Biology subjects

Morales-Cruz, A.

Publications and source records attributed to Morales-Cruz, A..

13 recordsLinked to original sources

bioRxiv2026

The dynamics of introgression across an adaptive radiation: examining hybrid speciation and parallel adaptation in North American Vitis

Hybridization between species can contribute to parallel adaptive events and, in some cases, speciation. However, the prevalence of introgression is rarely measured across multiple species, meaning that it is rarely integrated with landscape-scale processes or connected to adaptive repeatability. Here, we analyzed whole-genome resequencing data from 639 accessions representing 48 Vitis species. Vitis is notable for the domesticated grapevine (V. vinifera), multiple economically important North American species, and as an example of a temperate adaptive radiation. Our dataset included population-level sampling for 19 species, from which we reconstructed individual- and species-level phylogenetic frameworks for the genus. The analyses uncovered widespread evidence of introgression, comprising [~]14% of the average Vitis genome. Introgression was associated with geographic distribution between species, and highly admixed individuals were more frequently found near ecological niche margins. Genetic analyses further indicated that previously recognized hybrid taxa, V. x doaniana and V. x champinii, likely represent hybrid swarms rather than distinct species. We also assessed patterns of adaptive repeatability across eight species with denser population sampling. For six of the eight species, most of the detected sweeps overlapped with sweeps in other species; on average, more recently diverged species shared more overlapping sweeps. Parallel sweep events were driven mostly by introgression, although a substantial fraction ([~]40%) was attributed to selection on ancestral standing variation. By integrating population genomic data across many species, this study highlights the central role of shared genetic variation across an adaptive radiation.

evolutionary biology↗

bioRxiv2026

Positional grammar of transcription factor binding partitions developmental and stress-response regulation in plants

Understanding how transcription factor binding site (TFBS) position influences gene regulation remains a fundamental challenge in plants. Here, we integrate conserved multiDAP TFBS maps for 244 transcription factors (TFs) with single-nucleus chromatin accessibility, cell type-resolved gene expression, and hormone-response datasets across Brassicaceae species to determine how TFBS position relates to regulatory function. Although conserved TFBSs are enriched near transcription start sites (TSSs), TSS-proximal accessibility poorly predicts cell type-specific expression. Instead, cell type-specific expression correlates best with conserved TFBSs embedded in cell type-restricted chromatin, with TF family-specific distributions across distal promoters and introns. In contrast, TSS-proximal TFBSs in broadly accessible chromatin are associated with rapid transcriptional responses to abiotic and biotic stress hormones. Coding sequence TFBSs mark a distinct regulatory context in which the same DNA sequence encodes both amino acid sequence and TF motifs, including evidence that CDS-localized ABR1 binding may contribute to repression during hormone response. Finally, distal upstream regions contain conserved multi-family TF clusters with enhancer-like features overlapping rare cell type-specific accessible chromatin and enriched near genes controlling embryonic, meristematic, and hormone-dependent developmental patterning. Together, these results support a positional grammar in which TFBS position and chromatin context jointly partition developmental, stress-responsive, and repressive regulatory output in plants.

genomics↗

bioRxiv2024

An atlas of conserved transcription factor binding sites reveals the cell type-resolved gene regulatory landscape of flowering plants

Transcription factors (TFs) are proteins that bind DNA to control where and when genes are expressed. In plants, dozens of TF families interact with distinct sets of binding sites (TFBSs) that reflect each TFs role in organismal function and species-specific adaptations. However, defining these roles and understanding broader patterns of regulatory evolution remains challenging, as predicted TFBSs may lack a clear impact on transcription, and experimentally-derived TF binding maps to date are modest in scale or restricted to model organisms. Here, we present a scalable TFBS assay that we leveraged to create an atlas of nearly 3,000 genome-wide binding site maps for 360 TFs in 10 species spanning 150 million years of flowering plant evolution. We find that TF orthologs from distant species retain nearly identical binding preferences, suggesting that regulatory evolution primarily arises from gain and loss of TFBSs. Within lineages however, conserved TFBSs are over-represented and found in regions harboring signatures of functional regulatory elements. Moreover, genes with conserved TFBSs showed a striking enrichment for cell type-specific expression in single-nuclei RNA atlases, providing a robust marker of each TFs activity and developmental role. Finally, we compare distant lineages, illustrating how ancient regulatory modules were recruited and rewired to enable adaptations underlying the evolutionary success of grasses.

genomics↗

bioRxiv2023

Comparative pangenomic insights into the distinct evolution of virulence factors among grapevine trunk pathogens

