVRN2a and HvVRN2b. While the effect of HvVRN2 presence is well-known, its outcome on the transcriptome and other genes outside the flowering/vernalization pathway remains unknown. C_LIO_LINear-isogenic lines with presence/absence of HvVRN2, were subjected to different lengths of vernalization treatments, identifying the expression dynamics of both HvVRN2 genes and wider transcriptional responses controlled by VRN2. C_LIO_LIOur work revealed previously unknown differences in expression levels of the two HvVRN2 genes, in responses to its main repressor, HvVRN1, and an effect on tillering. Besides, we shed new light on the repressing mechanism of VRN2 on flowering, using protein modelling. A regulatory network analysis pointed at new candidate genes for flowering regulation related to the vernalization pathway, and suggested additional biological roles for HvVRN2b. C_LIO_LIThis study re-establishes HvVRN2 as a central gene for understanding barley responses to environmental cues, beyond its previously accepted simple role, and expands the catalogue of genes related to the vernalization pathway, which may be targeted in barley breeding. C_LI

plant biology↗

bioRxiv2025

A pan-gene catalogue of Asian cultivated rice

The rice genome underpins fundamental research and breeding, but the Nipponbare (japonica) reference does not fully encompass the genetic diversity of Asian rice. To address this gap, the Rice Population Reference Panel (RPRP) was developed, comprising high-quality assemblies of 16 rice cultivars to represent japonica, indica, aus, and aromatic varietal groups. The RPRP has been consistently annotated, supported by extensive experimental data and here we report the computational assignment, characterization and dissemination of stably identified pan-genes. We identified 25,178 core pan-genes shared across all cultivars, alongside cultivar-specific and family-enriched genes. Core genes exhibit higher gene expression and proteomic evidence, higher confidence protein domains and AlphaFold structures, while cultivar-specific genes were enriched for domains under selective breeding pressure, such as for disease resistance. This resource, integrated into public databases, enables researchers to explore genetic and functional diversity via a population-aware "reference guide" across rice genomes, advancing both basic and applied research.

genomics↗

bioRxiv2024

Mapping the genomic landscape of peach and almond with PrunusMap

High throughput sequencing is accelerating plant breeding. Genotyping, quantitative trait locus or genome-wide association analyses are essential to locate alleles of interest in germplasm collections. These applications require accurately mapping nucleotide markers within growing collections of reference genome sequences. PrunusMap (https://prunusmap.eead.csic.es) is a user-friendly Web application designed to facilitate these tasks to Prunus breeders. It efficiently aligns markers and locates SNPs on peach and almond genomes, providing lists of nearby genes and curated proteins. It can align all markers from a genetic map in one step, producing their physical positions. By searching multiple maps, it can also solve the problem of finding equivalent gene identifiers across different annotations. Three intuitive tools, "Find markers", "Align sequences" and "Locate by position", are available to accelerate mapping analyses, particularly for users with limited bioinformatics expertise. New genomes, annotations or marker sets will be added based on their interest to the community.

bioinformatics↗

bioRxiv2023

ddRAD-seq-derived SNPs reveal novel association signatures for fruit-related traits in peach

Breeding for new peach cultivars with enhanced traits is a prime target in breeding programs. In this study, we used a discovery panel of 90 peach accessions in order to dissect the genetic architecture of 16 fruit-related traits. ddRAD-seq genotyping and the intersection between three variant callers yielded 13,045 high-confidence SNPs. These markers were subjected to an exhaustive association analysis by testing up to seven GWAS models. Blink was selected as the most adjusted, simultaneously balancing false positive and negative associations. Totally, we identified 16 association signals for six traits showing high broad-sense heritability: harvest date, fruit weight, flesh firmness, contents of flavonoids, anthocyanins and sorbitol. By assessing the allelic effect of significant markers on phenotypic attributes, nine SNP alleles were denoted favorable. A promising marker (SNC_034014.1_7012470) was found to be simultaneously associated with harvest date and fruit firmness conferring a positive allelic effect on both traits. We anticipate that this marker could be used to improve firmness in late harvested cultivars. Candidate causal genes were shortlisted when fulfilling the following criteria: i) position within the linkage disequilibrium block, ii) functional annotation and iii) expression pattern. A bibliographic review of previously reported QTLs mapping nearby the associated markers allowed us to benchmark the accuracy of our approach. Despite the moderate germplasm size, ddRAD-seq allowed us to produce an accurate representation of peachs genome resulting in SNP markers suitable for empirical association studies. Together with candidate genes, they lay the foundation for further genetic dissection of peach key traits.