The permanent organs of grapevines (V. vinifera L.), like other woody perennials, are colonized by various unrelated pathogenic ascomycete fungi secreting cell wall-degrading enzymes and phytotoxic secondary metabolites that contribute to host damage and disease symptoms. Trunk pathogens differ in the symptoms they induce and the extent and speed of damage. Isolates of the same species often display a wide virulence range, even within the same vineyard. This study focuses on Eutypa lata, Neofusicoccum parvum, and Phaeoacremonium minimum, causal agents of Eutypa dieback, Botryosphaeria dieback, and Esca, respectively. We sequenced fifty isolates from viticulture regions worldwide and built nucleotide-level, reference-free pangenomes for each species. Through examining genomic diversity and pangenome structure, we analyzed intraspecific conservation and variability of putative virulence factors, focusing on functions under positive selection, and recent gene-family dynamics of contraction and expansion. Our findings reveal contrasting distributions of putative virulence factors in the core, dispensable, and private genomes of each pangenome. For example, CAZymes were prevalent in the core genomes of each pangenome, whereas biosynthetic gene clusters were prevalent in the dispensable genomes of E. lata and P. minimum. The dispensable fractions were also enriched in Gypsy transposable elements and virulence factors under positive selection (polyketide synthases genes in E. lata and P. minimum glycosyltransferases in N. parvum). Our findings underscore the complexity of the genomic architecture in each species and provide insights into their adaptive strategies, enhancing our understanding of the underlying mechanisms of virulence.

genomics↗

bioRxiv2022

Multigenic resistance to Xylella fastidiosa in wild grapes (Vitis sps.) and its implications within a changing climate

Xylella fastidiosa is a bacterium that infects crops like grapevines, coffee, almonds, citrus and olives, causing economically devastating damage. There is, however, little understanding of the genes that contribute to resistance, the genomic architecture of resistance, and the potential role of climate in shaping resistance, in part because major crops like grapevines (V. vinifera) are not resistant to the bacterium. Here we studied a wild grapevine species, Vitis arizonica, that segregates for resistance to X. fastidiosa. Using genome-wide association, we identified candidate genes that mediate the host response to X. fastidiosa infection. We uncovered evidence that resistance requires genes from multiple genomic regions, based on data from breeding populations and from additional Vitis species. We also inferred that resistance evolved more than once in the wild, suggesting that wild Vitis species may be a rich source for resistance alleles and mechanisms. Finally, resistance in V. arizonica was climate dependent, because individuals from low (< 10{degrees}C) temperature locations in the wettest quarter were typically susceptible to infection, likely reflecting a lack of pathogen pressure in these climates. Surprisingly, climate was nearly as effective a predictor of resistance phenotypes as some genetic markers. This work underscores that pathogen pressure is likely to increase with climate, but it also provides genetic insight and tools for breeding and transforming resistant crops.

genetics↗

bioRxiv2022

Insights into the domestication of avocado and potential genetic contributors to heterodichogamy

O_LIThe domestication history of avocado (Persea americana) remains unclear, in part due to a lack of suitable genomic tools. C_LIO_LIWe created a reference genome from the Gwen varietal, which is closely related to the economically dominant Hass varietal. We also compiled a database of 34 resequenced accessions that represented the three botanical races of P. americana. C_LIO_LIOur genome assembly had an N50 of 3.37 megabases, a BUSCO score of 91% and was scaffolded with a genetic map, producing 12 pseudo-chromosomes with 49,450 genes. We used the Gwen genome as a reference to investigate the population genomics of avocado. Our analyses were consistent with three separate domestication events; we estimated that the Mexican race diverged from the Lowland (formerly known as West Indian) and Guatemalan races >1 million years ago. We also identified putative targets of selective sweeps in domestication events; within the Guatemalan race, putative candidate genes were enriched for fruit development and ripening. We also investigated divergence between heterodichogamous flowering types. C_LIO_LIWith the help of a new reference genome, we inferred the domestication history of avocado and identified genes that may contribute to heterodichogamy, including genes with functions in pollination and floral development. C_LI

genomics↗

bioRxiv2021

Climate Change, Crop Wild Relatives and Genomic Data: The persistence and agronomic utility of five Vitis species

Crop wild relatives (CWRs) have the capacity to contribute novel traits to agriculture. Given climate change, these contributions may be especially vital for the persistence of perennial crops, because perennials are often clonally propagated and consequently do not evolve rapidly. By studying the landscape genomics of samples from five Vitis CWRs (V. arizonica, V. mustangensis, V. riparia, V. berlandieri and V. girdiana) in the context of projected climate change, we addressed two goals. The first was to assess the relative potential of different CWR accessions to persist in the face of climate change. By integrating species distribution models with adaptive genetic variation, additional genetic features such as genomic load and a phenotype (resistance to Pierces Disease), we predicted that accessions from one species (V. mustangensis) are particularly well-suited to persist in future climates. The second goal was to identify which CWR accessions may contribute to bioclimatic adaptation for grapevine (V. vinifera) cultivation. To do so, we evaluated whether CWR accessions have the allelic capacity to persist if moved to locations where grapevines (V. vinifera) are cultivated in the United States. We identified six candidates from V. mustangensis and hypothesized that they may prove useful for contributing alleles that may mitigate climate impacts on viticulture. By identifying candidate germplasm, this work takes a conceptual step toward assessing the genomic and bioclimatic characteristics of CWRs.

evolutionary biology↗

bioRxiv2021

Extensive introgression among North American wild grapes (Vitis) fuels biotic and abiotic adaptation

Introgressive hybridization can introduce adaptive genetic variation into a species or population. To evaluate the evolutionary forces that contribute to introgression, we studied six Vitis species that are native to the Southwestern United States and potentially useful for breeding grapevine (V. vinifera) rootstocks. By creating a reference genome from one wild species, V. arizonica, and by resequencing 130 accessions, we focused on identifying putatively introgressed regions (pIRs) between species. We found that up to ~8% of extant genome is attributable to introgression between species. The pIRs tended to be gene poor, located in regions of high recombination and enriched for genes implicated in disease resistance functions. To assess potential pIR function, we explored SNP associations to bioclimatic variables and to bacterial levels after infection with the causative agent of Pierces Disease. pIRs were enriched for SNPs associated with both climate and bacterial levels, suggesting potential drivers of adaptive events. Altogether, this study yields insights into the genomic extent of introgression, potential pressures that shape adaptive introgression, and the history of economically important wild relatives of a critical crop.

evolutionary biology↗

bioRxiv2021

Phylogenomics of plant-associated Botryosphaeriaceae species

The Botryosphaeriaceae is a fungal family that includes many destructive vascular pathogens of woody plants (e.g., Botryosphaeria dieback of grape, Panicle blight of pistachio). Species in the genera Botryosphaeria, Diplodia, Dothiorella, Lasiodiplodia, Neofusicoccum, and Neoscytalidium attack a range of horticultural crops, but they vary in virulence and in their abilities to infect their hosts via different infection courts (flowers, green shoots, woody twigs). Isolates of seventeen species, originating from symptomatic apricot, grape, pistachio, and walnut were tested for pathogenicity to grapevine wood after four months of incubation in potted plants in the greenhouse. Results revealed significant variation in virulence in terms of the length of the internal wood lesions caused by these seventeen species. Phylogenomic comparisons of the seventeen species of wood-colonizing fungi revealed clade-specific expansion of gene families representing putative virulence factors involved in toxin production and mobilization, wood degradation, and nutrient uptake. Statistical analyses of the evolution of the size of gene families revealed expansions of secondary metabolism and transporter gene families in Lasiodiplodia and of secreted cell wall degrading enzymes (CAZymes) in Botryosphaeria and Neofusicoccum genomes. In contrast, Diplodia, Dothiorella, and Neoscytalidium generally showed a contraction in the number of members of these gene families. Overall, species with expansions of gene families, such as secreted CAZymes, secondary metabolism, and transporters, were the most virulent (i.e., were associated with the largest lesions), based on our pathogenicity tests and published reports. This study represents the first comparative phylogenomic investigation into the evolution of possible virulence factors from diverse, cosmopolitan members of the Botryosphaeriaceae.

genomics↗

bioRxiv2019

The unique genome architecture of the devastating West African cacao black pod pathogen Phytophthora megakarya

Phytophthora megakarya (Pmeg) and P. palmivora (Ppal) are oomycete pathogens that cause black pod rot of cacao (Theobroma cacao), the most economically important disease on cacao globally. While Ppal is a cosmopolitan pathogen, Pmeg, which is more aggressive on cacao than Ppal, has been reported only in West and Central Africa where it has been spreading and devastating cacao farms since the 1950s. In this study, we reconstructed the complete diploid genomes of multiple isolates of both species using single-molecule sequencing. Thirty-one additional genotypes were sequenced to analyze inter- and intra-species genomic diversity. These resources make it possible to better understand the molecular basis of virulence differences in closely related and consequential pathogens and study their evolutionary history. The Pmeg genome is exceptionally large (222 Mbp) and nearly twice the size Ppal (135 Mbp) and most known Phytophthora species ([~]100 Mbp on average). We show that the genomes of both species recently expanded by independent whole-genome duplications (WGD). WGD and the dramatic transposable element associated expansion of a few gene families led to the exceptionally large genome and transcriptome of Pmeg and the diversification of virulence-related genes including secreted RxLR effectors. Finally, this study provides evidence of adaptive evolution among well-known effectors and discusses the implications of effector expansion and diversification.