plant biology↗

bioRxiv2023

Building pangene sets from plant genome alignments confirms presence-absence variation

Consistent gene annotation in crops is becoming harder as genomes for new cultivars are frequently published. Gene sets from recently sequenced accessions have different gene identifiers to those on the reference accession, and might be of higher quality due to technical advances. For these reasons there is a need to define pangenes, which represent all known syntenic orthologues for a gene model and can be linked back to the original annotation sources. A pangene set effectively summarizes our current understanding of the coding potential of a crop and can be used to inform gene model annotation in new cultivars. Here we present an approach (get_pangenes) to identify and analyze pangenes that is not biased towards the reference annotation. The method involves computing Whole Genome Alignments (WGA), which are used to estimate gene model overlaps. After a benchmark on Arabidopsis, rice, wheat and barley datasets, we find that minimap2 performs better than the GSAlign WGA algorithm. Our results show that pangenes recapitulate known phylogeny-based orthologies while adding extra core gene models in rice. More importantly, get_pangenes can also produce clusters of genome segments (gDNA) that overlap with gene models annotated in other cultivars. By lifting-over CDS sequences, gDNA clusters can help refine gene models across individuals and confirm or reject observed gene Presence-Absence Variation. A collection of flowering-related genes from the barley pangenome are discussed in detail. Documentation and source code are available at https://github.com/Ensembl/plant-scripts.

genomics↗

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↗

bioRxiv2021

Efficient masking of plant genomes by combining kmer counting and curated repeats

Ii.Summary/AbstractThe annotation of repetitive sequences within plant genomes can help in the interpretation of observed phenotypes. Moreover, repeat masking is required for tasks such as whole-genome alignment, promoter analysis or pangenome exploration. While homology-based annotation methods are computationally expensive, k-mer strategies for masking are orders of magnitude faster. Here we benchmark a two-step approach, where repeats are first called by k-mer counting and then annotated by comparison to curated libraries. This hybrid protocol was tested on 20 plant genomes from Ensembl, using the kmer-based Repeat Detector (Red) and two repeat libraries (REdat and nrTEplants, curated for this work). We obtained repeated genome fractions that match those reported in the literature, but with shorter repeated elements than those produced with conventional annotators. Inspection of masked regions overlapping genes revealed no preference for specific protein domains. Half of Red masked sequences can be successfully classified with nrTEplants, with the complete protocol taking less than 2h on a desktop Linux box. The repeat library and the scripts to mask and annotate plant genomes can be obtained at https://github.com/Ensembl/plant-scripts.

genomics↗

bioRxiv2021

Light spectra trigger divergent gene expression in barley cultivars

Light spectra influence barley development, causing a diverse range of responses among cultivars that are poorly understood. Here, we exposed three barley genotypes with different light sensitivities to two light sources: fluorescent bulbs, over-representing green and red wavebands, and metal halide lamps, with a more balanced spectrum. We used RNA sequencing to identify the main genes and pathways involved in the different responses, and RT-qPCR to validate the expression values. Different grades of sensitivity to light spectra were associated with transcriptional reprogramming, plastid signals, and photosynthesis. The genotypes were especially divergent in the expression of genes regulated by transcription factors from MADS-box, WRKY, and NAC families, and in specific photoreceptors such as phytochromes and cryptochromes. Variations in light spectra also affected the expression of circadian clock, flowering time, and frost tolerance genes, among others, resembling plant responses to temperature. The relation between PPD-H1, HvVRN1, and HvFT1 expression might explain genotypic differences. Light-sensitive genotypes experienced a partial reversion of the vernalization process and senescence-related stress under the less favorable light quality conditions. The observed light-quality sensitivities reveal a complex mechanism of adaptation to regions with specific light quality features and/or possible regulation of light spectra in plant development during early spring. HighlightDevelopment genes were affected by light quality in the barley varieties tested. Different grades of sensitivity were related to the expression of transcription factors, senescence, light signaling and cold-regulated genes.

plant biology↗

bioRxiv2020

The Ensembl COVID-19 resource: Ongoing integration of public SARS-CoV-2 data

The COVID-19 pandemic has seen unprecedented use of SARS-CoV-2 genome sequencing for epidemiological tracking and identification of emerging variants. Understanding the potential impact of these variants on the infectivity of the virus and the efficacy of emerging therapeutics and vaccines has become a cornerstone of the fight against the disease. To support the maximal use of genomic information for SARS-CoV-2 research, we launched the Ensembl COVID-19 browser, incorporating a new Ensembl gene set, multiple variant sets (including novel variation calls), and annotation from several relevant resources integrated into the reference SARS-CoV-2 assembly. This work included key adaptations of existing Ensembl genome annotation methods to model ribosomal slippage, stringent filters to elucidate the highest confidence variants and utilisation of our comparative genomics pipelines on viruses for the first time. Since May 2020, the content has been regularly updated and tools such as the Ensembl Variant Effect Predictor have been integrated. The Ensembl COVID-19 browser is freely available at https://covid-19.ensembl.org.

bioinformatics↗

bioRxiv2020

Motif analysis in co-expression networks reveals regulatory elements in plants: The peach as a model

Identification of functional regulatory elements encoded in plant genomes is a fundamental need to understand gene regulation. While much attention has been given to model species as Arabidopsis thaliana, little is known about regulatory motifs in other plant genera. Here, we describe an accurate bottom-up approach using the online workbench RSAT::Plants for a versatile ab-initio motif discovery taking Prunus persica as a model. These predictions rely on the construction of a co-expression network to generate modules with similar expression trends and assess the effect of increasing upstream region length on the sensitivity of motif discovery. Applying two discovery algorithms, 18 out of 45 modules were found to be enriched in motifs typical of well-known transcription factor families (bHLH, bZip, BZR, CAMTA, DOF, E2FE, AP2-ERF, Myb-like, NAC, TCP, WRKY) and a novel motif. Our results indicate that small number of input sequences and short promoter length are preferential to minimize the amount of uninformative signals in peach. The spatial distribution of TF binding sites revealed an unbalanced distribution where motifs tend to lie around the transcriptional start site region. The reliability of this approach was also benchmarked in Arabidopsis thaliana, where it recovered the expected motifs from promoters of genes containing ChIPseq peaks. Overall, this paper presents a glimpse of the peach regulatory components at genome scale and provides a general protocol that can be applied to many other species. Additionally, a RSAT Docker container was released to facilitate similar analyses on other species or to reproduce our results. One sentence summaryMotifs prediction depends on the promoter size. A proximal promoter region defined as an interval of -500 bp to +200 bp seems to be the adequate stretch to predict de novo regulatory motifs in peach

genomics↗

bioRxiv2019

RSAT Var-tools: an accessible and flexible framework to predict the impact of regulatory variants on transcription factor binding

Gene regulatory regions contain short and degenerated DNA sites recognized by transcription factors (TFs). When such regions harbor SNPs, the DNA motifs where TFs bind may be affected, thereby altering the transcriptional regulation of the target genes. Such regulatory SNPs have been implicated as causal variants in GWAS studies. In this study, we describe the application of the programs Var-tools designed to predict regulatory variants, and present four case studies to illustrate their usage and applications. In brief, Var-tools facilitate i) obtaining variation information, ii) interconversion of variation file formats, iii) retrieval of sequences surrounding variants, and iv) calculating the change on predicted TF affinity scores between alleles, using motif scanning approaches. Notably, the tools support the analysis of haplotypes. The tools are included within the well-maintained suite Regulatory Sequence Analysis Tools (RSAT, http://rsat.eu), and accessible through a web interface that currently enables analysis of five metazoa and ten plant genomes. Vart-tools can also be used in command-line with any locally-installed Ensembl genome. Users can input personal collections of variants and motifs, providing flexibility in the analysis.