genomics↗

bioRxiv2018

Profiling grapevine trunk pathogens in planta: A case for community-targeted DNA metabarcoding

DNA metabarcoding, commonly used in exploratory microbial ecology studies, is a promising method for the simultaneous in planta-detection of multiple pathogens associated with disease complexes, such as the grapevine trunk diseases. Their detection is particularly challenging, due to the presence within an individual wood lesion of multiple co-infecting trunk pathogens and other wood-colonizing fungi, which span a broad range of taxa in the Fungal Kingdom. As such, we designed metabarcoding primers, using as template the ribosomal internal transcribed spacer of grapevine trunk-associated Ascomycete fungi (GTAA) and compared them to two universal primer widely used in microbial ecology. We first performed in silico simulations and then tested the primers by high-throughput amplicon sequencing of (i) multiple combinations of mock communities, (ii) time-course experiments with controlled inoculations, and (iii) diseased field samples from vineyards under natural levels of infection. All analyses showed that GTAA had greater affinity and sensitivity, compared to those of the universal primers. Importantly, with GTAA, profiling of mock communities and comparisons with shotgun-sequencing metagenomics of field samples gave an accurate representation of genera of important trunk pathogens, namely Phaeomoniella, Phaeoacremonium, and Eutypa, the abundances of which were greatly over- or under-estimated with universal primers. Overall, our findings not only demonstrate that DNA metabarcoding gives qualitatively and quantitatively accurate results when applied to grapevine trunk diseases, but also that primer customization and testing are crucial to ensure the validity of DNA metabarcoding results.

microbiology↗

bioRxiv2018

Whole-genome resequencing and pan-transcriptome reconstruction highlight the impact of genomic structural variation on secondary metabolism gene clusters in the grapevine Esca pathogen Phaeoacremonium minimum

The Ascomycete fungus Phaeoacremonium minimum is one of the primary causal agents of Esca, a widespread and damaging grapevine trunk disease. Variation in virulence among Pm. minimum isolates has been reported, but the underlying genetic basis of the phenotypic variability remains unknown. The goal of this study was to characterize intraspecific genetic diversity and explore its potential impact on virulence functions associated with secondary metabolism, cellular transport, and cell wall decomposition. We generated a chromosome-scale genome assembly, using single molecule real-time sequencing, and resequenced the genomes and transcriptomes of multiple isolates to identify sequence and structural polymorphisms. Numerous insertion and deletion events were found for a total of about 1 Mbp in each isolate. Structural variation in this extremely gene dense genome frequently caused presence/absence polymorphisms of multiple adjacent genes, mostly belonging to biosynthetic clusters associated with secondary metabolism. Because of the observed intraspecific diversity in gene content due to structural variation we concluded that a transcriptome reference developed from a single isolate is insufficient to represent the virulence factor repertoire of the species. We therefore compiled a pan-transcriptome reference of Pm. minimum comprising a non-redundant set of 15,245 protein-coding sequences. Using naturally infected field samples expressing Esca symptoms, we demonstrated that mapping of meta-transcriptomics data on a multi-species reference that included the Pm. minimum pan-transcriptome allows the profiling of an expanded set of virulence factors, including variable genes associated with secondary metabolism and cellular transport.

genomics↗

bioRxiv2017

Closed-reference metatranscriptomics enables in planta profiling of putative virulence activities in the grapevine trunk-disease complex

Grapevines, like other perennial crops, are affected by so-called trunk diseases, which damage the trunk and other woody tissues. Mature grapevines typically contract more than one trunk disease and often multiple grapevine trunk pathogens (GTPs) are recovered from infected tissues. The co-existence of different GTP species in complex and dynamic microbial communities complicates the study of the molecular mechanisms underlying disease development especially under vineyard conditions. The objective of this study was to develop and optimize a community-level transcriptomics (i.e., metatranscriptomics) approach that can monitor simultaneously the virulence activities of multiple GTPs in planta. The availability of annotated genomes for the most relevant co-infecting GTPs in diseased grapevine wood provided the unprecedented opportunity to generate a multi-species reference for mapping and quantifying DNA and RNA sequencing reads. We first evaluated popular sequence read mappers using permutations of multiple simulated datasets. Alignment parameters of the selected mapper were optimized to increase the specificity and sensitivity for its application to metagenomics and metatranscriptomics analyses. Initial testing on grapevine wood experimentally inoculated with individual GTPs confirmed the validity of the method. Using naturally-infected field samples expressing a variety of trunk disease symptoms, we show that our approach provides quantitative assessments of species composition as well as genome-wide transcriptional profiling of potential virulence factors, namely cell wall degradation, secondary metabolism and nutrient uptake for all co-infecting GTPs.

genomics↗