bioinformatics↗

bioRxiv2018

GET_PHYLOMARKERS, a software package to select optimal orthologous clusters for phylogenomics and inferring pan-genome phylogenies, used for a critical geno-taxonomic revision of the genus Stenotrophomonas

The massive accumulation of genome-sequences in public databases promoted the proliferation of genome-level phylogenetic analyses in many areas of biological research. However, due to diverse evolutionary and genetic processes, many loci have undesirable properties for phylogenetic reconstruction. These, if undetected, can result in erroneous or biased estimates, particularly when estimating species trees from concatenated datasets. To deal with these problems, we developed GET_PHYLOMARKERS, a pipeline designed to identify high-quality markers to estimate robust genome phylogenies from the orthologous clusters, or the pan-genome matrix (PGM), computed by GET_HOMOLOGUES. In the first context, a set of sequential filters are applied to exclude recombinant alignments and those producing anomalous or poorly resolved trees. Multiple sequence alignments and maximum likelihood (ML) phylogenies are computed in parallel on multi-core computers. A ML species tree is estimated from the concatenated set of top-ranking alignments at the DNA or protein levels, using either FastTree or IQ-TREE (IQT). The latter is used by default due to its superior performance revealed in an extensive benchmark analysis. In addition, parsimony and ML phylogenies can be estimated from the PGM.\n\nWe demonstrate the practical utility of the software by analyzing 170 Stenotrophomonas genome sequences available in RefSeq and 10 new complete genomes of environmental S. maltophilia complex (Smc) isolates reported herein. A combination of core-genome and PGM analyses was used to revise the molecular systematics of the genus. An unsupervised learning approach that uses a goodness of clustering statistic identified 20 groups within the Smc at a core-genome average nucleotide identity of 95.9% that are perfectly consistent with strongly supported clades on the core- and pan-genome trees. In addition, we identified 14 misclassified RefSeq genome sequences, 12 of them labeled as S. maltophilia, demonstrating the broad utility of the software for phylogenomics and geno-taxonomic studies. The code, a detailed manual and tutorials are freely available for Linux/UNIX servers under the GNU GPLv3 license at https://github.com/vinuesa/get_phylomarkers. A docker image bundling GET_PHYLOMARKERS with GET_HOMOLOGUES is available at https://hub.docker.com/r/csicunam/get_homologues/, which can be easily run on any platform.

genomics↗

bioRxiv2017

A new multi-genomic approach for the study of biogeochemical cycles at global scale: the molecular reconstruction of the sulfur cycle

Despite the great advances in microbial ecology and the explosion of high throughput sequencing, our ability to understand and integrate the global biogeochemical cycles is still limited. Here we propose a novel approach to summarize the complexity of the Sulfur cycle based on the minimum ecosystem concept, the microbial mat model and the relative entropy of protein domains involved in S-metabolism. This methodology produces a single value, called the Sulfur Score (SS), which informs about the specific S-related molecular machinery. After curating an inventory of microorganisms, pathways and genes taking part in this cycle, we benchmark the performance of the SS on a collection of 2,107 non-redundant RefSeq genomes, 900 metagenomes from MG-RAST and 35 metagenomes analyzed for the first time. We find that the SS is able to correctly classify microorganisms known to be involved in the S-cycle, yielding an Area Under the ROC Curve of 0.985. Moreover, when sorting environments the top-scoring metagenomes were hydrothermal vents, microbial mats and deep-sea sediments, among others. This methodology can be generalized to the analysis of other biogeochemical cycles or processes. Provided that an inventory of relevant pathways and microorganisms can be compiled, entropy-based scores could be used to detect environmental patterns and informative samples in multi-genomic scale.

bioinformatics↗